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Scala M, Bradley CA, Howe JL, Trost B, Salazar NB, Shum C, Reuter MS, MacDonald JR, Ko SY, Frankland PW, Granger L, Anadiotis G, Pullano V, Brusco A, Keller R, Parisotto S, Pedro HF, Lusk L, McDonnell PP, Helbig I, Mullegama SV, Douine ED, Russell BE, Nelson SF, Zara F, Scherer SW. Genetic variants in DDX53 contribute to Autism Spectrum Disorder associated with the Xp22.11 locus. medRxiv 2023:2023.12.21.23300383. [PMID: 38234782 PMCID: PMC10793518 DOI: 10.1101/2023.12.21.23300383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Autism Spectrum Disorder (ASD) exhibits an ~4:1 male-to-female sex bias and is characterized by early-onset impairment of social/communication skills, restricted interests, and stereotyped behaviors. Disruption of the Xp22.11 locus has been associated with ASD in males. This locus includes the three-exon PTCHD1 gene, an adjacent multi-isoform long noncoding RNA (lncRNA) named PTCHD1-AS (spanning ~1Mb), and a poorly characterized single-exon RNA helicase named DDX53 that is intronic to PTCHD1-AS. While the relationship between PTCHD1/PTCHD1-AS and ASD is being studied, the role of DDX53 has not been examined, in part because there is no apparent functional murine orthologue. Through clinical testing, here, we identified 6 males and 1 female with ASD from 6 unrelated families carrying rare, predicted-damaging or loss-of-function variants in DDX53. Then, we examined databases, including the Autism Speaks MSSNG and Simons Foundation Autism Research Initiative, as well as population controls. We identified 24 additional individuals with ASD harboring rare, damaging DDX53 variations, including the same variants detected in two families from the original clinical analysis. In this extended cohort of 31 participants with ASD (28 male, 3 female), we identified 25 mostly maternally-inherited variations in DDX53, including 18 missense changes, 2 truncating variants, 2 in-frame variants, 2 deletions in the 3' UTR and 1 copy number deletion. Our findings in humans support a direct link between DDX53 and ASD, which will be important in clinical genetic testing. These same autism-related findings, coupled with the observation that a functional orthologous gene is not found in mouse, may also influence the design and interpretation of murine-modelling of ASD.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Clarrisa A. Bradley
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer L. Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nelson Bautista Salazar
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Carole Shum
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S. Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R. MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sangyoon Y. Ko
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Paul W. Frankland
- Program in Neurosciences and Mental Health, The Hospital for Sick Children and Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - George Anadiotis
- Department of Genetics and Metabolism, Randall Children’s Hospital, Portland, OR 97227, USA
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Alfredo Brusco
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Roberto Keller
- Adult Autism Centre DSM ASL Città di Torino, 10138 Turin, Italy
| | - Sarah Parisotto
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Helio F. Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Laina Lusk
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pamela Pojomovsky McDonnell
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ingo Helbig
- Epilepsy Neurogenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Bianca E. Russell
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Giannina Gaslini, Genoa, Italy
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- McLaughlin Centre, Toronto, ON M5G 0A4, Canada
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Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind WH, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener MH, Byers PHH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A. Neurol Genet 2023; 9:e200090. [PMID: 37560121 PMCID: PMC10409571 DOI: 10.1212/nxg.0000000000200090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
Objectives Transcript sequencing of patient-derived samples has been shown to improve the diagnostic yield for solving cases of suspected Mendelian conditions, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods We applied short-read and full-length transcript sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts the branch point critical for intron 6 splicing. Full-length long-read isoform complementary DNA (cDNA) sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates 5 distinct altered splicing transcripts. All 5 altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.
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Affiliation(s)
- Andrew B Stergachis
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Elizabeth E Blue
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Madelyn A Gillentine
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Lee-Kai Wang
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ulrike Schwarze
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Adriana Sedeño Cortés
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Jane Ranchalis
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Aimee Allworth
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Austin E Bland
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Sirisak Chanprasert
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Jingheng Chen
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Daniel Doherty
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Andrew B Folta
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ian Glass
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Martha Horike-Pyne
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Alden Y Huang
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Alyna T Khan
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Kathleen A Leppig
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Danny E Miller
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Ghayda Mirzaa
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Azma Parhin
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Wendy H Raskind
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Elisabeth A Rosenthal
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Sam Sheppeard
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Samuel Strohbehn
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Virginia P Sybert
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Thao T Tran
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Mark H Wener
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Peter H H Byers
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Stanley F Nelson
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Michael J Bamshad
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Katrina M Dipple
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Gail P Jarvik
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Suzanne Hoppins
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
| | - Fuki M Hisama
- From the Department of Medicine (A.B.S., E.E.B., A.S.C., J.R., A.A., A.E.B., S.C., A.B.F., M.H.-P., A.P., W.H.R., E.A.R., S. Sheppeard, S. Strohbehn, V.P.S., P.H.H.B., G.P.J., F.M.H.), Genome Sciences (A.B.S., G.P.J.), University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine (A.B.S., E.E.B., D.D., I.G., D.E.M., G.M., M.J.B., K.M.D., G.P.J., F.M.H.); University of Washington (E.E.B., J.C., A.T.K.), Institute of Public Health Genetics; Department of Laboratories (M.A.G.), Seattle Children's Hospital, WA; Institute for Precision Health (L.-K.W., A.Y.H., S.F.N.), David Geffen School of Medicine, University of California Los Angeles; Department of Laboratory Medicine and Pathology (U.S., D.E.M., T.T.T., M.H.W., P.H.H.B.), University of Washington School of Medicine; Department of Pediatrics (D.D., I.G., D.E.M., G.M., M.J.B., K.M.D.), Department of Biostatistics (A.T.K.), University of Washington; Group Health Cooperative (K.A.L.), Kaiser Permanente Washington; Seattle Children's Research Institute (G.M.), Center for Integrative Brain Research; and Department of Biochemistry (S.H.), University of Washington School of Medicine, Seattle, WA
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3
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Ulm JW, Barthélémy F, Nelson SF. Elucidation of bioinformatic-guided high-prospect drug repositioning candidates for DMD via Swanson linking of target-focused latent knowledge from text-mined categorical metadata. Front Cell Dev Biol 2023; 11:1226707. [PMID: 37664462 PMCID: PMC10469615 DOI: 10.3389/fcell.2023.1226707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Duchenne Muscular Dystrophy (DMD)'s complex multi-system pathophysiology, coupled with the cost-prohibitive logistics of multi-year drug screening and follow-up, has hampered the pursuit of new therapeutic approaches. Here we conducted a systematic historical and text mining-based pilot feasibility study to explore the potential of established or previously tested drugs as prospective DMD therapeutic agents. Our approach utilized a Swanson linking-inspired method to uncover meaningful yet largely hidden deep semantic connections between pharmacologically significant DMD targets and drugs developed for unrelated diseases. Specifically, we focused on molecular target-based MeSH terms and categories as high-yield bioinformatic proxies, effectively tagging relevant literature with categorical metadata. To identify promising leads, we comprehensively assembled published reports from 2011 and sampling from subsequent years. We then determined the earliest year when distinct MeSH terms or category labels of the relevant cellular target were referenced in conjunction with the drug, as well as when the pertinent target itself was first conclusively identified as holding therapeutic value for DMD. By comparing the earliest year when the drug was identifiable as a DMD treatment candidate with that of the first actual report confirming this, we computed an Index of Delayed Discovery (IDD), which serves as a metric of Swanson-linked latent knowledge. Using these findings, we identified data from previously unlinked articles subsetted via MeSH-derived Swanson linking or from target classes within the DrugBank repository. This enabled us to identify new but untested high-prospect small-molecule candidates that are of particular interest in repurposing for DMD and warrant further investigations.
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Affiliation(s)
- J. Wes Ulm
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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4
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Nieves-Rodriguez S, Barthélémy F, Woods JD, Douine ED, Wang RT, Scripture-Adams DD, Chesmore KN, Galasso F, Miceli MC, Nelson SF. Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD. Front Genet 2023; 14:1216066. [PMID: 37576554 PMCID: PMC10415210 DOI: 10.3389/fgene.2023.1216066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.
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Affiliation(s)
- Shirley Nieves-Rodriguez
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeremy D. Woods
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Emilie D. Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Richard T. Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Deirdre D. Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin N. Chesmore
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Francesca Galasso
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - M. Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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5
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Wilkes MC, Chae HD, Scanlon V, Cepika AM, Wentworth EP, Saxena M, Eskin A, Chen Z, Glader B, Grazia Roncarolo M, Nelson SF, Sakamoto KM. SATB1 Chromatin Loops Regulate Megakaryocyte/Erythroid Progenitor Expansion by Facilitating HSP70 and GATA1 Induction. Stem Cells 2023; 41:560-569. [PMID: 36987811 PMCID: PMC10267687 DOI: 10.1093/stmcls/sxad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/21/2023] [Indexed: 03/30/2023]
Abstract
Diamond Blackfan anemia (DBA) is an inherited bone marrow failure syndrome associated with severe anemia, congenital malformations, and an increased risk of developing cancer. The chromatin-binding special AT-rich sequence-binding protein-1 (SATB1) is downregulated in megakaryocyte/erythroid progenitors (MEPs) in patients and cell models of DBA, leading to a reduction in MEP expansion. Here we demonstrate that SATB1 expression is required for the upregulation of the critical erythroid factors heat shock protein 70 (HSP70) and GATA1 which accompanies MEP differentiation. SATB1 binding to specific sites surrounding the HSP70 genes promotes chromatin loops that are required for the induction of HSP70, which, in turn, promotes GATA1 induction. This demonstrates that SATB1, although gradually downregulated during myelopoiesis, maintains a biological function in early myeloid progenitors.
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Affiliation(s)
- Mark C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Hee-Don Chae
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Vanessa Scanlon
- Department of Laboratory Medicine, Yale Stem Cell Center, Yale Cooperative Center of Excellence in Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Alma-Martina Cepika
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ethan P Wentworth
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Mallika Saxena
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ascia Eskin
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Zugen Chen
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Bert Glader
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Maria Grazia Roncarolo
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
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6
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Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
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Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
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7
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Wong S, Tan YX, Loh AYT, Tan KY, Lee H, Aziz Z, Nelson SF, Özkan E, Kayserili H, Escande-Beillard N, Reversade B. RAF1 deficiency causes a lethal syndrome that underscores RTK signaling during embryogenesis. EMBO Mol Med 2023; 15:e17078. [PMID: 37066513 PMCID: PMC10165362 DOI: 10.15252/emmm.202217078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 04/18/2023] Open
Abstract
Somatic and germline gain-of-function point mutations in RAF, one of the first oncogenes to be discovered in humans, delineate a group of tumor-prone syndromes known as the RASopathies. In this study, we document the first human phenotype resulting from the germline loss-of-function of the proto-oncogene RAF1 (a.k.a. CRAF). In a consanguineous family, we uncovered a homozygous p.Thr543Met variant segregating with a neonatal lethal syndrome with cutaneous, craniofacial, cardiac, and limb anomalies. Structure-based prediction and functional tests using human knock-in cells showed that threonine 543 is essential to: (i) ensure RAF1's stability and phosphorylation, (ii) maintain its kinase activity toward substrates of the MAPK pathway, and (iii) protect from stress-induced apoptosis mediated by ASK1. In Xenopus embryos, mutant RAF1T543M failed to phenocopy the effects of normal and overactive FGF/MAPK signaling, confirming its hypomorphic activity. Collectively, our data disclose the genetic and molecular etiology of a novel lethal syndrome with progeroid features, highlighting the importance of RTK signaling for human development and homeostasis.
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Affiliation(s)
- Samantha Wong
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Experimental Drug Development Centre, A*STAR, Singapore, Singapore
| | - Yu Xuan Tan
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - Abigail Yi Ting Loh
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kiat Yi Tan
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- 3billion, Inc, Seoul, South Korea
| | - Zainab Aziz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hülya Kayserili
- Department of Medical Genetics, Koç University, School of Medicine, Istanbul, Turkey
| | - Nathalie Escande-Beillard
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Department of Medical Genetics, Koç University, School of Medicine, Istanbul, Turkey
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Medical Genetics, Koç University, School of Medicine, Istanbul, Turkey
- Department of Physiology, Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Smart-Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
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8
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Andrews JC, Mok JW, Kanca O, Jangam S, Tifft C, Macnamara EF, Russell BE, Wang LK, Nelson SF, Bellen HJ, Yamamoto S, Malicdan MCV, Wangler MF. De Novo Variants in MRTFB have gain of function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features. Genet Med 2023:100833. [PMID: 37013900 DOI: 10.1016/j.gim.2023.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
PURPOSE Myocardin-Related Transcription Factor B (MRTFB) is an important transcriptional regulator which promotes the activity of an estimated 300 genes but is not known to underlie a Mendelian disorder. METHODS Probands were identified through the efforts of the Undiagnosed Disease Network. As the MRTFB protein is highly conserved between vertebrate and invertebrate model organisms, we generated a humanized Drosophila model expressing the human MRTFB protein in the same spatial and temporal pattern as the fly gene. Actin binding assays were used to validate the effect of the variants on MRTFB. RESULTS Here we report two pediatric probands with de novo variants in MRTFB (p.R104G and p.A91P) and mild dysmorphic features, intellectual disability, global developmental delays, speech apraxia, and impulse control issues. Expression of the variants within wing tissues of a fruit fly model resulted in changes in wing morphology. The MRTFBR104G and MRTFBA91P variants also display a decreased level of actin binding within critical RPEL domains, resulting in increased transcriptional activity and changes in the organization of the Actin cytoskeleton. CONCLUSION The MRTFBR104G and MRTFBA91P variants affect the regulation of the protein and underlie a novel neurodevelopmental disorder. Overall, our data suggests these variants act as a gain of function.
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9
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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10
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Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind W, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener M, Byers PH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, Hisama FM. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A. bioRxiv 2023:2023.02.07.526487. [PMID: 36798371 PMCID: PMC9934537 DOI: 10.1101/2023.02.07.526487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Objectives Transcript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. Methods We applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. Results We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). Discussion This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.
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Affiliation(s)
- Andrew B Stergachis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Elizabeth E Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
| | | | - Lee-Kai Wang
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Adriana Sedeño Cortés
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Austin E Bland
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Jingheng Chen
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
| | - Daniel Doherty
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B Folta
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Alyna T Khan
- University of Washington, Institute of Public Health Genetics, Seattle, WA, USA
- University of Washington, Department of Biostatistics, Seattle, WA, USA
| | - Kathleen A Leppig
- Group Health Cooperative, Kaiser Permanente Washington, Seattle, WA, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Ghayda Mirzaa
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Azma Parhin
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Wendy Raskind
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Virginia P Sybert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Thao T Tran
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Mark Wener
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Peter H Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Stanley F Nelson
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Katrina M Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Gail P Jarvik
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Suzanne Hoppins
- University of Washington School of Medicine, Department of Biochemistry, Seattle, WA, USA
| | - Fuki M Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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11
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Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
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Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
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Barnard AM, Hammers DW, Triplett WT, Kim S, Forbes SC, Willcocks RJ, Daniels MJ, Senesac CR, Lott DJ, Arpan I, Rooney WD, Wang RT, Nelson SF, Sweeney HL, Vandenborne K, Walter GA. Evaluating Genetic Modifiers of Duchenne Muscular Dystrophy Disease Progression Using Modeling and MRI. Neurology 2022; 99:e2406-e2416. [PMID: 36240102 PMCID: PMC9687406 DOI: 10.1212/wnl.0000000000201163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Duchenne muscular dystrophy (DMD) is a progressive muscle degenerative disorder with a well-characterized disease phenotype but considerable interindividual heterogeneity that is not well understood. The aim of this study was to evaluate the effects of dystrophin variations and genetic modifiers of DMD on rate and age of muscle replacement by fat. METHODS One hundred seventy-five corticosteroid treated participants from the ImagingDMD natural history study underwent repeated magnetic resonance spectroscopy (MRS) of the vastus lateralis (VL) and soleus (SOL) to determine muscle fat fraction (FF). MRS was performed annually in most instances; however, some individuals had additional visits at 3 or 6 monthss intervals. FF changes over time were modeled using nonlinear mixed effects to estimate disease trajectories based on the age that the VL or SOL reached half-maximum change in FF (mu) and the time required for FF change (sigma). Computed mu and sigma values were evaluated for dystrophin variations that have demonstrated the ability to lead to a mild phenotype as well as compared between different genetic polymorphism groups. RESULTS Participants with dystrophin gene deletions amenable to exon 8 skipping (n = 4) had minimal increases in SOL FF and had an increase in VL mu value by 4.4 years compared with a reference cohort (p = 0.039). Participants with nonsense variations within exons that may produce milder phenotypes (n = 11) also had minimal increases in SOL and VL FFs. No differences in estimated FF trajectories were seen for individuals amenable to exon 44 skipping (n = 10). Modeling of the SPP1, LTBP4, and thrombospondin-1 (THBS1) genetic modifiers did not result in significant differences in muscle FF trajectories between genotype groups (p > 0.05); however, trends were noted for the polymorphisms associated with long-range regulation of LTBP4 and THBS1 that deserve further follow-up. DISCUSSION The results of this study link the historically mild phenotypes seen in individuals amenable to exon 8 skipping and with certain nonsense variations with alterations in trajectories of lower extremity muscle replacement by fat.
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Affiliation(s)
- Alison M Barnard
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - David W Hammers
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - William T Triplett
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Sarah Kim
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Sean C Forbes
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Rebecca J Willcocks
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Michael J Daniels
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Claudia R Senesac
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Donovan J Lott
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Ishu Arpan
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - William D Rooney
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Richard T Wang
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Stanley F Nelson
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - H Lee Sweeney
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Krista Vandenborne
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Glenn A Walter
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville.
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13
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Scripture-Adams DD, Chesmore KN, Barthélémy F, Wang RT, Nieves-Rodriguez S, Wang DW, Mokhonova EI, Douine ED, Wan J, Little I, Rabichow LN, Nelson SF, Miceli MC. Single nuclei transcriptomics of muscle reveals intra-muscular cell dynamics linked to dystrophin loss and rescue. Commun Biol 2022; 5:989. [PMID: 36123393 PMCID: PMC9485160 DOI: 10.1038/s42003-022-03938-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 02/05/2023] Open
Abstract
In Duchenne muscular dystrophy, dystrophin loss leads to chronic muscle damage, dysregulation of repair, fibro-fatty replacement, and weakness. We develop methodology to efficiently isolate individual nuclei from minute quantities of frozen skeletal muscle, allowing single nuclei sequencing of irreplaceable archival samples and from very small samples. We apply this method to identify cell and gene expression dynamics within human DMD and mdx mouse muscle, characterizing effects of dystrophin rescue by exon skipping therapy at single nuclei resolution. DMD exon 23 skipping events are directly observed and increased in myonuclei from treated mice. We describe partial rescue of type IIa and IIx myofibers, expansion of an MDSC-like myeloid population, recovery of repair/remodeling M2-macrophage, and repression of inflammatory POSTN1 + fibroblasts in response to exon skipping and partial dystrophin restoration. Use of this method enables exploration of cellular and transcriptomic mechanisms of dystrophin loss and repair within an intact muscle environment. Our initial findings will scaffold our future work to more directly examine muscular dystrophies and putative recovery pathways.
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Affiliation(s)
- Deirdre D Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kevin N Chesmore
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard T Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shirley Nieves-Rodriguez
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Derek W Wang
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | - Ekaterina I Mokhonova
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jijun Wan
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Isaiah Little
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura N Rabichow
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA.
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14
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Paul F, Ng C, Mohamad Sahari UB, Nafissi S, Nilipoor Y, Tavasoli AR, Bonnard C, Wong PM, Nabavizadeh N, Altunoğlu U, Estiar MA, Majoie CB, Lee H, Nelson SF, Gan-Or Z, Rouleau GA, Van Veldhoven PP, Massie R, Hennekam RC, Kariminejad A, Reversade B. RABENOSYN separation-of-function mutations uncouple endosomal recycling from lysosomal degradation, causing a distinct Mendelian Disorder. Hum Mol Genet 2022; 31:3729-3740. [PMID: 35652444 DOI: 10.1093/hmg/ddac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Rabenosyn (RBSN) is a conserved endosomal protein necessary for regulating internalized cargo. Here, we present clinical, genetic, cellular and biochemical evidence that two distinct RBSN missense variants are responsible for a novel Mendelian disorder consisting of progressive muscle weakness, facial dysmorphisms, ophthalmoplegia and intellectual disability. Using exome sequencing, we identified recessively-acting germline alleles p.Arg180Gly and p.Gly183Arg which are both situated in the FYVE domain of RBSN. We find that these variants abrogate binding to its cognate substrate PI3P and thus prevent its translocation to early endosomes. Although the endosomal recycling pathway was unaltered, mutant p.Gly183Arg patient fibroblasts exhibit accumulation of cargo tagged for lysosomal degradation. Our results suggest that these variants are separation-of-function alleles, which cause a delay in endosomal maturation without affecting cargo recycling. We conclude that distinct germline mutations in RBSN cause non-overlapping phenotypes with specific and discrete endolysosomal cellular defects.
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Affiliation(s)
- Franziska Paul
- Laboratory of Human Genetics & Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Calista Ng
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Umar Bin Mohamad Sahari
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Shahriar Nafissi
- Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Yalda Nilipoor
- Pediatric Pathology Research Centre, Research Institute for Children Health, Shahid Beheshti Medical University, Tehran, Iran
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Tehran University Of Medical Sciences, Tehran, Iran
| | - Carine Bonnard
- Model Development, A*STAR Skin Research Labs (ASRL), Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
| | - Nasrinsadat Nabavizadeh
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
| | - Umut Altunoğlu
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
| | - Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
| | - Charles B Majoie
- Department of Radiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Hane Lee
- 3billion Inc., Seoul, South Korea
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Paul P Van Veldhoven
- Laboratory of Lipid Biochemistry and Protein Interactions (LIPIT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Rami Massie
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
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15
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Wilkes MC, Scanlon V, Shibuya A, Celika AM, Eskin A, Chen Z, Narla A, Glader B, Roncarolo MG, Nelson SF, Sakamoto KM. Downregulation of SATB1 by miRNAs Reduces Megakaryocyte/Erythroid Progenitor Expansion in pre-clinical models of Diamond Blackfan Anemia. Exp Hematol 2022; 111:66-78. [PMID: 35460833 PMCID: PMC9255422 DOI: 10.1016/j.exphem.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/27/2022]
Abstract
Diamond Blackfan Anemia (DBA) is an inherited bone marrow failure syndrome that is associated with anemia, congenital anomalies, and cancer predisposition. It is categorized as a ribosomopathy, because over 80% or patients have haploinsufficiency of either a small or large subunit-associated ribosomal protein (RP). The erythroid pathology is predominantly due to a block and delay in early committed erythropoiesis with reduced Megakaryocyte/Erythroid Progenitors (MEPs). To understand the molecular pathways leading to pathogenesis of DBA, we performed RNA-seq on mRNA and miRNA from RPS19-deficient human hematopoietic stem and progenitor cells (HSPCs) and compared an existing database documenting transcript fluctuations across stages of early normal erythropoiesis. We determined the chromatin regulator, SATB1 was prematurely downregulated through the coordinated action of upregulated miR-34 and miR-30 during differentiation in ribosomal-insufficiency. Restoration of SATB1 rescued MEP expansion, leading to a modest improvement in erythroid and megakaryocyte expansion in RPS19-insufficiency. However, SATB1 expression did not impact expansion of committed erythroid progenitors, indicating ribosomal insufficiency impacts multiple stages during erythroid differentiation.
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Affiliation(s)
- Mark C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | - Vanessa Scanlon
- Yale Stem Cell Center, Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut 06509, USA
| | - Aya Shibuya
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | - Alma-Martina Celika
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Ascia Eskin
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Zugen Chen
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Anupama Narla
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | - Bert Glader
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | - Maria Grazia Roncarolo
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, California 94305, USA.
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16
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Barthélémy F, Santoso JW, Rabichow L, Jin R, Little I, Nelson SF, McCain ML, Miceli MC. Modeling Patient-Specific Muscular Dystrophy Phenotypes and Therapeutic Responses in Reprogrammed Myotubes Engineered on Micromolded Gelatin Hydrogels. Front Cell Dev Biol 2022; 10:830415. [PMID: 35465312 PMCID: PMC9020228 DOI: 10.3389/fcell.2022.830415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
In vitro models of patient-derived muscle allow for more efficient development of genetic medicines for the muscular dystrophies, which often present mutation-specific pathologies. One popular strategy to generate patient-specific myotubes involves reprogramming dermal fibroblasts to a muscle lineage through MyoD induction. However, creating physiologically relevant, reproducible tissues exhibiting multinucleated, aligned myotubes with organized striations is dependent on the introduction of physicochemical cues that mimic the native muscle microenvironment. Here, we engineered patient-specific control and dystrophic muscle tissues in vitro by culturing and differentiating MyoD–directly reprogrammed fibroblasts isolated from one healthy control subject, three patients with Duchenne muscular dystrophy (DMD), and two Limb Girdle 2A/R1 (LGMD2A/R1) patients on micromolded gelatin hydrogels. Engineered DMD and LGMD2A/R1 tissues demonstrated varying levels of defects in α-actinin expression and organization relative to control, depending on the mutation. In genetically relevant DMD tissues amenable to mRNA reframing by targeting exon 44 or 45 exclusion, exposure to exon skipping antisense oligonucleotides modestly increased myotube coverage and alignment and rescued dystrophin protein expression. These findings highlight the value of engineered culture substrates in guiding the organization of reprogrammed patient fibroblasts into aligned muscle tissues, thereby extending their value as tools for exploration and dissection of the cellular and molecular basis of genetic muscle defects, rescue, and repair.
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Affiliation(s)
- Florian Barthélémy
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeffrey W. Santoso
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Laura Rabichow
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rongcheng Jin
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Isaiah Little
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Megan L. McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
- *Correspondence: M. Carrie Miceli, ; Megan L. McCain,
| | - M. Carrie Miceli
- Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: M. Carrie Miceli, ; Megan L. McCain,
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17
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Yang JO, Shaybekyan H, Zhao Y, Kang X, Fishbein GA, Khanlou N, Alejos JC, Halnon N, Satou G, Biniwale R, Lee H, Van Arsdell G, Nelson SF, Touma M. Case Report: Whole Exome Sequencing Identifies Compound Heterozygous Variants in TSFM Gene Causing Juvenile Hypertrophic Cardiomyopathy. Front Cardiovasc Med 2022; 8:798985. [PMID: 35071363 PMCID: PMC8770926 DOI: 10.3389/fcvm.2021.798985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/08/2021] [Indexed: 02/04/2023] Open
Abstract
We report a case of hypertrophic cardiomyopathy and lactic acidosis in a 3-year-old female. Cardiac and skeletal muscles biopsies exhibited mitochondrial hyperplasia with decreased complex IV activity. Whole exome sequencing identified compound heterozygous variants, p.Arg333Trp and p.Val119Leu, in TSFM, a nuclear gene that encodes a mitochondrial translation elongation factor, resulting in impaired oxidative phosphorylation and juvenile hypertrophic cardiomyopathy.
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Affiliation(s)
- Jamie O Yang
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hapet Shaybekyan
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yan Zhao
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xuedong Kang
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Negar Khanlou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Juan C Alejos
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nancy Halnon
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gary Satou
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Reshma Biniwale
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Glen Van Arsdell
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F Nelson
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Marlin Touma
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, David Geffen School of Medicine, Children's Discovery and Innovation Institute, University of California, Los Angeles, Los Angeles, CA, United States.,The Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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18
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Marcogliese PC, Dutta D, Ray SS, Dang NDP, Zuo Z, Wang Y, Lu D, Fazal F, Ravenscroft TA, Chung H, Kanca O, Wan J, Douine ED, Network UD, Pena LDM, Yamamoto S, Nelson SF, Might M, Meyer KC, Yeo NC, Bellen HJ. Loss of IRF2BPL impairs neuronal maintenance through excess Wnt signaling. Sci Adv 2022; 8:eabl5613. [PMID: 35044823 PMCID: PMC8769555 DOI: 10.1126/sciadv.abl5613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 05/12/2023]
Abstract
De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction of Pits. Loss of irf2bpl in zebrafish also causes neurological defects with an associated increase in wnt1 transcription and downstream signaling. WNT1 is also increased in patient-derived astrocytes, and pharmacological inhibition of Wnt suppresses the neurological phenotypes. Last, IRF2BPL and the Wnt antagonist, CKIα, physically and genetically interact, showing that IRF2BPL and CkIα antagonize Wnt transcription and signaling.
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Affiliation(s)
- Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shrestha Sinha Ray
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Nghi D. P. Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Yuchun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Di Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Fatima Fazal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Thomas A. Ravenscroft
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - JiJun Wan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Undiagnosed Diseases Network
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Loren D. M. Pena
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Matthew Might
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Kathrin C. Meyer
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Apkon S, Kinnett K, Cripe L, Duan D, Jackson JL, Kornegay JN, Mah ML, Nelson SF, Rao V, Scavina M, Wong BL, Flanigan KM. Parent Project Muscular Dystrophy Females with Dystrophinopathy Conference, Orlando, Florida June 26 - June 27, 2019. J Neuromuscul Dis 2021; 8:315-322. [PMID: 33361607 PMCID: PMC10497321 DOI: 10.3233/jnd-200555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Susan Apkon
- Department of Physical Medicine and Rehabilitation, University of Colorado Denver and Children’s Hospital Colorado, Aurora, CO, USA
| | - Kathi Kinnett
- Parent Project Muscular Dystrophy, Hackensack, NJ, USA
| | - Linda Cripe
- The Heart Center, Nationwide Children’s Hospital and the Ohio State University, Columbus, OH, USA
| | - Dongsheng Duan
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Jamie L. Jackson
- Center for Biobehavioral Health, Abigail Wexner Research Institute at Nationwide Children’s Hospital; Assistant Professor of Pediatrics and Psychology, The Ohio State University, Columbus, OH, USA
| | - Joe N. Kornegay
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4458 TAMU, College Station, TX, USA
| | - May Ling Mah
- The Heart Center, Nationwide Children’s Hospital and the Ohio State University, Columbus, OH, USA
| | - Stanley F. Nelson
- Department of Human Genetics, Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Vamshi Rao
- Department of Pediatrics, Division of Neurology, Ann and Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mena Scavina
- Department of Neurology, Nemours/duPont Hospital for Children, Wilmington, DE, USA
| | - Brenda L. Wong
- Department of Pediatrics and Neurology, University of Massachusetts Medical School, Worcester, MA USA
| | - Kevin M. Flanigan
- Center for Gene Therapy, Nationwide Children’s Hospital and Departments of Pediatrics and Neurology, Ohio State University, Columbus, Ohio, USA
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20
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Findley L, Mulvihill JJ, Bentley A, Bernstein JA, Bican A, Botto L, Briere L, Butte MJ, Cope H, Fogel BL, Hom J, Kravets E, Mak BC, Martin MG, Martinez-Agosto JA, Nelson SF, Newman J, Palmer CGS, Parker NH, Rosenfeld JA, Ruzhnikov M, Schoch K, Spillmann R. Corrigendum to eP296-The yield of thorough record review in the Undiagnosed Diseases Network, Volume 132, Supplement 1, April 2021, Page S187, https://doi.org/10.1016/S1096-7192(21)00378-4. Mol Genet Metab 2021. [PMID: 34663553 DOI: 10.1016/j.ymgme.2021.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Abbey Bentley
- Baylor College of Medicine, United States of America
| | | | - Anna Bican
- Harvard University, United States of America
| | - Lorenzo Botto
- Baylor College of Medicine, United States of America
| | | | | | - Heidi Cope
- Vanderbilt University, United States of America
| | | | - Jason Hom
- Duke University, United States of America
| | | | - Bryan C Mak
- University of Utah, United States of America
| | | | | | | | - John Newman
- Harvard University, United States of America
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21
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Mehta Z, Zhao Y, Xuedong K, Alejos JC, Halnon N, Nelson SF, Touma M. Abstract MP212: Integrated Genomics Analysis Identifies Recessive Ciliopathy Mutations In Primary Endocardial Fibroelastosis: A Rare Neonatal Cardiomyopathy. Circ Res 2021. [DOI: 10.1161/res.129.suppl_1.mp212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Among neonatal cardiomyopathies, primary endocardial fibroelastosis (pEFE) remains a mysterious disease of the endomyocardium, affecting 1/5000 live births and accounting for 25% of the entire pediatric dilated cardiomyopathy (DCM) population with a devastating course and grave prognosis.
Objective:
We aimed to investigate potential genetic contributions to pEFE etiology.
Methods:
We performed integrative genomic analysis in 8 infants with confirmed pathological diagnosis of pEFE using whole exome sequencing (WES), RNA-seq and functional genomics studies. Patient-derived fibroblasts, neonatal rat ventricular myocytes and neonatal rat cardiac fibroblasts were used for cellular assays. Real-time cell migration and proliferation analyses were performed using xCELLigence technology.
Results:
Whole exome sequencing detected novel and deleterious
de novo
single nucleotide variants, or inherited homozygous rare variants in 11 cilia-related genes in seven out of the eight affected probands. In particular, a novel homozygous variant [c.1938delA] in
ALMS1
was identified in a female proband, pEFE4. This variant resulted in a frameshift introducing a premature stop codon and complete absence of the ALMS1 protein in the proband fibroblasts and explanted heart. Loss of function mutations of
ALMS1
have been implicated in Alstrom syndrome [OMIM 203800], a rare recessive ciliopathy. RNA-sequencing of the proband’s dermal fibroblasts revealed significantly dysregulated cellular signaling and function, including the induction of epithelial mesenchymal transition (EMT), potentially mediated by TGFβ signaling activation. The proband fibroblasts exhibited enhanced migration activity. Herein, we present the unique pathological features of pEFE compared to DCM and utilize integrated WES with RNA-seq analysis to elucidate the molecular mechanisms by which the novel causal
ALMS1
variant contributes to the unique pathology of pEFE in a female infant with Alstrom syndrome.
Conclusions:
Our report provides insights into pEFE etiology and suggests, for the first time to our knowledge, ciliopathy as a potential underlying mechanism for this poorly understood and incurable form of neonatal cardiomyopathy.
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Affiliation(s)
- Zubin Mehta
- DAVID GEFFEN SCHOOL MEDICINE, UNIVERSITY OF CALIFORNIA, LOS ANGELES, CA
| | - Yan Zhao
- UCLA DAVID GEFFEN SCHOOL MEDICINE, Los Angeles, CA
| | - Kang Xuedong
- UCLA DAVID GEFFEN SCHOOL MEDICINE, Los Angeles, CA
| | | | - Nancy Halnon
- UCLA DAVID GEFFEN SCHOOL MEDICINE, Los Angeles, CA
| | | | - Marlin Touma
- UCLA DAVID GEFFEN SCHOOL MEDICINE, Los Angeles, CA
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22
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Zhao Y, Wang LK, Eskin A, Kang X, Fajardo VM, Mehta Z, Pineles S, Schmidt RJ, Nagiel A, Satou G, Garg M, Federman M, Reardon LC, Lee SL, Biniwale R, Grody WW, Halnon N, Khanlou N, Quintero-Rivera F, Alejos JC, Nakano A, Fishbein GA, Van Arsdell GS, Nelson SF, Touma M. Recessive ciliopathy mutations in primary endocardial fibroelastosis: a rare neonatal cardiomyopathy in a case of Alstrom syndrome. J Mol Med (Berl) 2021; 99:1623-1638. [PMID: 34387706 PMCID: PMC8541947 DOI: 10.1007/s00109-021-02112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/28/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022]
Abstract
Abstract Among neonatal cardiomyopathies, primary endocardial fibroelastosis (pEFE) remains a mysterious disease of the endomyocardium that is poorly genetically characterized, affecting 1/5000 live births and accounting for 25% of the entire pediatric dilated cardiomyopathy (DCM) with a devastating course and grave prognosis. To investigate the potential genetic contribution to pEFE, we performed integrative genomic analysis, using whole exome sequencing (WES) and RNA-seq in a female infant with confirmed pathological diagnosis of pEFE. Within regions of homozygosity in the proband genome, WES analysis revealed novel parent-transmitted homozygous mutations affecting three genes with known roles in cilia assembly or function. Among them, a novel homozygous variant [c.1943delA] of uncertain significance in ALMS1 was prioritized for functional genomic and mechanistic analysis. Loss of function mutations of ALMS1 have been implicated in Alstrom syndrome (AS) [OMIM 203800], a rare recessive ciliopathy that has been associated with cardiomyopathy. The variant of interest results in a frameshift introducing a premature stop codon. RNA-seq of the proband’s dermal fibroblasts confirmed the impact of the novel ALMS1 variant on RNA-seq reads and revealed dysregulated cellular signaling and function, including the induction of epithelial mesenchymal transition (EMT) and activation of TGFβ signaling. ALMS1 loss enhanced cellular migration in patient fibroblasts as well as neonatal cardiac fibroblasts, while ALMS1-depleted cardiomyocytes exhibited enhanced proliferation activity. Herein, we present the unique pathological features of pEFE compared to DCM and utilize integrated genomic analysis to elucidate the molecular impact of a novel mutation in ALMS1 gene in an AS case. Our report provides insights into pEFE etiology and suggests, for the first time to our knowledge, ciliopathy as a potential underlying mechanism for this poorly understood and incurable form of neonatal cardiomyopathy. Key message Primary endocardial fibroelastosis (pEFE) is a rare form of neonatal cardiomyopathy that occurs in 1/5000 live births with significant consequences but unknown etiology. Integrated genomics analysis (whole exome sequencing and RNA sequencing) elucidates novel genetic contribution to pEFE etiology. In this case, the cardiac manifestation in Alstrom syndrome is pEFE. To our knowledge, this report provides the first evidence linking ciliopathy to pEFE etiology. Infants with pEFE should be examined for syndromic features of Alstrom syndrome. Our findings lead to a better understanding of the molecular mechanisms of pEFE, paving the way to potential diagnostic and therapeutic applications.
Supplementary information The online version contains supplementary material available at 10.1007/s00109-021-02112-z.
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Affiliation(s)
- Yan Zhao
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Children's Discovery and Innovation Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee-Kai Wang
- Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xuedong Kang
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Children's Discovery and Innovation Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Viviana M Fajardo
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Zubin Mehta
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Children's Discovery and Innovation Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Stacy Pineles
- Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Aaron Nagiel
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Ophthalmology, Roski Eye Institute, University of Southern California, Los Angeles, CA, USA
| | - Gary Satou
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Meena Garg
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Myke Federman
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Leigh C Reardon
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Ahmanson/UCLA Adult Congenital Heart Disease Center, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Steven L Lee
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Reshma Biniwale
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Wayne W Grody
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nancy Halnon
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Negar Khanlou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine and Department of Pediatrics, University of California Irvine, CA, Irvine, USA
| | - Juan C Alejos
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA
| | - Atsushi Nakano
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Glen S Van Arsdell
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA.,Institute for Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Marlin Touma
- Department of Pediatrics, 3762 MacDonald Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, 675 Charles E. Young Dr S, CA, 90095, Los Angeles, USA. .,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Pediatrics, Children's Discovery and Innovation Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,The Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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23
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Marbach F, Stoyanov G, Erger F, Stratakis CA, Settas N, London E, Rosenfeld JA, Torti E, Haldeman-Englert C, Sklirou E, Kessler E, Ceulemans S, Nelson SF, Martinez-Agosto JA, Palmer CGS, Signer RH, Andrews MV, Grange DK, Willaert R, Person R, Telegrafi A, Sievers A, Laugsch M, Theiß S, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP. Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain. Genet Med 2021; 23:1465-1473. [PMID: 33833410 PMCID: PMC8354857 DOI: 10.1038/s41436-021-01152-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022] Open
Abstract
PURPOSE We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA). METHODS Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development. RESULTS Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs. CONCLUSION Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.
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Affiliation(s)
- Felix Marbach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Georgi Stoyanov
- Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Florian Erger
- Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Nikolaos Settas
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Edra London
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | | | | | - Evgenia Sklirou
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elena Kessler
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sophia Ceulemans
- Genetics/Dysmorphology, Rady Children's Hospital, San Diego, CA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute for Society and Genetics, UCLA, Los Angeles, CA, USA
| | - Rebecca H Signer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marisa V Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | | | | | | | - Aaron Sievers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Magdalena Laugsch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Susanne Theiß
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - YuZhu Cheng
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Biomedicine West Wing, International Centre for Life, Times Square, Newcastle upon Tyne, UK
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amber Stocco
- INTEGRIS Pediatric Neurology, Oklahoma City, OK, USA
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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24
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Huang Y, Grand K, Kimonis V, Butler MG, Jain S, Huang AYW, Martinez-Agosto JA, Nelson SF, Sanchez-Lara PA. Mosaic de novo SNRPN gene variant associated with Prader-Willi syndrome. J Med Genet 2021; 59:719-722. [PMID: 34099539 DOI: 10.1136/jmedgenet-2020-107674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/11/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Prader-Willi syndrome (PWS) is an imprinting disorder caused by the absence of paternal expressed genes in the Prader-Willi critical region (PWCR) on chromosome 15q11.2-q13. Three molecular mechanisms have been known to cause PWS, including a deletion in the PWCR, uniparental disomy 15 and imprinting defects. RESULTS We report the first case of PWS associated with a single-nucleotide SNRPN variant in a 10-year-old girl presenting with clinical features consistent with PWS, including infantile hypotonia and feeding difficulty, developmental delay with cognitive impairment, excessive eating with central obesity, sleep disturbances, skin picking and related behaviour issues. Whole-exome sequencing revealed a de novo mosaic nonsense variant of the SNRPN gene (c.73C>T, p.R25X) in 10% of DNA isolated from buccal cells and 19% of DNA from patient-derived lymphoblast cells. DNA methylation study did not detect an abnormal methylation pattern in the SNRPN locus. Parental origin studies showed a paternal source of an intronic single-nucleotide polymorphism within the locus in proximity to the SNRPN variant. CONCLUSIONS This is the first report that provides evidence of a de novo point mutation of paternal origin in SNRPN as a new disease-causing mechanism for PWS. This finding suggests that gene sequencing should be considered as part of the diagnostic workup in patients with clinical suspicion of PWS.
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Affiliation(s)
- Yue Huang
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Virginia Kimonis
- Department of Pediatrics, UCI and Children's Hospital of Orange County, Irvine, California, USA
| | - Merlin G Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Suparna Jain
- Pediatric Endocrinology, Department of Pediatrics, Cedar-Sinai Medical Center, Los Angeles, California, USA
| | - Alden Yen-Wen Huang
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
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25
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Mannucci I, Dang NDP, Huber H, Murry JB, Abramson J, Althoff T, Banka S, Baynam G, Bearden D, Beleza-Meireles A, Benke PJ, Berland S, Bierhals T, Bilan F, Bindoff LA, Braathen GJ, Busk ØL, Chenbhanich J, Denecke J, Escobar LF, Estes C, Fleischer J, Groepper D, Haaxma CA, Hempel M, Holler-Managan Y, Houge G, Jackson A, Kellogg L, Keren B, Kiraly-Borri C, Kraus C, Kubisch C, Le Guyader G, Ljungblad UW, Brenman LM, Martinez-Agosto JA, Might M, Miller DT, Minks KQ, Moghaddam B, Nava C, Nelson SF, Parant JM, Prescott T, Rajabi F, Randrianaivo H, Reiter SF, Schuurs-Hoeijmakers J, Shieh PB, Slavotinek A, Smithson S, Stegmann APA, Tomczak K, Tveten K, Wang J, Whitlock JH, Zweier C, McWalter K, Juusola J, Quintero-Rivera F, Fischer U, Yeo NC, Kreienkamp HJ, Lessel D. Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders. Genome Med 2021; 13:90. [PMID: 34020708 PMCID: PMC8140440 DOI: 10.1186/s13073-021-00900-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/28/2021] [Indexed: 12/27/2022] Open
Abstract
Background We aimed to define the clinical and variant spectrum and to provide novel molecular insights into the DHX30-associated neurodevelopmental disorder. Methods Clinical and genetic data from affected individuals were collected through Facebook-based family support group, GeneMatcher, and our network of collaborators. We investigated the impact of novel missense variants with respect to ATPase and helicase activity, stress granule (SG) formation, global translation, and their effect on embryonic development in zebrafish. SG formation was additionally analyzed in CRISPR/Cas9-mediated DHX30-deficient HEK293T and zebrafish models, along with in vivo behavioral assays. Results We identified 25 previously unreported individuals, ten of whom carry novel variants, two of which are recurrent, and provide evidence of gonadal mosaicism in one family. All 19 individuals harboring heterozygous missense variants within helicase core motifs (HCMs) have global developmental delay, intellectual disability, severe speech impairment, and gait abnormalities. These variants impair the ATPase and helicase activity of DHX30, trigger SG formation, interfere with global translation, and cause developmental defects in a zebrafish model. Notably, 4 individuals harboring heterozygous variants resulting either in haploinsufficiency or truncated proteins presented with a milder clinical course, similar to an individual harboring a de novo mosaic HCM missense variant. Functionally, we established DHX30 as an ATP-dependent RNA helicase and as an evolutionary conserved factor in SG assembly. Based on the clinical course, the variant location, and type we establish two distinct clinical subtypes. DHX30 loss-of-function variants cause a milder phenotype whereas a severe phenotype is caused by HCM missense variants that, in addition to the loss of ATPase and helicase activity, lead to a detrimental gain-of-function with respect to SG formation. Behavioral characterization of dhx30-deficient zebrafish revealed altered sleep-wake activity and social interaction, partially resembling the human phenotype. Conclusions Our study highlights the usefulness of social media to define novel Mendelian disorders and exemplifies how functional analyses accompanied by clinical and genetic findings can define clinically distinct subtypes for ultra-rare disorders. Such approaches require close interdisciplinary collaboration between families/legal representatives of the affected individuals, clinicians, molecular genetics diagnostic laboratories, and research laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00900-3.
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Affiliation(s)
- Ilaria Mannucci
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Nghi D P Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Hannes Huber
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Jaclyn B Murry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeff Abramson
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thorsten Althoff
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gareth Baynam
- Faculty of Medicine and Health Sciences, University of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia.,Telethon Kids Institute, Perth, Australia
| | - David Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Ana Beleza-Meireles
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jirat Chenbhanich
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246, Hamburg, Germany
| | - Luis F Escobar
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Caroline Estes
- Peyton Manning Children's Hospital, Ascension Health, Indianapolis, IN, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yolanda Holler-Managan
- Division of Neurology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.,Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Boris Keren
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Cliniques et Expérimentales-INSERM U1084, Université de Poitiers, Poitiers, France
| | - Ulf W Ljungblad
- Department of Pediatrics, Vestfold Hospital, 3116, Tønsberg, Norway
| | | | - Julian A Martinez-Agosto
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pediatrics, Division of Medical Genetics at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kelly Q Minks
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | | | - Caroline Nava
- Département de Génétique, Hôpital La Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics at David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, USA.,Center for Duchenne Muscular Dystrophy, University of California Los Angeles, Los Angeles, CA, USA
| | - John M Parant
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hanitra Randrianaivo
- UF de Génétique Médicale, GHSR, CHU de La Réunion, Saint Pierre, La Réunion, France
| | - Simone F Reiter
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | | | - Perry B Shieh
- Department of Neurology at David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Smithson
- Clinical Genetics Department, University Hospitals Bristol and Weston, Bristol, UK
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kinga Tomczak
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA
| | - Jordan H Whitlock
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL, 35210, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | | | | | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, Biocenter of the University of Würzburg, 97070, Würzburg, Germany
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, USA.
| | - Hans-Jürgen Kreienkamp
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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26
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Sheppard SE, Campbell IM, Harr MH, Gold N, Li D, Bjornsson HT, Cohen JS, Fahrner JA, Fatemi A, Harris JR, Nowak C, Stevens CA, Grand K, Au M, Graham JM, Sanchez-Lara PA, Campo MD, Jones MC, Abdul-Rahman O, Alkuraya FS, Bassetti JA, Bergstrom K, Bhoj E, Dugan S, Kaplan JD, Derar N, Gripp KW, Hauser N, Innes AM, Keena B, Kodra N, Miller R, Nelson B, Nowaczyk MJ, Rahbeeni Z, Ben-Shachar S, Shieh JT, Slavotinek A, Sobering AK, Abbott MA, Allain DC, Amlie-Wolf L, Au PYB, Bedoukian E, Beek G, Barry J, Berg J, Bernstein JA, Cytrynbaum C, Chung BHY, Donoghue S, Dorrani N, Eaton A, Flores-Daboub JA, Dubbs H, Felix CA, Fong CT, Fung JLF, Gangaram B, Goldstein A, Greenberg R, Ha TK, Hersh J, Izumi K, Kallish S, Kravets E, Kwok PY, Jobling RK, Knight Johnson AE, Kushner J, Lee BH, Levin B, Lindstrom K, Manickam K, Mardach R, McCormick E, McLeod DR, Mentch FD, Minks K, Muraresku C, Nelson SF, Porazzi P, Pichurin PN, Powell-Hamilton NN, Powis Z, Ritter A, Rogers C, Rohena L, Ronspies C, Schroeder A, Stark Z, Starr L, Stoler J, Suwannarat P, Velinov M, Weksberg R, Wilnai Y, Zadeh N, Zand DJ, Falk MJ, Hakonarson H, Zackai EH, Quintero-Rivera F. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. Am J Med Genet A 2021; 185:1649-1665. [PMID: 33783954 DOI: 10.1002/ajmg.a.62124] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.
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Affiliation(s)
- Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian M Campbell
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, Massachusetts, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Iceland
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, The Feingold Center for Children, Boston, Massachusetts, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Miguel Del Campo
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Marilyn C Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah Dugan
- Division of Medical Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Julie D Kaplan
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nada Derar
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Natalie Hauser
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Beth Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Neslida Kodra
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Rebecca Miller
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Beverly Nelson
- Department of Clinical Skills, St. George's University, True Blue, Grenada
| | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shay Ben-Shachar
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph T Shieh
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Andrew K Sobering
- Department of Biochemistry, St. George's University, True Blue, Grenada
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, Massachusetts, USA
| | - Dawn C Allain
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Ping Yee Billie Au
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Geoffrey Beek
- Children's Hospital of Minnesota, Minneapolis, Minnesota, USA
| | - James Barry
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Janet Berg
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA
| | - Alison Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carolyn A Felix
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chin-To Fong
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Balram Gangaram
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Amy Goldstein
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rotem Greenberg
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thoa K Ha
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Joseph Hersh
- Weisskopf Child Evaluation Center, Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elijah Kravets
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Pui-Yan Kwok
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Rebekah K Jobling
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Jessica Kushner
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Bo Hoon Lee
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Kandamurugu Manickam
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rebecca Mardach
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - D Ross McLeod
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Minks
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Colleen Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA.,Department of Human Genetics, Center for Duchenne Muscular Dystrophy University of California Los Angeles, California, Los Angeles, USA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pavel N Pichurin
- Clinical Genomics Center, University of California Los Angeles, Los Angeles, California, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Zoe Powis
- Quest Diagnostics Kalamzoo, Kalamzoo, Michigan, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Caleb Rogers
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Carey Ronspies
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Audrey Schroeder
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lois Starr
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Milen Velinov
- NYS Institute for Basic Research in developmental Disabilities, Staten Island, New York, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Yael Wilnai
- Genetic Institute, Sourasky Medical Center, Te-Aviv, Tel Aviv, Israel
| | - Neda Zadeh
- Genetics Center and CHOC Children's Hospital, Orange, California, USA
| | - Dina J Zand
- Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Fabiola Quintero-Rivera
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, California, Los Angeles, USA
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27
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Hüffmeier U, Kraus C, Reuter MS, Uebe S, Abbott MA, Ahmed SA, Rawson KL, Barr E, Li H, Bruel AL, Faivre L, Tran Mau-Them F, Botti C, Brooks S, Burns K, Ward DI, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Nelson SF, Zacher P, Abou Jamra R, Klöckner C, McGaughran J, Kohlhase J, Schuhmann S, Moran E, Pappas J, Raas-Rothschild A, Sacoto MJG, Henderson LB, Palculict TB, Mullegama SV, Zghal Elloumi H, Reich A, Schrier Vergano SA, Wahl E, Reis A, Zweier C. EIF3F-related neurodevelopmental disorder: refining the phenotypic and expanding the molecular spectrum. Orphanet J Rare Dis 2021; 16:136. [PMID: 33736665 PMCID: PMC7977188 DOI: 10.1186/s13023-021-01744-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND An identical homozygous missense variant in EIF3F, identified through a large-scale genome-wide sequencing approach, was reported as causative in nine individuals with a neurodevelopmental disorder, characterized by variable intellectual disability, epilepsy, behavioral problems and sensorineural hearing-loss. To refine the phenotypic and molecular spectrum of EIF3F-related neurodevelopmental disorder, we examined independent patients. RESULTS 21 patients were homozygous and one compound heterozygous for c.694T>G/p.(Phe232Val) in EIF3F. Haplotype analyses in 15 families suggested that c.694T>G/p.(Phe232Val) was a founder variant. All affected individuals had developmental delays including delayed speech development. About half of the affected individuals had behavioral problems, altered muscular tone, hearing loss, and short stature. Moreover, this study suggests that microcephaly, reduced sensitivity to pain, cleft lip/palate, gastrointestinal symptoms and ophthalmological symptoms are part of the phenotypic spectrum. Minor dysmorphic features were observed, although neither the individuals' facial nor general appearance were obviously distinctive. Symptoms in the compound heterozygous individual with an additional truncating variant were at the severe end of the spectrum in regard to motor milestones, speech delay, organic problems and pre- and postnatal growth of body and head, suggesting some genotype-phenotype correlation. CONCLUSIONS Our study refines the phenotypic and expands the molecular spectrum of EIF3F-related syndromic neurodevelopmental disorder.
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Affiliation(s)
- Ulrike Hüffmeier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Miriam S Reuter
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, MA, USA
| | - Syed A Ahmed
- Department of Genetics, Southern California Permanente Medical Group, Kaiser Permanente, Riverside, CA, USA
| | - Kristyn L Rawson
- Department of Genetics, Southern California Permanente Medical Group, Kaiser Permanente, Riverside, CA, USA
| | - Eileen Barr
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hong Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ange-Line Bruel
- UMR-Inserm 1231 GAD Team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, 21000, Dijon, France
- Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau de Biologie Hospitalo-Universitaire, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Laurence Faivre
- UMR-Inserm 1231 GAD Team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, 21000, Dijon, France
- Centre de Génétique, Centre de Référence «Anomalies du Développement et Syndromes Malformatifs» et FHU TRANSLAD, Hôpital D'Enfants, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR-Inserm 1231 GAD Team, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, 21000, Dijon, France
- Laboratoire de Génétique Chromosomique et Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau de Biologie Hospitalo-Universitaire, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Christina Botti
- Division of Medical Genetics, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Susan Brooks
- Division of Medical Genetics, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | | | | | - Marina Dutra-Clarke
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Julian A Martinez-Agosto
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Stanley F Nelson
- Division of Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Pia Zacher
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Woman's Hospital, Brisbane, Australia
- School of Medicine, The University of Queensland, St Lucia, Brisbane, Australia
| | | | - Sarah Schuhmann
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Ellen Moran
- Clinical Genetics, Hassenfeld Children's Hospital at NYU Langone, NYU Langone, Orthopedic Hospital, New York, NY, USA
| | - John Pappas
- Division of Clinical Genetic Services, Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Annick Raas-Rothschild
- Sackler School of Medicine at Tel Aviv University, Tel Aviv, Israel
- Institute of Rare Diseases, Edmond & Lily Safra Children Hospital, Tel Hashomer, Israel
| | | | | | | | | | | | - Adi Reich
- GeneDx, Gaithersburg, MD, 20877, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Erica Wahl
- Division of Genetics, UBMD Pediatrics, Buffalo, NY, USA
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054, Erlangen, Germany
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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28
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Bishop DP, Westerhausen MT, Barthelemy F, Lockwood T, Cole N, Gibbs EM, Crosbie RH, Nelson SF, Miceli MC, Doble PA, Wanagat J. Quantitative immuno-mass spectrometry imaging of skeletal muscle dystrophin. Sci Rep 2021; 11:1128. [PMID: 33441839 PMCID: PMC7806610 DOI: 10.1038/s41598-020-80495-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Emerging and promising therapeutic interventions for Duchenne muscular dystrophy (DMD) are confounded by the challenges of quantifying dystrophin. Current approaches have poor precision, require large amounts of tissue, and are difficult to standardize. This paper presents an immuno-mass spectrometry imaging method using gadolinium (Gd)-labeled anti-dystrophin antibodies and laser ablation-inductively coupled plasma-mass spectrometry to simultaneously quantify and localize dystrophin in muscle sections. Gd is quantified as a proxy for the relative expression of dystrophin and was validated in murine and human skeletal muscle sections following k-means clustering segmentation, before application to DMD patients with different gene mutations where dystrophin expression was measured up to 100 µg kg-1 Gd. These results demonstrate that immuno-mass spectrometry imaging is a viable approach for pre-clinical to clinical research in DMD. It rapidly quantified relative dystrophin in single tissue sections, efficiently used valuable patient resources, and may provide information on drug efficacy for clinical translation.
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Affiliation(s)
- David P Bishop
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mika T Westerhausen
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Florian Barthelemy
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thomas Lockwood
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nerida Cole
- ARC Training Centre in Biodevices, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Elizabeth M Gibbs
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Rachelle H Crosbie
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philip A Doble
- Atomic Medicine Initiative, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
- Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, 10945 Le Conte Avenue, Suite 2339, Los Angeles, CA, 90095, USA.
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29
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Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez-Agosto JA, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Expansion of NEUROD2 phenotypes to include developmental delay without seizures. Am J Med Genet A 2021; 185:1076-1080. [PMID: 33438828 DOI: 10.1002/ajmg.a.62064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 01/23/2023]
Abstract
De novo heterozygous variants in the brain-specific transcription factor Neuronal Differentiation Factor 2 (NEUROD2) have been recently associated with early-onset epileptic encephalopathy and developmental delay. Here, we report an adolescent with developmental delay without seizures who was found to have a novel de novo heterozygous NEUROD2 missense variant, p.(Leu163Pro). Functional testing using an in vivo assay of neuronal differentiation in Xenopus laevis tadpoles demonstrated that the patient variant of NEUROD2 displays minimal protein activity, strongly suggesting a loss of function effect. In contrast, a second rare NEUROD2 variant, p.(Ala235Thr), identified in an adolescent with developmental delay but lacking parental studies for inheritance, showed normal in vivo NEUROD2 activity. We thus provide clinical, genetic, and functional evidence that NEUROD2 variants can lead to developmental delay without accompanying early-onset seizures, and demonstrate how functional testing can complement genetic data when determining variant pathogenicity.
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Affiliation(s)
- Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebecca H Signer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA
| | | | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julian A Martinez-Agosto
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Christina G S Palmer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Institute for Society and Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Hane Lee
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Thomas Mitzelfelt
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elysa Marco
- Cortica, San Rafael, California, USA.,Pediatric Brain Center, University of California San Francisco, San Francisco, California, USA
| | - Martin G Martin
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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30
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Barthelemy F, Woods JD, Nieves‐Rodriguez S, Douine ED, Wang R, Wanagat J, Miceli MC, Nelson SF. A well-tolerated core needle muscle biopsy process suitable for children and adults. Muscle Nerve 2020; 62:688-698. [PMID: 32820569 PMCID: PMC7756388 DOI: 10.1002/mus.27041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Serial muscle biopsies within clinical trials for Duchenne muscular dystrophy (DMD) are critical to document therapeutic responses. Less invasive means of sampling muscle are needed. We analyzed a retrospective consecutive case-series cohort of vacuum-assisted core needle muscle biopsy procedures performed on healthy and dystrophic individuals at a single institution assessing for safety and reliability of obtaining sufficient high-quality biopsy tissue for histologic assessment in adult and pediatric subjects. Of 471 muscle cores from 128 biopsy procedures, 377-550 mg of total muscle tissue was obtained per procedure with mean core weight of 129 mg (SD, 25.1 mg). All biopsies were adequate for histological assessment. There were no significant adverse events. This core needle biopsy approach, when combined with improved sample processing, provides a safe means to consistently obtain muscle samples for diagnostic and clinical trial applications.
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Affiliation(s)
- Florian Barthelemy
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and SciencesUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jeremy D. Woods
- Department of PediatricsUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Shirley Nieves‐Rodriguez
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Richard Wang
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jonathan Wanagat
- Department of MedicineDavid Geffen School of Medicine at UCLALos AngelesCaliforniaUSA
| | - M. Carrie Miceli
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and SciencesUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of MedicineUniversity of California, Los AngelesLos AngelesCaliforniaUSA
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31
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Trott J, Alpagu Y, Tan EK, Shboul M, Dawood Y, Elsy M, Wollmann H, Tano V, Bonnard C, Eng S, Narayanan G, Junnarkar S, Wearne S, Strutt J, Kumar A, Tomaz LB, Goy PA, Mzoughi S, Jennings R, Hagoort J, Eskin A, Lee H, Nelson SF, Al-Kazaleh F, El-Khateeb M, Fathallah R, Shah H, Goeke J, Langley SR, Guccione E, Hanley N, De Bakker BS, Reversade B, Dunn NR. Mitchell-Riley syndrome iPSCs exhibit reduced pancreatic endoderm differentiation due to a mutation in RFX6. Development 2020; 147:dev194878. [PMID: 33033118 DOI: 10.1242/dev.194878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022]
Abstract
Mitchell-Riley syndrome (MRS) is caused by recessive mutations in the regulatory factor X6 gene (RFX6) and is characterised by pancreatic hypoplasia and neonatal diabetes. To determine why individuals with MRS specifically lack pancreatic endocrine cells, we micro-CT imaged a 12-week-old foetus homozygous for the nonsense mutation RFX6 c.1129C>T, which revealed loss of the pancreas body and tail. From this foetus, we derived iPSCs and show that differentiation of these cells in vitro proceeds normally until generation of pancreatic endoderm, which is significantly reduced. We additionally generated an RFX6HA reporter allele by gene targeting in wild-type H9 cells to precisely define RFX6 expression and in parallel performed in situ hybridisation for RFX6 in the dorsal pancreatic bud of a Carnegie stage 14 human embryo. Both in vitro and in vivo, we find that RFX6 specifically labels a subset of PDX1-expressing pancreatic endoderm. In summary, RFX6 is essential for efficient differentiation of pancreatic endoderm, and its absence in individuals with MRS specifically impairs formation of endocrine cells of the pancreas head and tail.
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Affiliation(s)
- Jamie Trott
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Yunus Alpagu
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Ee Kim Tan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Mohammad Shboul
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 2210, Jordan
| | - Yousif Dawood
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Obstetrics and Gynaecology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Michael Elsy
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Heike Wollmann
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Carine Bonnard
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Shermaine Eng
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Gunaseelan Narayanan
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Seetanshu Junnarkar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Stephen Wearne
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - James Strutt
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Aakash Kumar
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Lucian B Tomaz
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Pierre-Alexis Goy
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Slim Mzoughi
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Rachel Jennings
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Jaco Hagoort
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA 90095, USA
| | - Fawaz Al-Kazaleh
- Department of Obstetrics and Gynecology, University of Jordan, Amman 19241, Jordan
| | - Mohammad El-Khateeb
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and Genetics, Amman 19241, Jordan
| | - Harsha Shah
- Department of Obstetrics and Gynaecology, Queen Charlotte's & Chelsea Hospital, Imperial College London, Du Cane Road, London W12 0HS, UK
| | - Jonathan Goeke
- Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
| | - Neil Hanley
- Faculty of Biology, Medicine & Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Bernadette S De Bakker
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bruno Reversade
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Institute of Molecular and Cellular Biology, Agency for Science Technology and Research (A*STAR), 61 Biopolis Drive, 138673, Singapore
- Department of Paediatrics, National University of Singapore, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 12, 119228, Singapore
- Koç University School of Medicine, Medical Genetics Department, Istanbul 34450, Turkey
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore
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32
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Merselis LC, Jiang SY, Nelson SF, Lee H, Prabaker KK, Baker JL, Munson GP, Butte MJ. MPEG1/Perforin-2 Haploinsufficiency Associated Polymicrobial Skin Infections and Considerations for Interferon-γ Therapy. Front Immunol 2020; 11:601584. [PMID: 33224153 PMCID: PMC7670069 DOI: 10.3389/fimmu.2020.601584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
Introduction Macrophage expressed gene 1 (MPEG1) is highly expressed in macrophages and other phagocytes. The gene encodes a bactericidal pore-forming protein, dubbed Perforin-2. Structural-, animal-, and cell-based studies have established that perforin-2 facilitates the destruction of phagocytosed microbes upon its activation within acidic phagosomes. Relative to wild-type controls, Mpeg1 knockout mice suffer significantly higher mortality rates when challenged with gram-negative or -positive pathogens. Only four variants of MPEG1 have been functionally characterized, each in association with pulmonary infections. Here we report a new MPEG1 non-sense variant in a patient with the a newly described association with persistent polymicrobial infections of the skin and soft tissue. Case Description A young adult female patient was evaluated for recurrent abscesses and cellulitis of the breast and demonstrated a heterozygous, rare variant in MPEG1 p.Tyr430*. Multiple courses of broad-spectrum antimicrobials and surgical incision and drainage failed to resolve the infection. Functional studies revealed that the truncation variant resulted in significantly reduced capacity of the patient’s phagocytes to kill intracellular bacteria. Patient-derived macrophages responded to interferon gamma (IFN-γ) by significantly increasing the expression of MPEG1. IFN-γ treatment supported perforin-2 dependent bactericidal activity and wound healing. Conclusions This case expands the phenotype of MPEG1 deficiency to include severe skin and soft tissue infection. We showed that haploinsufficiency of perforin-2 reduced the bactericidal capacity of human phagocytes. Interferon-gamma therapy increases expression of perforin-2, which may compensate for such variants. Thus, treatment with IFN-γ could help prevent infections.
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Affiliation(s)
- Leidy C Merselis
- University of Miami Miller School of Medicine, Department of Microbiology and Immunology, Miami, FL, United States
| | - Shirley Y Jiang
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, United States
| | - Stanley F Nelson
- Department of Human Genetics, University of California Los Angeles, Los Angeles CA, United States.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States.,California Center for Rare Diseases, Institute for Precision Health, University of California Los Angeles, Los Angeles, CA, United States
| | - Hane Lee
- Department of Human Genetics, University of California Los Angeles, Los Angeles CA, United States.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Kavitha K Prabaker
- Division of Infectious Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Jennifer L Baker
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, United States
| | - George P Munson
- University of Miami Miller School of Medicine, Department of Microbiology and Immunology, Miami, FL, United States
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, United States.,California Center for Rare Diseases, Institute for Precision Health, University of California Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
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33
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Diaz F, Khosa S, Niyazov D, Lee H, Person R, Morrow MM, Signer R, Dorrani N, Zheng A, Herzog M, Freundlich R, Birath JB, Cervantes-Manzo Y, Martinez-Agosto JA, Palmer C, Nelson SF, Fogel BL, Mishra SK. Novel NUDT2 variant causes intellectual disability and polyneuropathy. Ann Clin Transl Neurol 2020; 7:2320-2325. [PMID: 33058507 PMCID: PMC7664258 DOI: 10.1002/acn3.51209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
Exome or genome sequencing was performed to identify the genetic etiology for the clinical presentation of global developmental delay, intellectual disability, and sensorimotor neuropathy with associated distal weakness in two unrelated families. A homozygous frameshift variant c.186delA (p.A63Qfs*3) in the NUDT2 gene was identified in cases 1 and 2 from one family and a third case from another family. Variants in NUDT2 were previously shown to cause intellectual disability, but here we expand the phenotype by demonstrating its association with distal upper and lower extremity weakness due to a sensorimotor polyneuropathy with demyelinating and/or axonal features.
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Affiliation(s)
- Frank Diaz
- Department of Neurology, Olive View-UCLA Medical Center, Sylmar, California, USA.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaweta Khosa
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Children's Health Center, New Orleans, Louisiana, USA.,The University of Queensland, Queensland, Australia
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | | | | | - Rebecca Signer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Allison Zheng
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Matthew Herzog
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Robert Freundlich
- Department of Neurology, Olive View-UCLA Medical Center, Sylmar, California, USA.,Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | | | - J Brandon Birath
- Department of Neurology, Olive View-UCLA Medical Center, Sylmar, California, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Yurivia Cervantes-Manzo
- Department of Neurology, Olive View-UCLA Medical Center, Sylmar, California, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Christina Palmer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Brent L Fogel
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Shri K Mishra
- Department of Neurology, Olive View-UCLA Medical Center, Sylmar, California, USA.,Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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34
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Fliedner A, Kirchner P, Wiesener A, van de Beek I, Waisfisz Q, van Haelst M, Scott DA, Lalani SR, Rosenfeld JA, Azamian MS, Xia F, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Noh GJ, Lippa N, Alkelai A, Aggarwal V, Agre KE, Gavrilova R, Mirzaa GM, Straussberg R, Cohen R, Horist B, Krishnamurthy V, McWalter K, Juusola J, Davis-Keppen L, Ohden L, van Slegtenhorst M, de Man SA, Ekici AB, Gregor A, van de Laar I, Zweier C, Nelson SF, Grody WW, Lee H, Deignan JL, Kang SH, Arboleda VA, Senaratne TN, Dorrani N, Dutra-Clarke MS, Kianmahd J, Hinkamp FL, Neustadt AM, Martinez-Agosto JA, Fogel BL, Quintero-Rivera F. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Am J Hum Genet 2020; 107:544-554. [PMID: 32730804 DOI: 10.1016/j.ajhg.2020.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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35
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Ulm JW, Nelson SF. COVID-19 drug repurposing: Summary statistics on current clinical trials and promising untested candidates. Transbound Emerg Dis 2020; 68:313-317. [PMID: 32619318 PMCID: PMC7362058 DOI: 10.1111/tbed.13710] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
Repurposing of existing anti-viral drugs, immunological modulators and supportive therapies represents a promising path towards rapidly developing new control strategies to mitigate the devastating public health consequences of the COVID-19 pandemic. A comprehensive text-mining and manual curation approach was used to comb and summarize the most pertinent information from existing clinical trials and previous efforts to develop therapies against related betacoronaviruses, particularly SARS and MERS. In contrast to drugs in current trials, which have been derived overwhelmingly from studies on taxonomically unrelated RNA viruses, a number of untested small molecule anti-virals had previously demonstrated remarkable in vitro specificity for SARS-CoV or MERS-CoV, with high selectivity indices, EC50 and/or IC50 . Due to the rapid containment of the prior epidemics, however, these were generally not followed up with in vivo animal studies or clinical investigations and thus largely overlooked as treatment prospects in the current COVID-19 trials. This brief review summarizes and tabulates core information on recent or ongoing drug repurposing-focused clinical trials, while detailing the most promising untested candidates with prior documented success against the aetiologic agents of SARS and/or MERS.
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Affiliation(s)
- J Wes Ulm
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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36
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Szelinger S, Krate J, Ramsey K, Strom SP, Shieh PB, Lee H, Belnap N, Balak C, Siniard AL, Russell M, Richholt R, Both MD, Claasen AM, Schrauwen I, Nelson SF, Huentelman MJ, Craig DW, Yang SP, Moore SA, Sivakumar K, Narayanan V, Rangasamy S. Congenital myasthenic syndrome caused by a frameshift insertion mutation in GFPT1. Neurol Genet 2020; 6:e468. [PMID: 32754643 PMCID: PMC7357421 DOI: 10.1212/nxg.0000000000000468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Objective Description of a new variant of the glutamine-fructose-6-phosphate transaminase 1 (GFPT1) gene causing congenital myasthenic syndrome (CMS) in 3 children from 2 unrelated families. Methods Muscle biopsies, EMG, and whole-exome sequencing were performed. Results All 3 patients presented with congenital hypotonia, muscle weakness, respiratory insufficiency, head lag, areflexia, and gastrointestinal dysfunction. Genetic analysis identified a homozygous frameshift insertion in the GFPT1 gene (NM_001244710.1: c.686dupC; p.Arg230Ter) that was shared by all 3 patients. In one of the patients, inheritance of the variant was through uniparental disomy (UPD) with maternal origin. Repetitive nerve stimulation and single-fiber EMG was consistent with the clinical diagnosis of CMS with a postjunctional defect. Ultrastructural evaluation of the muscle biopsy from one of the patients showed extremely attenuated postsynaptic folds at neuromuscular junctions and extensive autophagic vacuolar pathology. Conclusions These results expand on the spectrum of known loss-of-function GFPT1 mutations in CMS12 and in one family demonstrate a novel mode of inheritance due to UPD.
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Affiliation(s)
- Szabolcs Szelinger
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Jonida Krate
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Keri Ramsey
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Strom
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Perry B Shieh
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Hane Lee
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Newell Belnap
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Chris Balak
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ashley L Siniard
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Megan Russell
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ryan Richholt
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matt De Both
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ana M Claasen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Isabelle Schrauwen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Stanley F Nelson
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matthew J Huentelman
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - David W Craig
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Yang
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Steven A Moore
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Kumaraswamy Sivakumar
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Vinodh Narayanan
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Sampathkumar Rangasamy
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
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Lee H, Nelson SF. The frontiers of sequencing in undiagnosed neurodevelopmental diseases. Curr Opin Genet Dev 2020; 65:76-83. [PMID: 32599523 DOI: 10.1016/j.gde.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Characterized by impairments in brain and central nervous system development, neurodevelopmental diseases causes are highly heterogeneous. Although many of these diseases are individually rare, collectively more than 3% of the children are reported to be affected with a type of neurodevelopmental diseases worldwide, and many remain undiagnosed even with current genomic tools. Identifying the genetic causes of these diseases allows better clinical management and expands our understanding of human neurodevelopment. Over the past decade, expansion of genomic sequencing and some methodologic improvements have improved molecular diagnostic yield as well as the discovery of novel genetic causes for wide spectrum of neurodevelopmental diseases. Here we review the current diagnostic workflow and propose ways of improving the diagnostic yield.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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38
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Zhao Y, Kang X, Barsegian A, He J, Guzman A, Lau RP, Biniwale R, Wadhra M, Reemtsen B, Garg M, Halnon N, Quintero-Rivera F, Grody WW, Van Arsdell G, Nelson SF, Touma M. Gene-environment regulation of chamber-specific maturation during hypoxemic perinatal circulatory transition. J Mol Med (Berl) 2020; 98:1009-1020. [PMID: 32533200 DOI: 10.1007/s00109-020-01933-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
Chamber-specific and temporally regulated perinatal cardiac growth and maturation is critical for functional adaptation of the heart and may be altered significantly in response to perinatal stress, such as systemic hypoxia (hypoxemia), leading to significant pathology, even mortality. Understanding transcriptome regulation of neonatal heart chambers in response to hypoxemia is necessary to develop chamber-specific therapies for infants with cyanotic congenital heart defects (CHDs). We sought to determine chamber-specific transcriptome programming during hypoxemic perinatal circulatory transition. We performed transcriptome-wide analysis on right ventricle (RV) and left ventricle (LV) of postnatal day 3 (P3) mouse hearts exposed to perinatal hypoxemia. Hypoxemia decreased baseline differences between RV and LV leading to significant attenuation of ventricular patterning (AVP), which involved several molecular pathways, including Wnt signaling suppression and cell cycle induction. Notably, robust changes in RV transcriptome in hypoxemic condition contributed significantly to the AVP. Remarkably, suppression of epithelial mesenchymal transition (EMT) and dysregulation of the TP53 signaling were prominent hallmarks of the AVP genes in neonatal mouse heart. Furthermore, members of the TP53-related gene family were dysregulated in the hypoxemic RVs of neonatal mouse and cyanotic Tetralogy of Fallot hearts. Integrated analysis of chamber-specific transcriptome revealed hypoxemia-specific changes that were more robust in RVs compared with LVs, leading to previously uncharacterized AVP induced by perinatal hypoxemia. Remarkably, reprogramming of EMT process and dysregulation of the TP53 network contributed to transcriptome remodeling of neonatal heart during hypoxemic circulatory transition. These insights may enhance our understanding of hypoxemia-induced pathogenesis in newborn infants with cyanotic CHD phenotypes. KEY MESSAGES: During perinatal circulatory transition, transcriptome programming is a major driving force of cardiac chamber-specific maturation and adaptation to hemodynamic load and external environment. During hypoxemic perinatal transition, transcriptome reprogramming may affect chamber-specific growth and development, particularly in newborns with congenital heart defects (CHDs). Chamber-specific transcriptome changes during hypoxemic perinatal transition are yet to be fully elucidated. Systems-based analysis of hypoxemic neonatal hearts at postnatal day 3 reveals chamber-specific transcriptome signatures during hypoxemic perinatal transition, which involve attenuation of ventricular patterning (AVP) and repression of epithelial mesenchymal transition (EMT). Key regulatory circuits involved in hypoxemia response were identified including suppression of Wnt signaling, induction of cellular proliferation and dysregulation of TP53 network.
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Affiliation(s)
- Yan Zhao
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Xuedong Kang
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexander Barsegian
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Jian He
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Alejandra Guzman
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Ryan P Lau
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Reshma Biniwale
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Madhuri Wadhra
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian Reemtsen
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Meena Garg
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA
| | - Nancy Halnon
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Glen Van Arsdell
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA.,Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Marlin Touma
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles 675 Charles E. Young Dr S, 3762 MacDonald Research Laboratories, Los Angeles, CA, 90024, USA. .,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,Children's Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,The Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA. .,Eli and Edythe Stem Cell Institute, University of California Los Angeles, Los Angeles, CA, USA. .,Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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Tsai M, Thauland TJ, Huang AY, Bun C, Fitzwater S, Krogstad P, Douine ED, Nelson SF, Lee H, Garcia-Lloret MI, Butte MJ. Disseminated Coccidioidomycosis Treated with Interferon-γ and Dupilumab. N Engl J Med 2020; 382:2337-2343. [PMID: 32521134 PMCID: PMC7333509 DOI: 10.1056/nejmoa2000024] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe a case of life-threatening disseminated coccidioidomycosis in a previously healthy child. Like most patients with disseminated coccidioidomycosis, this child had no genomic evidence of any known, rare immune disease. However, comprehensive immunologic testing showed exaggerated production of interleukin-4 and reduced production of interferon-γ. Supplementation of antifungal agents with interferon-γ treatment slowed disease progression, and the addition of interleukin-4 and interleukin-13 blockade with dupilumab resulted in rapid resolution of the patient's clinical symptoms. This report shows that blocking of type 2 immune responses can treat infection. This immunomodulatory approach could be used to enhance immune clearance of refractory fungal, mycobacterial, and viral infections. (Supported by the Jeffrey Modell Foundation and the National Institutes of Health.).
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Affiliation(s)
- Monica Tsai
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Timothy J Thauland
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Alden Y Huang
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Chantana Bun
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Sean Fitzwater
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Paul Krogstad
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Emilie D Douine
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Stanley F Nelson
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Hane Lee
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Maria I Garcia-Lloret
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
| | - Manish J Butte
- From the Divisions of Immunology, Allergy, and Rheumatology (M.T., T.J.T., C.B., M.I.G.-L., M.J.B.) and Infectious Diseases (S.F., P.K.), Department of Pediatrics, the Department of Human Genetics (E.D.D., S.F.N., H.L.), the Department of Pathology and Laboratory Medicine (H.L.), and the California Center for Rare Diseases, Institute for Precision Health (A.Y.H., S.F.N., M.J.B.), University of California, Los Angeles, Los Angeles
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Woods JD, Khanlou N, Lee H, Signer R, Shieh P, Chen J, Herzog M, Palmer C, Martinez‐Agosto J, Nelson SF. Myopathy associated with homozygous PYROXD1 pathogenic variants detected by genome sequencing. Neuropathology 2020; 40:302-307. [PMID: 32037607 PMCID: PMC7317439 DOI: 10.1111/neup.12641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 12/01/2022]
Abstract
Biallelic pathogenic variants in the gene PYROXD1 have recently been described to cause early-onset autosomal recessive myopathy. Myopathy associated with PYROXD1 pathogenic variants is rare and reported in only 17 individuals. Known pathogenic variants in PYROXD1 include missense, insertion and essential splice-site variants. Here we describe a consanguineous family of individuals affected with late-onset myopathy and homozygous PYROXD1 missense variants (NM_024854.5:c.464A>G [p.Asn155Ser]) expanding our understanding of the possible disease phenotypes of PYROXD1-associated myopathy.
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Affiliation(s)
- Jeremy D. Woods
- Department of PediatricsUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Negar Khanlou
- Department of PathologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Hane Lee
- Department of PathologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Rebecca Signer
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Perry Shieh
- Department of NeurologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Johnathan Chen
- Department of RadiologyUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Matthew Herzog
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Christina Palmer
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Psychiatry and Behavioral SciencesUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | | | | | - Stanley F. Nelson
- Department of PediatricsUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Human GeneticsUniversity of California Los AngelesLos AngelesCaliforniaUSA
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41
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Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM, Kini U, Mackay JP, Pierson TM. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Genet Med 2020; 22:878-888. [PMID: 31949314 PMCID: PMC7920571 DOI: 10.1038/s41436-019-0747-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Determination of genotypic/phenotypic features of GATAD2B-associated neurodevelopmental disorder (GAND). METHODS Fifty GAND subjects were evaluated to determine consistent genotypic/phenotypic features. Immunoprecipitation assays utilizing in vitro transcription-translation products were used to evaluate GATAD2B missense variants' ability to interact with binding partners within the nucleosome remodeling and deacetylase (NuRD) complex. RESULTS Subjects had clinical findings that included macrocephaly, hypotonia, intellectual disability, neonatal feeding issues, polyhydramnios, apraxia of speech, epilepsy, and bicuspid aortic valves. Forty-one novelGATAD2B variants were identified with multiple variant types (nonsense, truncating frameshift, splice-site variants, deletions, and missense). Seven subjects were identified with missense variants that localized within two conserved region domains (CR1 or CR2) of the GATAD2B protein. Immunoprecipitation assays revealed several of these missense variants disrupted GATAD2B interactions with its NuRD complex binding partners. CONCLUSIONS A consistent GAND phenotype was caused by a range of genetic variants in GATAD2B that include loss-of-function and missense subtypes. Missense variants were present in conserved region domains that disrupted assembly of NuRD complex proteins. GAND's clinical phenotype had substantial clinical overlap with other disorders associated with the NuRD complex that involve CHD3 and CHD4, with clinical features of hypotonia, intellectual disability, cardiac defects, childhood apraxia of speech, and macrocephaly.
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Affiliation(s)
- Christine Shieh
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Brigitte Vanle
- Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Medical College of Wisconsin-Central Wisconsin, Wausau, WI, USA
| | - Margaret Au
- Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Hane Lee
- Department of Human Genetics and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Maria G Otero
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Choi
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ingrid P Taff
- Department of Neurology, Hofstra School of Medicine, Great Neck, NY, USA
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, Quillen College of Medicine, Mountain Home, TN, USA
| | | | - Luis Rohena
- Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, USA
- Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, USA
| | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, USA
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Sakkubai Naidu
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Ana Berta Sousa
- Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Geoffrey Beek
- Children's Hospitals and Clinics of Minnesota Department of Genetics, Minneapolis, MN, USA
| | - Donald Basel
- Department of Pediatrics, Division of Genetics; Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Roman Yusupov
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FlL, USA
| | | | - Lisa Ohden
- Department of Genetic Counseling, Sanford Children's Specialty Clinic, Sioux Falls, SD, USA
| | - Laura Davis-Keppen
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Richard Finkel
- Division of Pediatric Neurology, Department of Pediatrics, Nemours Children's Hospital, Orlando, FL, USA
| | - Andrew Dauber
- Division of Endocrinology, Children's National Health System, Washington, DC, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, UK
| | - Miranda Splitt
- Institute of Genetic Medicine, Northern Genetics Service, Newcastle upon Tyne Hospitals Trust, Newcastle, UK
| | - Katherine Lachlan
- Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health Division, Wessex Clinical Genetics Service, University Hospitals of Southampton NHS Trust, Southampton, UK
| | - Shane A McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jane Hurst
- Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - David R Fitzpatrick
- Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Juan I Young
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia and Department of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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42
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Lee CC, Hoang A, Segovia D, Herbst A, Barthelemy F, Gibbs E, Crosbie R, Nelson SF, Miceli C, Wanagat J. Enhanced Methods for Needle Biopsy and Cryopreservation of Skeletal Muscle in Older Adults. J Cytol Histol 2020; 11. [PMID: 32566369 PMCID: PMC7304549 DOI: 10.37421/jch.2020.11.553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human muscle biopsies are increasingly important for diagnosis, research, and to monitor therapeutic trials. We examined the use of a self-contained, vacuum-assisted biopsy system and a novel muscle freezing technique to improve, simplify, and standardize human muscle biopsy collection and cryopreservation in older adults. The VACORA vacuum-assisted biopsy system was deployed in muscle biopsies of 12 individuals ranging in age from 57 to 80 years. This office-based approach was well tolerated as it is minimally invasive, uses only local anesthetic, and has a quick recovery. To maximize biopsy sample quality and reproducibility, we developed a novel muscle sample freezing protocol. Fresh muscle biopsy samples were placed into readily available tissue cassettes followed by direct freezing in liquid nitrogen. After this modified snap freezing protocol, frozen muscle samples were enrobed in embedding medium for cryosectioning. We examined the effect of this freezing approach in histological sections of rodent and human muscle samples. The VACORA Biopsy System provided as many as four skeletal muscle core samples from a single biopsy site. Biopsy samples from 12 older adults weighed an average of 147.5 ± 11 mg each and had a consistent size and shape. There were no complications, and the residual scar is less than 10 mm. The freezing method using standard tissue cassettes with direct freezing in liquid nitrogen yielded high quality cryopreserved muscle tissue suitable for histological analysis without the need for isopentane and with little to no freeze-thaw damage. These enhancements have streamlined and improved the consistency of our muscle biopsy protocol and provide sufficient high-quality sample for multi-dimensional downstream studies of human muscle in aging and disease.
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Affiliation(s)
- Cathy C Lee
- VA Greater Los Angeles, Department of Veterans Affairs, Los Angeles, CA, USA.,Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Austin Hoang
- Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Segovia
- VA Greater Los Angeles, Department of Veterans Affairs, Los Angeles, CA, USA
| | - Allen Herbst
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Florian Barthelemy
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Elizabeth Gibbs
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Rachelle Crosbie
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carrie Miceli
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan Wanagat
- VA Greater Los Angeles, Department of Veterans Affairs, Los Angeles, CA, USA.,Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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43
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Yazdani S, Badjatiya A, Dorrani N, Lee H, Grody WW, Nelson SF, Dipple KM. Genetic characterization and long-term management of severely affected siblings with intellectual developmental disorder with cardiac arrhythmia syndrome. Mol Genet Metab Rep 2020; 23:100582. [PMID: 32280589 PMCID: PMC7138921 DOI: 10.1016/j.ymgmr.2020.100582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 11/30/2022] Open
Abstract
We report two brothers with severe global cognitive and motor delay, cortical visual impairment and sick sinus syndrome who were born to consanguineous parents. Standard genetic evaluations did not reveal the cause of their mental retardation. As expected, chromosomal microarray (CMA) revealed extensive regions of homozygosity. Exome sequencing revealed that both affected boys were homozygous for a nonsense mutation in the G-protein β5 (GNB5) gene (NM_016194.3:c.1032C > G; Tyr344Ter), and that the parents were carriers of this mutation. No other DNA variants that were explanatory for the sick sinus or the developmental delay/intellectual disability were identified, and no other clinical parameters are likely to have contributed to this unusual combination of phenotypes. The neurologic features of our patients are more severe than those of most of the other patients previously reported with GNB5 variants, probably because of the homozygous, complete loss-of-function (nonsense/stop-gain) nature of their variant, and their clinical course has been monitored for longer duration.
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Affiliation(s)
- Shahram Yazdani
- Departments of Pediatrics and Mattel Children's Hospital at UCLA, Los Angeles, CA, United States of America
| | - Anish Badjatiya
- Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Naghmeh Dorrani
- Departments of Pediatrics and Mattel Children's Hospital at UCLA, Los Angeles, CA, United States of America
| | - Hane Lee
- Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America.,Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Wayne W Grody
- Departments of Pediatrics and Mattel Children's Hospital at UCLA, Los Angeles, CA, United States of America.,Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America.,Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Stanley F Nelson
- Departments of Pediatrics and Mattel Children's Hospital at UCLA, Los Angeles, CA, United States of America.,Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America.,Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
| | - Katrina M Dipple
- Departments of Pediatrics and Mattel Children's Hospital at UCLA, Los Angeles, CA, United States of America.,Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
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44
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Kang X, Zhao Y, Van Arsdell G, Nelson SF, Touma M. Ppp1r1b-lncRNA inhibits PRC2 at myogenic regulatory genes to promote cardiac and skeletal muscle development in mouse and human. RNA 2020; 26:481-491. [PMID: 31953255 PMCID: PMC7075267 DOI: 10.1261/rna.073692.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical epigenetic regulators and play important roles in cardiac development and congenital heart disease. In a previous study, we identified a novel lncRNA, Ppp1r1b, with expression highly correlated with myogenesis. However, the molecular mechanism that underlies Ppp1r1b-lncRNA function in myogenic regulation is unknown. By silencing Ppp1r1b-lncRNA, mouse C2C12 and human skeletal myoblasts failed to develop fully differentiated myotubes. Myogenic differentiation was also impaired in PPP1R1B-lncRNA deficient human-induced pluripotent stem cell-derived cardiomyocytes (hiPSCs-CMs). The expression of myogenic transcription factors, including MyoD, Myogenin, and Tbx5, as well as sarcomere proteins, was significantly suppressed in Ppp1r1b-lncRNA inhibited myoblast cells and neonatal mouse heart. Histone modification analysis revealed increased H3K27 tri-methylation at MyoD1 and Myogenin promoters in GapmeR treated C2C12 cells. Furthermore, Ppp1r1b-lncRNA was found to bind to Ezh2, and chromatin isolation by RNA purification (ChIRP) assay revealed enriched interaction of Ppp1r1b-lncRNA with Myod1 and Tbx5 promoters, suggesting that Ppp1r1b-lncRNA induces transcription of myogenic transcription factors by interacting with the polycomb repressive complex 2 (PRC2) at the chromatin interface. Correspondingly, the silencing of Ppp1r1b-lncRNA increased EZH2 binding at promoter regions of myogenic transcription factors. Therefore, our results suggest that Ppp1r1b-lncRNA promotes myogenic differentiation through competing for PRC2 binding with chromatin of myogenic master regulators during heart and skeletal muscle development.
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Affiliation(s)
- Xuedong Kang
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yan Zhao
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Glen Van Arsdell
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Stanley F Nelson
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Human Genetics, Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Marlin Touma
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Human Genetics, Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Institute of Precision Health, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- The Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Children's Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Stem Cell Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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45
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Shieh C, Jones N, Vanle B, Au M, Huang AY, Silva APG, Lee H, Douine ED, Otero MG, Choi A, Grand K, Taff IP, Delgado MR, Hajianpour MJ, Seeley A, Rohena L, Vernon H, Gripp KW, Vergano SA, Mahida S, Naidu S, Sousa AB, Wain KE, Challman TD, Beek G, Basel D, Ranells J, Smith R, Yusupov R, Freckmann ML, Ohden L, Davis-Keppen L, Chitayat D, Dowling JJ, Finkel R, Dauber A, Spillmann R, Pena LDM, Metcalfe K, Splitt M, Lachlan K, McKee SA, Hurst J, Fitzpatrick DR, Morton JEV, Cox H, Venkateswaran S, Young JI, Marsh ED, Nelson SF, Martinez JA, Graham JM, Kini U, Mackay JP, Pierson TM. Correction: GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Genet Med 2020; 22:822. [PMID: 32047287 PMCID: PMC11000750 DOI: 10.1038/s41436-020-0760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Christine Shieh
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natasha Jones
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Brigitte Vanle
- Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Medical College of Wisconsin-Central Wisconsin, Wausau, WI, USA
| | - Margaret Au
- Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Hane Lee
- Department of Human Genetics and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Maria G Otero
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Choi
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ingrid P Taff
- Department of Neurology, Hofstra School of Medicine, Great Neck, NY, USA
| | - Mauricio R Delgado
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, Quillen College of Medicine, Mountain Home, TN, USA
| | | | - Luis Rohena
- Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, USA
- Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Hilary Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, USA
| | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, USA
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Sakkubai Naidu
- Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Ana Berta Sousa
- Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Thomas D Challman
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Geoffrey Beek
- Children's Hospitals and Clinics of Minnesota Department of Genetics, Minneapolis, MN, USA
| | - Donald Basel
- Department of Pediatrics, Division of Genetics, Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Roman Yusupov
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FlL, USA
| | | | - Lisa Ohden
- Department of Genetic Counseling, Sanford Children's Specialty Clinic, Sioux Falls, SD, USA
| | - Laura Davis-Keppen
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Richard Finkel
- Division of Pediatric Neurology, Department of Pediatrics, Nemours Children's Hospital, Orlando, FL, USA
| | - Andrew Dauber
- Division of Endocrinology, Children's National Health System, Washington, DC, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, UK
| | - Miranda Splitt
- Institute of Genetic Medicine, Northern Genetics Service, Newcastle upon Tyne Hospitals Trust, Newcastle, UK
| | - Katherine Lachlan
- Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health Division, Wessex Clinical Genetics Service, University Hospitals of Southampton NHS Trust, Southampton, UK
| | - Shane A McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jane Hurst
- Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, UK
| | - David R Fitzpatrick
- Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, UK
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Juan I Young
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia and Department of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez
- Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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46
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Zhao Y, Kang X, Gao F, Guzman A, Lau RP, Biniwale R, Wadehra M, Reemtsen B, Garg M, Halnon N, Quintero-Rivera F, Van Arsdell G, Coppola G, Nelson SF, Touma M. Gene-environment regulatory circuits of right ventricular pathology in tetralogy of fallot. J Mol Med (Berl) 2019; 97:1711-1722. [PMID: 31834445 DOI: 10.1007/s00109-019-01857-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/02/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022]
Abstract
The phenotypic spectrum of congenital heart defects (CHDs) is contributed by both genetic and environmental factors. Their interactions are profoundly heterogeneous but may operate on common pathways as in the case of hypoxia signaling during postnatal heart development in the context of CHDs. Tetralogy of Fallot (TOF) is the most common cyanotic (hypoxemic) CHD. However, how the hypoxic environment contributes to TOF pathogenesis after birth is poorly understood. We performed Genome-wide transcriptome analysis on right ventricle outflow tract (RVOT) specimens from cyanotic and noncyanotic TOF. Co-expression network analysis identified gene modules specifically associated with clinical diagnosis and hypoxemia status in the TOF hearts. In particular, hypoxia-dependent induction of myocyte proliferation is associated with E2F1-mediated cell cycle regulation and repression of the WNT11-RB1 axis. Genes enriched in epithelial mesenchymal transition (EMT), fibrosis, and sarcomere were also repressed in cyanotic TOF patients. Importantly, transcription factor analysis of the hypoxia-regulated modules suggested CREB1 as a putative regulator of hypoxia/WNT11-RB1 circuit. The study provides a high-resolution landscape of transcriptome programming associated with TOF phenotypes and unveiled hypoxia-induced regulatory circuit in cyanotic TOF. Hypoxia-induced cardiomyocyte proliferation involves negative modulation of CREB1 activity upstream of the WNT11-RB1 axis. KEY MESSAGES: Genetic and environmental factors contribute to congenital heart defects (CHDs). How hypoxia contributes to Tetralogy of Fallot (TOF) pathogenesis after birth is unclear. Systems biology-based analysis revealed distinct molecular signature in CHDs. Gene expression modules specifically associated with cyanotic TOF were uncovered. Key regulatory circuits induced by hypoxia in TOF pathogenesis after birth were unveiled.
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Affiliation(s)
- Yan Zhao
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, CA, USA
| | - Xuedong Kang
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA.,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, CA, USA
| | - Fuying Gao
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Alejandra Guzman
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA
| | - Ryan P Lau
- Department of Pathology and Laboratory Medicine, Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Reshma Biniwale
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Madhuri Wadehra
- Department of Pathology and Laboratory Medicine, Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Brian Reemtsen
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Meena Garg
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA
| | - Nancy Halnon
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Glen Van Arsdell
- Department of Cardiothoracic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Giovanni Coppola
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Stanley F Nelson
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Marlin Touma
- Department of Pediatrics, David Geffen School of Medicine, University of California, 10833 Le Conte Ave, MDCC-B2-375, Los Angeles, CA, 90095, USA. .,Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, University of California, Los Angeles, CA, USA. .,Department of Human Genetics, Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,Institute of Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,Department of Pediatrics, Children's Discovery and Innovation Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,The Molecular Biology Institute, University of California, Los Angeles, CA, USA. .,Eli and Edythe Stem Cell Institute, University of California, Los Angeles, CA, USA.
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47
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Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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48
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Gibbs EM, Barthélémy F, Douine ED, Hardiman NC, Shieh PB, Khanlou N, Crosbie RH, Nelson SF, Miceli MC. Large in-frame 5' deletions in DMD associated with mild Duchenne muscular dystrophy: Two case reports and a review of the literature. Neuromuscul Disord 2019; 29:863-873. [PMID: 31672265 PMCID: PMC7092699 DOI: 10.1016/j.nmd.2019.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
Duchenne muscular dystrophy is caused by mutations in the dystrophin-encoding DMD gene. While Duchenne is most commonly caused by large intragenic deletions that cause frameshift and complete loss of dystrophin expression, in-frame deletions in DMD can result in the expression of internally truncated dystrophin proteins and may be associated with a milder phenotype. In this study, we describe two individuals with large in-frame 5' deletions (exon 3-23 and exon 3-28) that remove the majority of the N-terminal region, including part of the actin binding and central rod domains. Both patients had progressive muscle weakness during childhood but are observed to have a relatively mild disease course compared to typical Duchenne. We show that in muscle biopsies from both patients, truncated dystrophin is expressed at the sarcolemma. We have additionally developed a patient-specific fibroblast-derived cell model, which can be inducibly reprogrammed to form myotubes that largely recapitulate biopsy findings for the patient with the exon 3-23 deletion, providing a culture model for future investigation of this unusual case. We discuss these mutations in the context of previously reported 5' in-frame DMD deletions and relevant animal models, and review the spectrum of phenotypes associated with these deletions.
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Affiliation(s)
- Elizabeth M Gibbs
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie C Hardiman
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Perry B Shieh
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - Negar Khanlou
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Rachelle H Crosbie
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - M Carrie Miceli
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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49
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Barthélémy F, Wang RT, Hsu C, Douine ED, Marcantonio EE, Nelson SF, Miceli MC. Targeting RyR Activity Boosts Antisense Exon 44 and 45 Skipping in Human DMD Skeletal or Cardiac Muscle Culture Models. Mol Ther Nucleic Acids 2019; 18:580-589. [PMID: 31678734 PMCID: PMC6838898 DOI: 10.1016/j.omtn.2019.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/15/2019] [Accepted: 09/12/2019] [Indexed: 12/23/2022]
Abstract
Systemic delivery of antisense oligonucleotides (AO) for DMD exon skipping has proven effective for reframing DMD mRNA, rescuing dystrophin expression, and slowing disease progression in animal models. In humans with Duchenne muscular dystrophy treated with AOs, low levels of dystrophin have been induced, and modest slowing of disease progression has been observed, highlighting the need for improved efficiency of human skipping drugs. Here, we demonstrate that dantrolene and Rycals S107 and ARM210 potentiate AO-mediated exon skipping of exon 44 or exon 45 in patient-derived myotube cultures with appropriate mutations. Further, dantrolene is shown to boost AO-mediated exon skipping in patient-derived, induced cardiomyocyte cultures. Our findings further validate the ryanodine receptors (RyR) as the likely target responsible for exon skip boosting and demonstrate potential applicability beyond exon 51 skipping. These data provide preclinical support of dantrolene trial as an adjuvant to AO-mediated exon-skipping therapy in humans and identify a novel Rycal, ARM210, for development as a potential exon-skipping booster. Further, they highlight the value of mutation-specific DMD culture models for basic discovery, preclinical drug screening and translation of personalized genetic medicines.
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Affiliation(s)
- Florian Barthélémy
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
| | - Richard T Wang
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Hsu
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie D Douine
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Stanley F Nelson
- Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Carrie Miceli
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, USA; Center for Duchenne Muscular Dystrophy, University of California, Los Angeles, Los Angeles, CA, USA; Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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50
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Abstract
Introduction:
Emerged as critical epigenetic regulators of the transcriptome, the long noncoding RNAs (lncRNAs) play important roles in cardiac development and might be targeted to treat human cardiomyocyte dysfunction in congenital heart disease. In our work, we identified a novel lncRNA that regulates myogenic differentiation.
Methods:
Antisense oligonucleotides (GapmeR) were used to suppress Ppp1r1b-lncRNA. Chromatin immunoprecipitation (CHIP) and chromatin isolation by RNA purification (CHIRP) were used to analyze gene specific histone modification level and lncRNA:chromatin interaction, respectively. RNA pull-down and RNA immunoprecipitation (RIP) were used to identify the protein molecules that interact with Ppp1r1b-lncRNA.
Results:
By silencing Ppp1r1b-lncRNA, C2C12, a skeletal myoblast cell line, and human-induced pluripotent stem cell derived cardiomyocytes failed to develop fully differentiated myotubes. Analysis of GapmeR injected neonatal mouse heart (
in vivo
) and siRNA silenced human myoblasts (
in vitro
) further confirmed the role of Ppp1r1b-lncRNA in normal myogenesis. Members of the MyoD family of muscle-specific transcription factors were not induced during myogenic differentiation in C2C12 cells treated with Ppp1r1b-lncRNA specific GapmeR. Proteins essential for striated muscle development were also suppressed in Ppp1r1b-lncRNA- deficient cells. Histone modification analysis revealed enrichment of histone tri-methylation at Myogenin and MyoD1 promoters in GapmeR treated C2C12 cells. Subsequently, lncRNA- protein complex isolation and lncRNA-DNA interaction assays confirmed Ppp1r1b-lncRNA function.
Conclusions:
Our findings support important role of Ppp1r1b-lncRNA in promoting myogenic differentiation. Ppp1r1b-lncRNA function is mediated by inhibiting histone methylation on promoters of key myogenic genes. Particularly, the identification of EZH2 in pulled Pp1r1b-lncRNA: protein complex supports that Polycomb repressive complex 2 is involved in Ppp1r1b-lncRNA modulated myoblast differentiation. The recovery of MyoD1 promoter DNA in isolated lncRNA: chromatin DNA interactome implies that Ppp1r1b-lncRNA regulates transcription by recruiting PRC2 complex to its target genes.
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Affiliation(s)
| | - Yan Zhao
- UCLA-David Geffen Sch Medicine, Los Angeles, CA
| | - Joseph Wu
- UCLA-David Geffen Sch Medicine, Los Angeles, CA
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