1
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Bejma TA, Beidler WS, VanSickle EA, Prokop JW, Brown WT, Scheurer-Monaghan A, Rossetti LZ. Expansion of the phenotypic spectrum of KARS1-related disorders to include arthrogryposis multiplex congenita and summary of experiences with lysine supplementation. Am J Med Genet A 2024:e63811. [PMID: 38980148 DOI: 10.1002/ajmg.a.63811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/19/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024]
Abstract
There are currently multiple disorders of aminoacyl-tRNA synthetases described, including KARS1-related disorder resulting from dysfunctional lysyl-tRNA synthetases. In this report, we describe four novel KARS1 variants in three affected individuals, two of whom displayed arthrogryposis-like phenotypes, suggestive of phenotypic expansion. We also highlight subjective clinical improvement in one subject following lysine supplementation in conjunction with a protein-fortified diet, suggesting its potential as a novel treatment modality for KARS1-related disorders. This report offers additional insight into the etiology and management of KARS1-related disorders and expands our ability to provide guidance to affected individuals and their families.
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Affiliation(s)
- Taylor A Bejma
- Michigan State University College of Human Medicine, Grand Rapids, Michigan, USA
| | | | - Elizabeth A VanSickle
- Division of Medical Genetics and Genomics, Corewell Health, Grand Rapids, Michigan, USA
| | - Jeremy W Prokop
- Office of Research, Corewell Health, Grand Rapids, Michigan, USA
| | - Wendy T Brown
- Department of Radiology, Helen DeVos Children's Hospital and Corewell Health, Advanced Radiology Services, Grand Rapids, Michigan, USA
| | | | - Linda Z Rossetti
- Michigan State University College of Human Medicine, Grand Rapids, Michigan, USA
- Division of Medical Genetics and Genomics, Corewell Health, Grand Rapids, Michigan, USA
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2
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Lee J, Sim KM, Kang M, Oh HJ, Choi HJ, Kim YE, Pack CG, Kim K, Kim KM, Oh SH, Kim I, Chang I. Understanding the molecular mechanism of pathogenic variants of BIR2 domain in XIAP-deficient inflammatory bowel disease. Sci Rep 2024; 14:853. [PMID: 38191507 PMCID: PMC10774423 DOI: 10.1038/s41598-023-50932-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) deficiency causes refractory inflammatory bowel disease. The XIAP protein plays a pivotal role in the pro-inflammatory response through the nucleotide-binding oligomerization domain-containing signaling pathway that is important in mucosal homeostasis. We analyzed the molecular mechanism of non-synonymous pathogenic variants (PVs) of XIAP BIR2 domain. We generated N-terminally green fluorescent protein-tagged XIAP constructs of representative non-synonymous PVs. Co-immunoprecipitation and fluorescence cross-correlation spectroscopy showed that wild-type XIAP and RIP2 preferentially interacted in live cells, whereas all non-synonymous PV XIAPs failed to interact properly with RIP2. Structural analysis showed that various structural changes by mutations, such as hydrophobic core collapse, Zn-finger loss, and spatial rearrangement, destabilized the two loop structures (174-182 and 205-215) that critically interact with RIP2. Subsequently, it caused a failure of RIP2 ubiquitination and loss of protein deficiency by the auto-ubiquitination of all XIAP mutants. These findings could enhance our understanding of the role of XIAP mutations in XIAP-deficient inflammatory bowel disease and may benefit future therapeutic strategies.
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Affiliation(s)
- Juhwan Lee
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Kyoung Mi Sim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Mooseok Kang
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Hyun Ju Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Ho Jung Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Yeong Eun Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Chan-Gi Pack
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyunggon Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Seak Hee Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Inki Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea.
- Department of Pharmacology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Iksoo Chang
- Creative Research Initiatives Center for Proteome Biophysics, Department of Brain Sciences and Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
- Department of Brain Sciences and Supercomputing Big Data Center, DGIST, Daegu, 42988, Korea.
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3
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Henderson ML, Zieba JK, Li X, Campbell DB, Williams MR, Vogt DL, Bupp CP, Edgerly YM, Rajasekaran S, Hartog NL, Prokop JW, Krueger JM. Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care. BIOTECH 2024; 13:1. [PMID: 38247731 PMCID: PMC10801589 DOI: 10.3390/biotech13010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost-benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success.
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Affiliation(s)
- Marian L. Henderson
- The Department of Biology, Calvin University, Grand Rapids, MI 49546, USA;
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Jacob K. Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Daniel B. Campbell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Michael R. Williams
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Daniel L. Vogt
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | | | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA;
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
| | - Nicholas L. Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Allergy & Immunology, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA;
| | - Jena M. Krueger
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA; (J.K.Z.); (X.L.); (D.B.C.); (M.R.W.); (D.L.V.); (C.P.B.); (S.R.); (N.L.H.)
- Department of Neurology, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
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4
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Rudolph HC, Stafford AM, Hwang HE, Kim CH, Prokop JW, Vogt D. Structure-Function of the Human WAC Protein in GABAergic Neurons: Towards an Understanding of Autosomal Dominant DeSanto-Shinawi Syndrome. BIOLOGY 2023; 12:589. [PMID: 37106788 PMCID: PMC10136313 DOI: 10.3390/biology12040589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/29/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
Dysfunction of the WW domain-containing adaptor with coiled-coil, WAC, gene underlies a rare autosomal dominant disorder, DeSanto-Shinawi syndrome (DESSH). DESSH is associated with facial dysmorphia, hypotonia, and cognitive alterations, including attention deficit hyperactivity disorder and autism. How the WAC protein localizes and functions in neural cells is critical to understanding its role during development. To understand the genotype-phenotype role of WAC, we developed a knowledgebase of WAC expression, evolution, human genomics, and structural/motif analysis combined with human protein domain deletions to assess how conserved domains guide cellular distribution. Then, we assessed localization in a cell type implicated in DESSH, cortical GABAergic neurons. WAC contains conserved charged amino acids, phosphorylation signals, and enriched nuclear motifs, suggesting a role in cellular signaling and gene transcription. Human DESSH variants are found within these regions. We also discovered and tested a nuclear localization domain that impacts the cellular distribution of the protein. These data provide new insights into the potential roles of this critical developmental gene, establishing a platform to assess further translational studies, including the screening of missense genetic variants in WAC. Moreover, these studies are essential for understanding the role of human WAC variants in more diverse neurological phenotypes, including autism spectrum disorder.
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Affiliation(s)
- Hannah C. Rudolph
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - April M. Stafford
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Hye-Eun Hwang
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
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5
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Underwood A, Rasicci DT, Hinds D, Mitchell JT, Zieba JK, Mills J, Arnold NE, Cook TW, Moustaqil M, Gambin Y, Sierecki E, Fontaine F, Vanderweele S, Das AS, Cvammen W, Sirpilla O, Soehnlen X, Bricker K, Alokaili M, Green M, Heeringa S, Wilstermann AM, Freeland TM, Qutob D, Milsted A, Jauch R, Triche TJ, Krawczyk CM, Bupp CP, Rajasekaran S, Francois M, Prokop JW. Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships. Genes (Basel) 2023; 14:222. [PMID: 36672963 PMCID: PMC9859272 DOI: 10.3390/genes14010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
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Affiliation(s)
- Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Daniel T Rasicci
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - David Hinds
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jackson T Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob K Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nicholas E Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Taylor W Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mehdi Moustaqil
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Yann Gambin
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Emma Sierecki
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Vanderweele
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Akansha S Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - William Cvammen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Olivia Sirpilla
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Xavier Soehnlen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Kristen Bricker
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Maram Alokaili
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Morgan Green
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Sadie Heeringa
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Amy M Wilstermann
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Thomas M. Freeland
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Dinah Qutob
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Amy Milsted
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 518057, China
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Mathias Francois
- The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
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6
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Mark PR, Murray SA, Yang T, Eby A, Lai A, Lu D, Zieba J, Rajasekaran S, VanSickle EA, Rossetti LZ, Guidugli L, Watkins K, Wright MS, Bupp CP, Prokop JW. Autosomal recessive LRP1-related syndrome featuring cardiopulmonary dysfunction, bone dysmorphology, and corneal clouding. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006169. [PMID: 36307211 PMCID: PMC9632358 DOI: 10.1101/mcs.a006169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/22/2022] [Indexed: 01/25/2023] Open
Abstract
We provide the first study of two siblings with a novel autosomal recessive LRP1-related syndrome identified by rapid genome sequencing and overlapping multiple genetic models. The patients presented with respiratory distress, congenital heart defects, hypotonia, dysmorphology, and unique findings, including corneal clouding and ascites. Both siblings had compound heterozygous damaging variants, c.11420G > C (p.Cys3807Ser) and c.12407T > G (p.Val4136Gly) in LRP1, in which segregation analysis helped dismiss additional variants of interest. LRP1 analysis using multiple human/mouse data sets reveals a correlation to patient phenotypes of Peters plus syndrome with additional severe cardiomyopathy and blood vessel development complications linked to neural crest cells.
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Affiliation(s)
- Paul R. Mark
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | | | - Tao Yang
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, USA
| | - Alexandra Eby
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Department of Science, Davenport University, Grand Rapids, Michigan 49512, USA
| | - Angela Lai
- Neonatal Intensive Care Unit, Bronson Methodist Hospital, Kalamazoo, Michigan 49007, USA
| | - Di Lu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, USA
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Office of Research, Spectrum Health, Grand Rapids, Michigan 49503, USA
| | | | - Linda Z. Rossetti
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Meredith S. Wright
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Caleb P. Bupp
- Division of Medical Genetics, Spectrum Health, Grand Rapids, Michigan 49503, USA;,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA;,Genetics and Genome Sciences Program, Michigan State University, East Lansing, Michigan 48824, USA;,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, USA
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7
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Charron JG, Hernandez A, Bilinovich SM, Vogt DL, Bedinger LA, Seaver LH, Williams M, Devries S, Campbell DB, Bupp CP, Prokop JW. N-methyl-d-aspartate (NMDA) receptor genetics: The power of paralog homology and protein dynamics in defining dominant genetic variants. Am J Med Genet A 2022; 188:556-568. [PMID: 34726335 PMCID: PMC10472328 DOI: 10.1002/ajmg.a.62554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Abstract
Predicting genotype-to-phenotype correlations from genomic variants has been challenging, particularly for genes that have a complex balance of dominant and recessive inheritance for phenotypes. Variants in NMDA receptor components GRIN1, GRIN2A, and GRIN2B cause a myriad of dominant disease phenotypes, with the most common being epilepsy and autism spectrum disorder. Starting from the analysis of a variant of uncertain significance (VUS, GRIN2A G760S), we realized the need for tools to map dominant variants for the components of the NMDA receptor. Some variants within GRIN1, GRIN2A, and GRIN2B exert dominant epilepsy and developmental delay, yet other amino acid variants are conserved and predicted to alter protein function but do not have dominant phenotypes. Common variant annotation tools are not powered to determine pathogenic dominant outcomes. To address this gap, we integrated sequence and structural analyses for GRIN1, GRIN2A, and GRIN2B. Using this approach, we determined that paralog homology mapping and topology can segregate dominant variants, with an elevation of intermolecular contacts between the subunits. Furthermore, demonstrating the general utility of our methodology, we show that 25 VUS within ClinVar also reach a dominant variant annotation, including the GRIN2A G760S variant. Our work suggests paralog homology and protein topology as a powerful strategy within the receptor complex to resolve dominant genetic variants relative to variants that would fit a recessive inheritance, requiring two damaging variants. These strategies should be tested in additional dominant genetic disorders to determine the broader utility.
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Affiliation(s)
- Jacob G Charron
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Department of Biology, Calvin University, Grand Rapids MI 49506, USA
| | - Angel Hernandez
- Pediatric Neurology, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Stephanie M Bilinovich
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Center for Research in Autism, Intellectual, and other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel L Vogt
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Center for Research in Autism, Intellectual, and other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI, 48824, USA
| | - Laura A Bedinger
- Division of Medical Genetics, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Laurie H Seaver
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Division of Medical Genetics, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Michael Williams
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Center for Research in Autism, Intellectual, and other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI, 48824, USA
| | - Seth Devries
- Pediatric Neurology, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Daniel B Campbell
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Center for Research in Autism, Intellectual, and other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI, 48824, USA
| | - Caleb P Bupp
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Division of Medical Genetics, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI. 49503
- Center for Research in Autism, Intellectual, and other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI, 48824, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
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8
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Epiregulin as an Alternative Ligand for Leptin Receptor Alleviates Glucose Intolerance without Change in Obesity. Cells 2022; 11:cells11030425. [PMID: 35159237 PMCID: PMC8834548 DOI: 10.3390/cells11030425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 11/16/2022] Open
Abstract
The leptin receptor (LepR) acts as a signaling nexus for the regulation of glucose uptake and obesity, among other metabolic responses. The functional role of LepR under leptin-deficient conditions remains unclear. This study reports that epiregulin (EREG) governed glucose uptake in vitro and in vivo in Lepob mice by activating LepR under leptin-deficient conditions. Single and long-term treatment with EREG effectively rescued glucose intolerance in comparative insulin and EREG tolerance tests in Lepob mice. The immunoprecipitation study revealed binding between EREG and LepR in adipose tissue of Lepob mice. EREG/LepR regulated glucose uptake without changes in obesity in Lepob mice via mechanisms, including ERK activation and translocation of GLUT4 to the cell surface. EREG-dependent glucose uptake was abolished in Leprdb mice which supports a key role of LepR in this process. In contrast, inhibition of the canonical epidermal growth factor receptor (EGFR) pathway implicated in other EREG responses, increased glucose uptake. Our data provide a basis for understanding glycemic responses of EREG that are dependent on LepR unlike functions mediated by EGFR, including leptin secretion, thermogenesis, pain, growth, and other responses. The computational analysis identified a conserved amino acid sequence, supporting an evolutionary role of EREG as an alternative LepR ligand.
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9
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Bauss J, Morris M, Shankar R, Olivero R, Buck LN, Stenger CL, Hinds D, Mills J, Eby A, Zagorski JW, Smith C, Cline S, Hartog NL, Chen B, Huss J, Carcillo JA, Rajasekaran S, Bupp CP, Prokop JW. CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications. Front Immunol 2021; 12:790041. [PMID: 34925370 PMCID: PMC8674737 DOI: 10.3389/fimmu.2021.790041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.
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Affiliation(s)
- Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Infectious Disease, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Leah N Buck
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Mathematics, University of North Alabama, Florence, AL, United States
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, AL, United States
| | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Joshua Mills
- Department of Biology, Grand Valley State University, Allendale, MI, United States
| | - Alexandra Eby
- Department of Science, Davenport University, Grand Rapids, MI, United States
| | - Joseph W Zagorski
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Caitlin Smith
- Department of Biology, Athens State University, Athens, AL, United States
| | - Sara Cline
- Department of Biology, Athens State University, Athens, AL, United States
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - John Huss
- Department of Philosophy, The University of Akron, Akron, OH, United States
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Office of Research, Spectrum Health, Grand Rapids, MI, United States.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Medical Genetics, Spectrum Health, Grand Rapids, MI, United States
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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10
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Prokop JW, Bupp CP, Frisch A, Bilinovich SM, Campbell DB, Vogt D, Schultz CR, Uhl KL, VanSickle E, Rajasekaran S, Bachmann AS. Emerging Role of ODC1 in Neurodevelopmental Disorders and Brain Development. Genes (Basel) 2021; 12:genes12040470. [PMID: 33806076 PMCID: PMC8064465 DOI: 10.3390/genes12040470] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 01/18/2023] Open
Abstract
Ornithine decarboxylase 1 (ODC1 gene) has been linked through gain-of-function variants to a rare disease featuring developmental delay, alopecia, macrocephaly, and structural brain anomalies. ODC1 has been linked to additional diseases like cancer, with growing evidence for neurological contributions to schizophrenia, mood disorders, anxiety, epilepsy, learning, and suicidal behavior. The evidence of ODC1 connection to neural disorders highlights the need for a systematic analysis of ODC1 genotype-to-phenotype associations. An analysis of variants from ClinVar, Geno2MP, TOPMed, gnomAD, and COSMIC revealed an intellectual disability and seizure connected loss-of-function variant, ODC G84R (rs138359527, NC_000002.12:g.10444500C > T). The missense variant is found in ~1% of South Asian individuals and results in 2.5-fold decrease in enzyme function. Expression quantitative trait loci (eQTLs) reveal multiple functionally annotated, non-coding variants regulating ODC1 that associate with psychiatric/neurological phenotypes. Further dissection of RNA-Seq during fetal brain development and within cerebral organoids showed an association of ODC1 expression with cell proliferation of neural progenitor cells, suggesting gain-of-function variants with neural over-proliferation and loss-of-function variants with neural depletion. The linkage from the expression data of ODC1 in early neural progenitor proliferation to phenotypes of neurodevelopmental delay and to the connection of polyamine metabolites in brain function establish ODC1 as a bona fide neurodevelopmental disorder gene.
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Affiliation(s)
- Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Center for Research in Autism, Intellectual, and Other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (J.W.P.); (A.S.B.)
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Spectrum Health Medical Genetics, Grand Rapids, MI 49503, USA;
| | - Austin Frisch
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
| | - Stephanie M. Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
| | - Daniel B. Campbell
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Center for Research in Autism, Intellectual, and Other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI 48824, USA
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Center for Research in Autism, Intellectual, and Other Neurodevelopmental Disabilities, Michigan State University, East Lansing, MI 48824, USA
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
| | - Chad R. Schultz
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
| | - Katie L. Uhl
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
| | | | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
| | - André S. Bachmann
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA; (C.P.B.); (A.F.); (S.M.B.); (D.B.C.); (D.V.); (C.R.S.); (K.L.U.); (S.R.)
- Correspondence: (J.W.P.); (A.S.B.)
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11
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Peng H, Cassel J, McCracken DS, Prokop JW, Sementino E, Cheung M, Collop PR, Polo A, Joshi S, Mandell JP, Ayyanathan K, Hinds D, Malkowicz SB, Harbour JW, Bowcock AM, Salvino J, Kennedy EJ, Testa JR, Rauscher FJ. Kinetic Characterization of ASXL1/2-Mediated Allosteric Regulation of the BAP1 Deubiquitinase. Mol Cancer Res 2021; 19:1099-1112. [PMID: 33731362 DOI: 10.1158/1541-7786.mcr-20-0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/22/2020] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
BAP1 is an ubiquitin hydrolase whose deubiquitinase activity is mediated by polycomb group-like protein ASXL2. Cancer-related BAP1 mutations/deletions lead to loss-of-function by targeting the catalytic ubiquitin C-terminal hydrolase (UCH) or UCH37-like domain (ULD) domains of BAP1, and the latter disrupts binding to ASXL2, an obligate partner for BAP1 enzymatic activity. However, the biochemical and biophysical properties of domains involved in forming the enzymatically active complex are unknown. Here, we report the molecular dynamics, kinetics, and stoichiometry of these interactions. We demonstrate that interactions between BAP1 and ASXL2 are direct, specific, and stable to biochemical and biophysical manipulations as detected by isothermal titration calorimetry (ITC), GST association, and optical biosensor assays. Association of the ASXL2-AB box greatly stimulates BAP1 activity. A stable ternary complex is formed, comprised of the BAP1-UCH, BAP1-ULD, and ASXL2-AB domains. Stoichiometric analysis revealed that one molecule of the ULD domain directly interacts with one molecule of the AB box. Real-time kinetic analysis of the ULD/AB protein complex to the BAP1-UCH domain, based on surface plasmon resonance, indicated that formation of the ULD/AB complex with the UCH domain is a single-step event with fast association and slow dissociation rates. In vitro experiments validated in cells that the ASXL-AB box directly regulates BAP1 activity. IMPLICATIONS: Collectively, these data elucidate molecular interactions between specific protein domains regulating BAP1 deubiquitinase activity, thus establishing a foundation for small-molecule approaches to reactivate latent wild-type BAP1 catalytic activity in BAP1-mutant cancers.
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Affiliation(s)
| | - Joel Cassel
- The Wistar Institute, Philadelphia, Pennsylvania
| | - Daniel S McCracken
- The Wistar Institute, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | | | | | - Paul R Collop
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | | | - Surbhi Joshi
- The Wistar Institute, Philadelphia, Pennsylvania
| | | | | | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - S Bruce Malkowicz
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Anne M Bowcock
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
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12
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Sanders M, Lawlor JMJ, Li X, Schuen JN, Millard SL, Zhang X, Buck L, Grysko B, Uhl KL, Hinds D, Stenger CL, Morris M, Lamb N, Levy H, Bupp C, Prokop JW. Genomic, transcriptomic, and protein landscape profile of CFTR and cystic fibrosis. Hum Genet 2021; 140:423-439. [PMID: 32734384 PMCID: PMC7855842 DOI: 10.1007/s00439-020-02211-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/25/2020] [Indexed: 01/18/2023]
Abstract
Cystic Fibrosis (CF) is caused most often by removal of amino acid 508 (Phe508del, deltaF508) within CFTR, yet dozens of additional CFTR variants are known to give rise to CF and many variants in the genome are known to contribute to CF pathology. To address CFTR coding variants, we developed a sequence-to-structure-to-dynamic matrix for all amino acids of CFTR using 233 vertebrate species, CFTR structure within a lipid membrane, and 20 ns of molecular dynamic simulation to assess known variants from the CFTR1, CFTR2, ClinVar, TOPmed, gnomAD, and COSMIC databases. Surprisingly, we identify 18 variants of uncertain significance within CFTR from diverse populations that are heritable and a likely cause of CF that have been understudied due to nonexistence in Caucasian populations. In addition, 15 sites within the genome are known to modulate CF pathology, where we have identified one genome region (chr11:34754985-34836401) that contributes to CF through modulation of expression of a noncoding RNA in epithelial cells. These 15 sites are just the beginning of understanding comodifiers of CF, where utilization of eQTLs suggests many additional genomics of CFTR expressing cells that can be influenced by genomic background of CFTR variants. This work highlights that many additional insights of CF genetics are needed, particularly as pharmaceutical interventions increase in the coming years.
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Affiliation(s)
- Morgan Sanders
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - John N Schuen
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Susan L Millard
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Xi Zhang
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Leah Buck
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Bethany Grysko
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Hara Levy
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA.
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA.
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13
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Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal AW, Kim Y, Kyle PB, Attipoe E, Johnson AC, Uhl KL, Sirpilla OL, Jahanbakhsh S, Robinson M, Levy S, Valdar W, Garrett MR, Solberg Woods LC. Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model. Sci Rep 2021; 11:2071. [PMID: 33483609 PMCID: PMC7822875 DOI: 10.1038/s41598-021-81550-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023] Open
Abstract
Chronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.
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Affiliation(s)
| | - Jeremy W Prokop
- HudsonAlpha Institute, Huntsville, AL, USA
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Hong He
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Katie Holl
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - John Littrell
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aaron W Deal
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yunjung Kim
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick B Kyle
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Esinam Attipoe
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ashley C Johnson
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Olivia L Sirpilla
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Seyedehameneh Jahanbakhsh
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | | | - Shawn Levy
- HudsonAlpha Institute, Huntsville, AL, USA
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Garrett
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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14
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Ngo J, Prokop JW, Umfleet J, Seaver LH. Perinatal Manifestations of DARS2-Associated Leukoencephalopathy With Brainstem and Spinal Cord Involvement and Lactate Elevation (LBSL). Child Neurol Open 2021; 8:2329048X211019173. [PMID: 34104671 PMCID: PMC8155743 DOI: 10.1177/2329048x211019173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/16/2021] [Accepted: 05/03/2021] [Indexed: 11/17/2022] Open
Abstract
Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is a progressive disorder associated with deficiency of mitochondrial aspartyl-tRNA synthetase, a homodimer encoded by the gene DARS2. There is a wide range in age of onset of symptoms, typically from childhood to adulthood, with very few cases of infantile onset disease reported. We report a child at age 10 years with perinatal onset of symptoms evidenced by congenital microcephaly with progression to severe but non-lethal epileptic encephalopathy and spastic quadriplegia. A comprehensive epilepsy focused gene panel performed as a trio with parents detected a novel homozygous DARS2 variant. This variant is located at the dimer interface in a critical catalytic domain and is expected to result in markedly reduced enzyme activity which likely explains the severe and early onset symptoms in this case.
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Affiliation(s)
- Julie Ngo
- Michigan State University College of Human Medicine, Grand Rapids, MI,
USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University
College of Human Medicine, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, MI, USA
| | - Jason Umfleet
- Spectrum Health Helen Devos Children’s Hospital Grand Rapids, MI, USA
| | - Laurie H. Seaver
- Department of Pediatrics and Human Development, Michigan State University
College of Human Medicine, Grand Rapids, MI, USA
- Spectrum Health Helen Devos Children’s Hospital Grand Rapids, MI, USA
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15
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Rapid whole-genome sequencing identifies a homozygous novel variant, His540Arg, in HSD17B4 resulting in D-bifunctional protein deficiency disorder diagnosis. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005496. [PMID: 33115767 PMCID: PMC7784488 DOI: 10.1101/mcs.a005496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023] Open
Abstract
Rapid whole-genome sequencing (rWGS) allows for a diagnosis to be made quickly and impact medical management, particularly in critically ill children. Variants identified by this approach are often not identified using other testing methodologies, such as carrier screening or gene sequencing panels, targeted panels, or chromosomal microarrays. However, rWGS can identify variants of uncertain significance (VUSs), which challenges clinicians in the rapid return of information to families. Here we present a case of the metabolic condition D-bifunctional protein deficiency in a neonate with epilepsy and hypotonia born to consanguineous parents. Sequencing revealed a homozygous VUS in HSD17B4, c.1619A > G (p.His540Arg). Preliminary results were delivered within 3 d of sample receipt. Previous parental carrier screening included the HSD17B4 gene but was reported as negative. The molecular finding directed the clinical team to assess phenotypic overlap and investigate next steps in terms of confirmation of the findings and potential medical management of the patient. Clinical metabolic testing of fatty acids confirmed the diagnosis. Computational analysis of HSD17B4 His540Arg showed the change to likely impact dimerization based on structural insights, with the histidine conserved and selected throughout all 223 species assessed for this amino acid. This variant clusters around several pathogenic and likely pathogenic variants in HSD17B4. This case demonstrates the utility of rWGS, the potential for receiving uncertain results, and the downstream implications for confirmation or rejection of a molecular diagnosis by the clinical team.
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16
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Afrin A, Prokop JW, Underwood A, Uhl KL, VanSickle EA, Baruwal R, Wajda M, Rajasekaran S, Bupp C. NAA10 variant in 38-week-gestation male patient: a case study. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005868. [PMID: 33335012 PMCID: PMC7784496 DOI: 10.1101/mcs.a005868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/30/2020] [Indexed: 11/24/2022] Open
Abstract
We present a male patient born at 38-wk gestation with rhizomelic shortening of extremities, hepatomegaly, ventriculomegaly, heart failure, severely depressed left ventricular function, biventricular hypertrophy, and biatrial enlargement. Additional physical findings included anteriorly displaced anus, vertebral anomalies, and brachydactyly. The patient's cardiac malformations led to persistent hypotension, sinus tachycardia, and multiorgan failure in the absence of arrhythmias. Rapid whole-exome sequencing was ordered on day of life (DOL) 8. The patient's family elected to withdraw supportive care, and he passed away that evening. Whole-exome sequencing returned posthumously and identified a variant in NAA10, E100K. The genotype-phenotype was closest to Ogden syndrome or amino-terminal acetyltransferase deficiency. Typical features of this rare X-linked syndrome include progeroid appearance, failure to thrive, developmental delays, hypotonia, and cardiac arrhythmias. Other family members were tested and the patient's mother, who has a history of mild intellectual disability, as well as a daughter born later, were identified as carriers. All carriers showed no cardiac findings. The carrier sister has manifested developmental delay and cortical atrophy. Protein modeling, evolution, dynamics, population variant assessments, and immunoprecipitation depict the deleterious nature of the variant on the interactions of NAA10 with NAA15 These findings had subsequent implications for posthumous diagnosis of the index patient, for female carriers, and regarding family planning. We highlight how these rapid genetic tests and variant characterization can potentially lead to informed decision-making between health-care providers and family members of patients with critical or lethal conditions when treatment options are limited.
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Affiliation(s)
- Antara Afrin
- College of Human Medicine,, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Jeremy W Prokop
- College of Human Medicine,, Michigan State University, Grand Rapids, Michigan 49503, USA.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Adam Underwood
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan 49503, USA.,Walsh University, North Canton, Ohio 44720, USA
| | - Katie L Uhl
- College of Human Medicine,, Michigan State University, Grand Rapids, Michigan 49503, USA.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Elizabeth A VanSickle
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | | | | | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan 49503, USA.,Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | - Caleb Bupp
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan 49503, USA.,Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
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17
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PEA15 loss of function and defective cerebral development in the domestic cat. PLoS Genet 2020; 16:e1008671. [PMID: 33290415 DOI: 10.1371/journal.pgen.1008671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Cerebral cortical size and organization are critical features of neurodevelopment and human evolution, for which genetic investigation in model organisms can provide insight into developmental mechanisms and the causes of cerebral malformations. However, some abnormalities in cerebral cortical proliferation and folding are challenging to study in laboratory mice due to the absence of gyri and sulci in rodents. We report an autosomal recessive allele in domestic cats associated with impaired cerebral cortical expansion and folding, giving rise to a smooth, lissencephalic brain, and that appears to be caused by homozygosity for a frameshift in PEA15 (phosphoprotein expressed in astrocytes-15). Notably, previous studies of a Pea15 targeted mutation in mice did not reveal structural brain abnormalities. Affected cats, however, present with a non-progressive hypermetric gait and tremors, develop dissociative behavioral defects and aggression with age, and exhibit profound malformation of the cerebrum, with a 45% average decrease in overall brain weight, and reduction or absence of the ectosylvian, sylvian and anterior cingulate gyrus. Histologically, the cerebral cortical layers are disorganized, there is substantial loss of white matter in tracts such as the corona radiata and internal capsule, but the cerebellum is relatively spared. RNA-seq and immunohistochemical analysis reveal astrocytosis. Fibroblasts cultured from affected cats exhibit increased TNFα-mediated apoptosis, and increased FGFb-induced proliferation, consistent with previous studies implicating PEA15 as an intracellular adapter protein, and suggesting an underlying pathophysiology in which increased death of neurons accompanied by increased proliferation of astrocytes gives rise to abnormal organization of neuronal layers and loss of white matter. Taken together, our work points to a new role for PEA15 in development of a complex cerebral cortex that is only apparent in gyrencephalic species.
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18
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Sirpilla O, Bauss J, Gupta R, Underwood A, Qutob D, Freeland T, Bupp C, Carcillo J, Hartog N, Rajasekaran S, Prokop JW. SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes. J Proteome Res 2020; 19:4275-4290. [PMID: 32686937 PMCID: PMC7418564 DOI: 10.1021/acs.jproteome.0c00421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.
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Affiliation(s)
- Olivia Sirpilla
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Jacob Bauss
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
| | - Ruchir Gupta
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Adam Underwood
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Dinah Qutob
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Tom Freeland
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Caleb Bupp
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Spectrum Health Medical
Genetics, Grand Rapids, Michigan 49503,
United States
| | - Joseph Carcillo
- Department of Critical Care Medicine
and Pediatrics, Children’s Hospital of Pittsburgh,
University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania 15421,
United States
| | - Nicholas Hartog
- Allergy & Immunology,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Pediatric Intensive Care
Unit, Helen DeVos Children’s Hospital,
Grand Rapids, Michigan 49503, United States
- Office of Research,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
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19
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Wu F, Zhou Y, Li L, Shen X, Chen G, Wang X, Liang X, Tan M, Huang Z. Computational Approaches in Preclinical Studies on Drug Discovery and Development. Front Chem 2020; 8:726. [PMID: 33062633 PMCID: PMC7517894 DOI: 10.3389/fchem.2020.00726] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of drug development in the costly late stage, it has been widely recognized that drug ADMET properties should be considered as early as possible to reduce failure rates in the clinical phase of drug discovery. Concurrently, drug recalls have become increasingly common in recent years, prompting pharmaceutical companies to increase attention toward the safety evaluation of preclinical drugs. In vitro and in vivo drug evaluation techniques are currently more mature in preclinical applications, but these technologies are costly. In recent years, with the rapid development of computer science, in silico technology has been widely used to evaluate the relevant properties of drugs in the preclinical stage and has produced many software programs and in silico models, further promoting the study of ADMET in vitro. In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling). Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction. We focus on some widely studied ADMT properties as well as PBPK simulation, and we list some applications that are related to the prediction categories and web tools. Finally, we discuss challenges and limitations in the preclinical area and propose some suggestions and prospects for the future.
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Yuquan Zhou
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Langhui Li
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianhuan Shen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ganying Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaoqing Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianyang Liang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Mengyuan Tan
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
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20
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Gupta R, Charron J, Stenger CL, Painter J, Steward H, Cook TW, Faber W, Frisch A, Lind E, Bauss J, Li X, Sirpilla O, Soehnlen X, Underwood A, Hinds D, Morris M, Lamb N, Carcillo JA, Bupp C, Uhal BD, Rajasekaran S, Prokop JW. SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics. J Biol Chem 2020; 295:11742-11753. [PMID: 32587094 PMCID: PMC7450099 DOI: 10.1074/jbc.ra120.014873] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 06/23/2020] [Indexed: 12/28/2022] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has challenged the speed at which laboratories can discover the viral composition and study health outcomes. The small ∼30-kb ssRNA genome of coronaviruses makes them adept at cross-species spread while enabling a robust understanding of all of the proteins the viral genome encodes. We have employed protein modeling, molecular dynamics simulations, evolutionary mapping, and 3D printing to gain a full proteome- and dynamicome-level understanding of SARS-CoV-2. We established the Viral Integrated Structural Evolution Dynamic Database (VIStEDD at RRID:SCR_018793) to facilitate future discoveries and educational use. Here, we highlight the use of VIStEDD for nsp6, nucleocapsid (N), and spike (S) surface glycoprotein. For both nsp6 and N, we found highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we developed a quantitative dynamics cross-correlation matrix to gain insights into its interactions with the angiotensin I-converting enzyme 2 (ACE2)-solute carrier family 6 member 19 (SLC6A19) dimer. Using this quantitative matrix, we elucidated 47 potential functional missense variants from genomic databases within ACE2/SLC6A19/transmembrane serine protease 2 (TMPRSS2), warranting genomic enrichment analyses in SARS-CoV-2 patients. These variants had ultralow frequency but existed in males hemizygous for ACE2. Two ACE2 noncoding variants (rs4646118 and rs143185769) present in ∼9% of individuals of African descent may regulate ACE2 expression and may be associated with increased susceptibility of African Americans to SARS-CoV-2. We propose that this SARS-CoV-2 database may aid research into the ongoing pandemic.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2
- Betacoronavirus/chemistry
- Betacoronavirus/genetics
- Black People/genetics
- COVID-19
- Coronavirus Infections/metabolism
- Coronavirus Infections/virology
- Coronavirus Nucleocapsid Proteins
- Databases, Protein
- Genetic Predisposition to Disease
- Genetic Variation
- Host-Pathogen Interactions
- Humans
- Male
- Molecular Dynamics Simulation
- Nucleocapsid Proteins/chemistry
- Nucleocapsid Proteins/metabolism
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Phosphoproteins
- Pneumonia, Viral/metabolism
- Pneumonia, Viral/virology
- Protein Interaction Maps
- Protein Processing, Post-Translational
- Proteome
- SARS-CoV-2
- Sequence Homology, Amino Acid
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- Black or African American
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Affiliation(s)
- Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Jacob Charron
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Calvin University, Grand Rapids, Michigan, USA
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Jared Painter
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Hunter Steward
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Taylor W Cook
- Grand Rapids Community College, Grand Rapids, Michigan, USA
| | - William Faber
- Grand Rapids Community College, Grand Rapids, Michigan, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Eric Lind
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Olivia Sirpilla
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Walsh University, North Canton, Ohio, USA
| | - Xavier Soehnlen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Walsh University, North Canton, Ohio, USA
| | | | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, Michigan, USA
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, Michigan, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA
- Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
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21
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Devries S, Mulder M, Charron JG, Prokop JW, Mark PR. SLC6A1 G443D associated with developmental delay and epilepsy. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005371. [PMID: 32660967 PMCID: PMC7476406 DOI: 10.1101/mcs.a005371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022] Open
Abstract
SLC6A1 is associated with an autosomal dominant early-onset seizure and epileptic encephalopathy associated with intellectual disability. We present a 2-yr-old girl with developmental delay and epilepsy, using a new computational filtering impact score to show the patient's variant ranks with other pathogenic variants. Genomic studies within the patient revealed a G443D variant of uncertain significance. Structural and evolutionary assessments establish this variant as a loss of function to the protein. Compiled metrics through our custom tools on sequence, structure, and protein dynamics combined with PolyPhen-2, PROVEAN, SIFT, and Align-GVGD reveal this variant to rank in the top functional outcome changes relative to gnomAD, TOPMed, and ClinVar variants known to date. The patient was resistant to multiple epileptic drugs, finally finding that valproic acid controls the seizures. This is consistent with additional groups studying SLC6A1 variants within patients.
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Affiliation(s)
- Seth Devries
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | - Monica Mulder
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | - Jacob G Charron
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing Michigan 48824, USA
| | - Paul R Mark
- Spectrum Health Division of Medical Genetics, Grand Rapids, Michigan 49503, USA
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22
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Prokop JW, Shankar R, Gupta R, Leimanis ML, Nedveck D, Uhl K, Chen B, Hartog NL, Van Veen J, Sisco JS, Sirpilla O, Lydic T, Boville B, Hernandez A, Braunreiter C, Kuk CC, Singh V, Mills J, Wegener M, Adams M, Rhodes M, Bachmann AS, Pan W, Byrne-Steele ML, Smith DC, Depinet M, Brown BE, Eisenhower M, Han J, Haw M, Madura C, Sanfilippo DJ, Seaver LH, Bupp C, Rajasekaran S. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19. Physiol Genomics 2020; 52:255-268. [PMID: 32437232 PMCID: PMC7303726 DOI: 10.1152/physiolgenomics.00045.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Mara L Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Derek Nedveck
- Office of Research, Spectrum Health, Grand Rapids, Michigan
| | - Katie Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Allergy and Immunology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Adult Allergy and Immunology, Spectrum Health, Grand Rapids, Michigan
| | - Jason Van Veen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Joshua S Sisco
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Olivia Sirpilla
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Walsh University, North Canton, Ohio
| | - Todd Lydic
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Brian Boville
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Angel Hernandez
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Chi Braunreiter
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - ChiuYing Cynthia Kuk
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Varinder Singh
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Marc Wegener
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Andre S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | | | | | | | | | | | | | - Jian Han
- iRepertoire Inc., Huntsville, Alabama
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Marcus Haw
- Congenital Heart Center, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Casey Madura
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Dominic J Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Laurie H Seaver
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Caleb Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Office of Research, Spectrum Health, Grand Rapids, Michigan
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23
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Gupta R, Charron J, Stenger CL, Painter J, Steward H, Cook TW, Faber W, Frisch A, Lind E, Bauss J, Li X, Sirpilla O, Soehnlen X, Underwood A, Hinds D, Morris M, Lamb N, Carcillo JA, Bupp C, Uhal BD, Rajasekaran S, Prokop JW. SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511397 DOI: 10.1101/2020.05.15.098616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.
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24
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MacKay CI, Bick D, Prokop JW, Muñoz I, Rouse J, Downs J, Leonard H. Expanding the phenotype of the CDKL5 deficiency disorder: Are seizures mandatory? Am J Med Genet A 2020; 182:1217-1222. [DOI: 10.1002/ajmg.a.61504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/03/2019] [Accepted: 01/17/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Conor I. MacKay
- Telethon Kids InstituteThe University of Western Australia Perth Western Australia Australia
| | - David Bick
- HudsonAlpha Institute for Biotechnology Huntsville Alabama
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human MedicineMichigan State University Grand Rapids Michigan
| | - Ivan Muñoz
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of Dundee Dundee Scotland
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of Dundee Dundee Scotland
| | - Jenny Downs
- Telethon Kids InstituteThe University of Western Australia Perth Western Australia Australia
- School of Physiotherapy and Exercise ScienceCurtin University Perth Western Australia Australia
| | - Helen Leonard
- Telethon Kids InstituteThe University of Western Australia Perth Western Australia Australia
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25
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Cochran JN, McKinley EC, Cochran M, Amaral MD, Moyers BA, Lasseigne BN, Gray DE, Lawlor JMJ, Prokop JW, Geier EG, Holt JM, Thompson ML, Newberry JS, Yokoyama JS, Worthey EA, Geldmacher DS, Love MN, Cooper GM, Myers RM, Roberson ED. Genome sequencing for early-onset or atypical dementia: high diagnostic yield and frequent observation of multiple contributory alleles. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003491. [PMID: 31836585 PMCID: PMC6913143 DOI: 10.1101/mcs.a003491] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/25/2019] [Indexed: 12/14/2022] Open
Abstract
We assessed the results of genome sequencing for early-onset dementia. Participants were selected from a memory disorders clinic. Genome sequencing was performed along with C9orf72 repeat expansion testing. All returned sequencing results were Sanger-validated. Prior clinical diagnoses included Alzheimer's disease, frontotemporal dementia, and unspecified dementia. The mean age of onset was 54 (41–76). Fifty percent of patients had a strong family history, 37.5% had some, and 12.5% had no known family history. Nine of 32 patients (28%) had a variant defined as pathogenic or likely pathogenic (P/LP) by American College of Medical Genetics and Genomics standards, including variants in APP, C9orf72, CSF1R, and MAPT. Nine patients (including three with P/LP variants) harbored established risk alleles with moderate penetrance (odds ratios of ∼2–5) in ABCA7, AKAP9, GBA, PLD3, SORL1, and TREM2. All six patients harboring these moderate penetrance variants but not P/LP variants also had one or two APOE ε4 alleles. One patient had two APOE ε4 alleles with no other established contributors. In total, 16 patients (50%) harbored one or more genetic variants likely to explain symptoms. We identified variants of uncertain significance (VUSs) in ABI3, ADAM10, ARSA, GRID2IP, MME, NOTCH3, PLCD1, PSEN1, TM2D3, TNK1, TTC3, and VPS13C, also often along with other variants. In summary, genome sequencing for early-onset dementia frequently identified multiple established or possible contributory alleles. These observations add support for an oligogenic model for early-onset dementia.
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Affiliation(s)
| | - Emily C McKinley
- Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Meagan Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michelle D Amaral
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Bryan A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.,Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan 48824, USA
| | - Ethan G Geier
- Department of Neurology, Memory and Aging Center, University of California San Francisco, San Francisco, California 94158, USA
| | - James M Holt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - J Scott Newberry
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jennifer S Yokoyama
- Department of Neurology, Memory and Aging Center, University of California San Francisco, San Francisco, California 94158, USA
| | | | - David S Geldmacher
- Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Marissa Natelson Love
- Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Erik D Roberson
- Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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26
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Knop J, Spilgies LM, Rufli S, Reinhart R, Vasilikos L, Yabal M, Owsley E, Jost PJ, Marsh RA, Wajant H, Robinson MD, Kaufmann T, Wong WWL. TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death Dis 2019; 10:700. [PMID: 31541082 PMCID: PMC6754467 DOI: 10.1038/s41419-019-1938-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023]
Abstract
The pediatric immune deficiency X-linked proliferative disease-2 (XLP-2) is a unique disease, with patients presenting with either hemophagocytic lymphohistiocytosis (HLH) or intestinal bowel disease (IBD). Interestingly, XLP-2 patients display high levels of IL-18 in the serum even while in stable condition, presumably through spontaneous inflammasome activation. Recent data suggests that LPS stimulation can trigger inflammasome activation through a TNFR2/TNF/TNFR1 mediated loop in xiap−/− macrophages. Yet, the direct role TNFR2-specific activation plays in the absence of XIAP is unknown. We found TNFR2-specific activation leads to cell death in xiap−/− myeloid cells, particularly in the absence of the RING domain. RIPK1 kinase activity downstream of TNFR2 resulted in a TNF/TNFR1 cell death, independent of necroptosis. TNFR2-specific activation leads to a similar inflammatory NF-kB driven transcriptional profile as TNFR1 activation with the exception of upregulation of NLRP3 and caspase-11. Activation and upregulation of the canonical inflammasome upon loss of XIAP was mediated by RIPK1 kinase activity and ROS production. While both the inhibition of RIPK1 kinase activity and ROS production reduced cell death, as well as release of IL-1β, the release of IL-18 was not reduced to basal levels. This study supports targeting TNFR2 specifically to reduce IL-18 release in XLP-2 patients and to reduce priming of the inflammasome components.
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Affiliation(s)
- Janin Knop
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Lisanne M Spilgies
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Stefanie Rufli
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Ramona Reinhart
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Lazaros Vasilikos
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Monica Yabal
- III. Medizinische Klink, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Erika Owsley
- UC Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, USA
| | - Philipp J Jost
- III. Medizinische Klink, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Rebecca A Marsh
- UC Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, USA
| | - Harald Wajant
- Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Thomas Kaufmann
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - W Wei-Lynn Wong
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland.
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27
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Shepard CJ, Cline SG, Hinds D, Jahanbakhsh S, Prokop JW. Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms. Physiol Genomics 2019; 51:562-577. [PMID: 31482761 DOI: 10.1152/physiolgenomics.00120.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genetics of multiple sclerosis (MS) are highly polygenic with few insights into mechanistic associations with pathology. In this study, we assessed MS genetics through linkage disequilibrium and missense variant interpretation to yield a MS gene network. This network of 96 genes was taken through pathway analysis, tissue expression profiles, single cell expression segregation, expression quantitative trait loci (eQTLs), genome annotations, transcription factor (TF) binding profiles, structural genome looping, and overlap with additional associated genetic traits. This work revealed immune system dysfunction, nerve cell myelination, energetic control, transcriptional regulation, and variants that overlap multiple autoimmune disorders. Tissue-specific expression and eQTLs of MS genes implicate multiple immune cell types including macrophages, neutrophils, and T cells, while the genes in neural cell types enrich for oligodendrocyte and myelin sheath biology. There are eQTLs in linkage with lead MS variants in 25 genes including the multitissue eQTL, rs9271640, for HLA-DRB1/DRB5. Using multiple functional genomic databases, we identified noncoding variants that disrupt TF binding for GABPA, CTCF, EGR1, YY1, SPI1, CLOCK, ARNTL, BACH1, and GFI1. Overall, this paper suggests multiple genetic mechanisms for MS associated variants while highlighting the importance of a systems biology and network approach when elucidating intersections of the immune and nervous system.
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Affiliation(s)
- C Joy Shepard
- Department of Biology, Athens State University, Athens, Alabama.,Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sara G Cline
- Department of Biology, Athens State University, Athens, Alabama
| | - David Hinds
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Seyedehameneh Jahanbakhsh
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
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28
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Hiatt SM, Thompson ML, Prokop JW, Lawlor JMJ, Gray DE, Bebin EM, Rinne T, Kempers M, Pfundt R, van Bon BW, Mignot C, Nava C, Depienne C, Kalsner L, Rauch A, Joset P, Bachmann-Gagescu R, Wentzensen IM, McWalter K, Cooper GM. Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder. Am J Hum Genet 2019; 104:701-708. [PMID: 30879638 PMCID: PMC6451696 DOI: 10.1016/j.ajhg.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/01/2019] [Indexed: 01/08/2023] Open
Abstract
Developmental delay and intellectual disability (DD and ID) are heterogeneous phenotypes that arise in many rare monogenic disorders. Because of this rarity, developing cohorts with enough individuals to robustly identify disease-associated genes is challenging. Social-media platforms that facilitate data sharing among sequencing labs can help to address this challenge. Through one such tool, GeneMatcher, we identified nine DD- and/or ID-affected probands with a rare, heterozygous variant in the gene encoding the serine/threonine-protein kinase BRSK2. All probands have a speech delay, and most present with intellectual disability, motor delay, behavioral issues, and autism. Six of the nine variants are predicted to result in loss of function, and computational modeling predicts that the remaining three missense variants are damaging to BRSK2 structure and function. All nine variants are absent from large variant databases, and BRSK2 is, in general, relatively intolerant to protein-altering variation among humans. In all six probands for whom parents were available, the mutations were found to have arisen de novo. Five of these de novo variants were from cohorts with at least 400 sequenced probands; collectively, the cohorts span 3,429 probands, and the observed rate of de novo variation in these cohorts is significantly higher than the estimated background-mutation rate (p = 2.46 × 10-6). We also find that exome sequencing provides lower coverage and appears less sensitive to rare variation in BRSK2 than does genome sequencing; this fact most likely reduces BRSK2's visibility in many clinical and research sequencing efforts. Altogether, our results implicate damaging variation in BRSK2 as a source of neurodevelopmental disease.
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Affiliation(s)
- Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jeremy W Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - E Martina Bebin
- Department of Neurology, University of Alabama Birmingham, Birmingham, AL 35294, USA
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France; Centres de Référence Maladies Rares, Déficiences Intellectuelles de Causes Rares, Paris 75013, France; Groupes de Recherche Clinique Paris Sorbonne Déficience Intellectuelle et Autisme, Paris 75013, France
| | - Caroline Nava
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France; Faculté de Médecine, Institut du Cerveau et de la Moelle épinière, Sorbonne Université, Paris 75013, France
| | - Christel Depienne
- Faculté de Médecine, Institut du Cerveau et de la Moelle épinière, Sorbonne Université, Paris 75013, France; Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Louisa Kalsner
- Connecticut Children's Medical Center, Farmington, CT 06032, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland; Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program, University of Zurich, Zurich 8032, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren 8952, Switzerland
| | | | | | | | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
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29
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Korakavi N, Prokop JW, Seaver LH. Evolution of the phenotype of craniosynostosis with dental anomalies syndrome and report of IL11RA variant population frequencies in a Crouzon-like autosomal recessive syndrome. Am J Med Genet A 2019; 179:668-673. [PMID: 30811827 DOI: 10.1002/ajmg.a.61070] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/18/2018] [Accepted: 01/26/2019] [Indexed: 11/06/2022]
Abstract
In 2011, biallelic loss-of-function variants in the interleukin receptor 11 alpha gene IL11RA were found to be associated with a Crouzon-like craniosynostosis syndrome with associated dental anomalies (CRSDA). Since then, a total of 41 similar patients have been reported with IL11RA variants. We report two adult brothers diagnosed with Crouzon syndrome as children, in which the clinical diagnosis of CRSDA was made on reevaluation. Laboratory testing detected biallelic IL11RA variants, c.916_924dup (p.Thr306_Ser308dup) and c.781C > T (p.Arg261Cys), both of which have now been reported in other families. Protein modeling and conservation analysis show that these two mutation sites cluster together near a WSXWS motif that likely plays a significant role in regulating IL11RA protein function. Population analysis from gnomAD shows that Non-Finnish Europeans (similar to ethnicity of this family), have an allele frequency for p.Thr306_Ser308dup of 0.014% and p.Arg261Cys of 0.008%. We found other ethnicities have functional IL11RA missense variants at higher frequencies. With this report, we provide a summary of the clinical findings including details of middle ear anomalies associated with conductive hearing loss. We also provide data supporting the populations at risk for this condition to increase recognition and diagnosis of this rare autosomal recessive craniosynostosis syndrome.
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Affiliation(s)
- Nisha Korakavi
- Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, Michigan
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Laurie H Seaver
- Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, Michigan.,Division of Medical Genetics and Genomics, Spectrum Health Helen DeVos Children's Hospital, Grand Rapids, Michigan
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30
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Seaver LH, DeRoos S, Andersen NJ, Betz B, Prokop J, Lannen N, Jordan R, Rajasekaran S. Lethal NARS2-Related Disorder Associated With Rapidly Progressive Intractable Epilepsy and Global Brain Atrophy. Pediatr Neurol 2018; 89:26-30. [PMID: 30327238 DOI: 10.1016/j.pediatrneurol.2018.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/25/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Infantile epileptic encephalopathy is a heterogeneous condition that has been associated with variants in more than 200 genes. The variability in findings and prognosis creates challenges to making the correct diagnosis and initiating the appropriate therapy. Biallelic variants in NARS2, a mitochondrial aminoacyl-tRNA synthetase gene, were recently associated with neurodegenerative disorders that include epilepsy. METHODS We describe two infant brothers who presented with focal status epilepticus that progressed to lethal epileptic encephalopathy. We compared the cost of diagnostic laboratory evaluation for each child. Detailed NARS2 protein analysis was performed using a sequence-to-structure-to-function workflow, merging multiple homologous structures, to suggest biologic impact of the NARS2 variants. RESULTS Brain magnetic resonance imaging showed rapid progression to generalized atrophy. Extensive metabolic, infectious, chromosomal and genetic testing of the first infant failed to reach a specific diagnosis. The younger brother presented similarly. Rapid whole exome sequencing was performed revealing novel biallelic variants in NARS2. The variants c.167A>G (p.Gln56Arg) and c.631T>A (p.Phe211Ile) were confirmed in a reserved sample from the older brother. Management was then redirected toward palliative care and the child died at age nine months. CONCLUSIONS NARS2-related disorder should be considered in infants presenting with refractory seizures and rapid brain atrophy. Metabolic screening tests may be normal or yield nonspecific findings. Rapid whole exome sequencing in children with fulminant onset intractable epilepsy may minimize extensive diagnostic evaluation and aid in prognosis and medical management.
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Affiliation(s)
- Laurie H Seaver
- Helen DeVos Children's Hospital, Grand Rapids, Michigan; College of Human Medicine Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan.
| | - Steven DeRoos
- Helen DeVos Children's Hospital, Grand Rapids, Michigan; College of Human Medicine Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan
| | | | - Brad Betz
- Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Jeremy Prokop
- College of Human Medicine Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan
| | - Nick Lannen
- Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Renee Jordan
- Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Helen DeVos Children's Hospital, Grand Rapids, Michigan; College of Human Medicine Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan
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31
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Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
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Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P, Simon MEH, Smith R, Hurst JA, McLaughlin H, Person R, Crunk A, Wangler MF, Streff H, Symonds JD, Zuberi SM, Elliott KS, Sanders VR, Masunga A, Hopkin RJ, Dubbs HA, Ortiz-Gonzalez XR, Pfundt R, Brunner HG, Fisher SE, Kleefstra T, Cooper GM. De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder. Hum Genet 2018; 137:375-388. [PMID: 29740699 PMCID: PMC5973976 DOI: 10.1007/s00439-018-1887-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/21/2018] [Indexed: 01/15/2023]
Abstract
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.
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Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Krysta L Engel
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paulien Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Jane A Hurst
- Great Ormond Street Hospital for Children, London, UK
| | | | | | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | | | - Victoria R Sanders
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Abigail Masunga
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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33
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Prokop JW, Yeo NC, Ottmann C, Chhetri SB, Florus KL, Ross EJ, Sosonkina N, Link BA, Freedman BI, Coppola CJ, McDermott-Roe C, Leysen S, Milroy LG, Meijer FA, Geurts AM, Rauscher FJ, Ramaker R, Flister MJ, Jacob HJ, Mendenhall EM, Lazar J. Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD. J Am Soc Nephrol 2018; 29:1525-1535. [PMID: 29476007 DOI: 10.1681/asn.2017080856] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Background Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, SHROOM3 is an associated risk gene for CKD, yet causative mechanism(s) of SHROOM3 allele(s) are unknown.Methods We used our analytic pipeline that integrates genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiologic data to characterize coding and noncoding variants to study the human SHROOM3 risk locus for CKD.Results We identified a novel SHROOM3 transcriptional start site, which results in a shorter isoform lacking the PDZ domain and is regulated by a common noncoding sequence variant associated with CKD (rs17319721, allele frequency: 0.35). This variant disrupted allele binding to the transcription factor TCF7L2 in podocyte cell nuclear extracts and altered transcription levels of SHROOM3 in cultured cells, potentially through the loss of repressive looping between rs17319721 and the novel start site. Although common variant mechanisms are of high utility, sequencing is beginning to identify rare variants involved in disease; therefore, we used our biophysical tools to analyze an average of 112,849 individual human genome sequences for rare SHROOM3 missense variants, revealing 35 high-effect variants. The high-effect alleles include a coding variant (P1244L) previously associated with CKD (P=0.01, odds ratio=7.95; 95% CI, 1.53 to 41.46) that we find to be present in East Asian individuals at an allele frequency of 0.0027. We determined that P1244L attenuates the interaction of SHROOM3 with 14-3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD.Conclusions These data demonstrate multiple new SHROOM3-dependent genetic/molecular mechanisms that likely affect CKD.
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Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; .,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan
| | - Nan Cher Yeo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Kacie L Florus
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Emily J Ross
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee
| | | | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy and
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; and
| | - Candice J Coppola
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Chris McDermott-Roe
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Seppe Leysen
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Femke A Meijer
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Aron M Geurts
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Frank J Rauscher
- Gene Expression & Regulation Program, Wistar Institute, Philadelphia, Pennsylvania
| | - Ryne Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Michael J Flister
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Howard J Jacob
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama;
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34
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Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih SW, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister MJ, Mott R, Valdar W, Solberg Woods LC. Genetic Fine-Mapping and Identification of Candidate Genes and Variants for Adiposity Traits in Outbred Rats. Obesity (Silver Spring) 2018; 26:213-222. [PMID: 29193816 PMCID: PMC5740008 DOI: 10.1002/oby.22075] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Obesity is a major risk factor for multiple diseases and is in part heritable, yet the majority of causative genetic variants that drive excessive adiposity remain unknown. Here, outbred heterogeneous stock (HS) rats were used in controlled environmental conditions to fine-map novel genetic modifiers of adiposity. METHODS Body weight and visceral fat pad weights were measured in male HS rats that were also genotyped genome-wide. Quantitative trait loci (QTL) were identified by genome-wide association of imputed single-nucleotide polymorphism (SNP) genotypes using a linear mixed effect model that accounts for unequal relatedness between the HS rats. Candidate genes were assessed by protein modeling and mediation analysis of expression for coding and noncoding variants, respectively. RESULTS HS rats exhibited large variation in adiposity traits, which were highly heritable and correlated with metabolic health. Fine-mapping of fat pad weight and body weight revealed three QTL and prioritized five candidate genes. Fat pad weight was associated with missense SNPs in Adcy3 and Prlhr and altered expression of Krtcap3 and Slc30a3, whereas Grid2 was identified as a candidate within the body weight locus. CONCLUSIONS These data demonstrate the power of HS rats for identification of known and novel heritable mediators of obesity traits.
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Affiliation(s)
- Gregory R. Keele
- Department of Genetics, University of North Carolina at Chapel Hill, NC
| | | | - Hong He
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Katie Holl
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - John Littrell
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Aaron Deal
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, NC
| | - Sanja Francic
- University College London Genetics Institute, London, UK
| | - Leilei Cui
- University College London Genetics Institute, London, UK
| | | | - Karl W. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI
| | - Michael Tschannen
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Shirng-Wern Tsaih
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Maie Zagloul
- Department of Genetics, University of North Carolina at Chapel Hill, NC
| | - Yunjung Kim
- Department of Genetics, University of North Carolina at Chapel Hill, NC
| | - Brittany Baur
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Joseph Fox
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | | | | | - Michael J. Flister
- Medical College of Wisconsin, Departments of Pediatrics and Physiology, Milwaukee, WI
| | - Richard Mott
- University College London Genetics Institute, London, UK
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, NC
| | - Leah C Solberg Woods
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, NC
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