1
|
Kohler JN, Legro NR, Baldridge D, Shin J, Bowman A, Ugur B, Jackstadt MM, Shriver LP, Patti GJ, Zhang B, Feng W, McAdow AR, Goddard P, Ungar RA, Jensen T, Smith KS, Fresard L, Alvarez R, Bonner D, Reuter CM, McCormack C, Kravets E, Marwaha S, Holt JM, Worthey E, Ashley EA, Montgomery SB, Fisher P, Postlethwait J, De Camilli P, Solnica-Krezel L, Bernstein JA, Wheeler MT. Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genet Med 2024:101166. [PMID: 38767059 DOI: 10.1016/j.gim.2024.101166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
PURPOSE The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings. METHODS We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort. RESULTS These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated dysregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation. CONCLUSION Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.
Collapse
Affiliation(s)
- Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics - Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Nicole R Legro
- Department of Obstetrics and Gynecology, MedStar Washington Hospital Center andGeorgetown University Hospital, Washington, District of Columbia, 20009, USA.
| | - Dustin Baldridge
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Jimann Shin
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Angela Bowman
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Berrak Ugur
- Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, New Haven, CT, 6520, USA
| | - Madelyn M Jackstadt
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA; Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA; Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA; Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA; Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA; Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA; Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Bo Zhang
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Wenjia Feng
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Anthony R McAdow
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Pagé Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tanner Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin S Smith
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Raquel Alvarez
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics - Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chloe M Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics - Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Colleen McCormack
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
| | - Elijah Kravets
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
| | - James M Holt
- PacBio, 1305 O'Brien Drive Menlo Park, CA, 94025, USA
| | | | - Euan A Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Paul Fisher
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics - Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, 6520, USA
| | - Lila Solnica-Krezel
- Model Organism Screening Center, Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63130, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Department of Pediatrics - Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, 94305, USA; Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| |
Collapse
|
2
|
Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
Collapse
Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
| | | |
Collapse
|
3
|
Kamps-Hughes N, Carlton VEH, Fresard L, Osazuwa S, Starks E, Vincent JJ, Albritton S, Nussbaum RL, Nykamp K. A Systematic Method for Detecting Abnormal mRNA Splicing and Assessing Its Clinical Impact in Individuals Undergoing Genetic Testing for Hereditary Cancer Syndromes. J Mol Diagn 2023; 25:156-167. [PMID: 36563937 DOI: 10.1016/j.jmoldx.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Nearly 14% of disease-causing germline variants result from the disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing are classified as variants of uncertain significance. An analytic workflow-splice effect event resolver (SPEER)-was developed and validated to use mRNA sequencing to reveal significant deviations in splicing, pinpoint the DNA variants potentially involved, and measure the deleterious effects of the altered splicing on mRNA transcripts, providing evidence for assessing the pathogenicity of the variant. SPEER was used to analyze leukocyte RNA encoding 63 hereditary cancer syndrome-related genes in 20,317 patients. Among 3563 patients (17.5%) with at least one DNA variant predicted to affect splicing, 971 (4.8%) had altered splicing with a deleterious effect on the transcript, and 40 had altered splicing due to a DNA variant located outside of the reportable range of the test. Integrating SPEER results into the interpretation of variants allowed variants of uncertain significance to be reclassified as pathogenic or likely pathogenic in 0.4%, and as benign or likely benign in 5.9%, of the 20,317 patients. SPEER-based evidence was associated with a significantly greater effect on classifications of pathogenic or likely pathogenic and benign or likely benign in nonwhite versus non-Hispanic white patients, illustrating that evidence derived from mRNA splicing analysis may help to reduce ethnic/ancestral disparities in genetic testing.
Collapse
|
4
|
Fresard L, Nykamp K, Kamp-Hughes N, Vincent J, Albritton S, Carlton V, Kang HC, Krempely K, Pardo C. 14. Providing more answers for patients with supplemental RNA analysis. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
5
|
Burke EA, Sturgeon M, Zastrow DB, Fernandez L, Prybol C, Marwaha S, Frothingham EP, Ward PA, Eng CM, Fresard L, Montgomery SB, Enns GM, Fisher PG, Wolfe LA, Harding B, Carrington B, Bishop K, Sood R, Huang Y, Elkahloun A, Toro C, Bassuk AG, Wheeler MT, Markello TC, Gahl WA, Malicdan MCV. Compound heterozygous KCTD7 variants in progressive myoclonus epilepsy. J Neurogenet 2021; 35:74-83. [PMID: 33970744 DOI: 10.1080/01677063.2021.1892095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
KCTD7 is a member of the potassium channel tetramerization domain-containing protein family and has been associated with progressive myoclonic epilepsy (PME), characterized by myoclonus, epilepsy, and neurological deterioration. Here we report four affected individuals from two unrelated families in which we identified KCTD7 compound heterozygous single nucleotide variants through exome sequencing. RNAseq was used to detect a non-annotated splicing junction created by a synonymous variant in the second family. Whole-cell patch-clamp analysis of neuroblastoma cells overexpressing the patients' variant alleles demonstrated aberrant potassium regulation. While all four patients experienced many of the common clinical features of PME, they also showed variable phenotypes not previously reported, including dysautonomia, brain pathology findings including a significantly reduced thalamus, and the lack of myoclonic seizures. To gain further insight into the pathogenesis of the disorder, zinc finger nucleases were used to generate kctd7 knockout zebrafish. Kctd7 homozygous mutants showed global dysregulation of gene expression and increased transcription of c-fos, which has previously been correlated with seizure activity in animal models. Together these findings expand the known phenotypic spectrum of KCTD7-associated PME, report a new animal model for future studies, and contribute valuable insights into the disease.
Collapse
Affiliation(s)
- Elizabeth A Burke
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Morgan Sturgeon
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Diane B Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Cameron Prybol
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Laure Fresard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Brian Harding
- Departments of Pathology and Lab Medicine (Neuropathology), Children's Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | | | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, MD, USA
| |
Collapse
|
6
|
Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ, Adkins JN, Amar D, Dasari S, Drugan JK, Evans CR, Fernandez FM, Li Y, Lindholm ME, Nogiec CD, Radom-Aizik S, Sanford JA, Schenk S, Snyder MP, Tomlinson L, Tracy RP, Trappe S, Vanderboom P, Walsh MJ, Lee Alekel D, Bekirov I, Boyce AT, Boyington J, Fleg JL, Joseph LJ, Laughlin MR, Maruvada P, Morris SA, McGowan JA, Nierras C, Pai V, Peterson C, Ramos E, Roary MC, Williams JP, Xia A, Cornell E, Rooney J, Miller ME, Ambrosius WT, Rushing S, Stowe CL, Jack Rejeski W, Nicklas BJ, Pahor M, Lu CJ, Trappe T, Chambers T, Raue U, Lester B, Bergman BC, Bessesen DH, Jankowski CM, Kohrt WM, Melanson EL, Moreau KL, Schauer IE, Schwartz RS, Kraus WE, Slentz CA, Huffman KM, Johnson JL, Willis LH, Kelly L, Houmard JA, Dubis G, Broskey N, Goodpaster BH, Sparks LM, Coen PM, Cooper DM, Haddad F, Rankinen T, Ravussin E, Johannsen N, Harris M, Jakicic JM, Newman AB, Forman DD, Kershaw E, Rogers RJ, Nindl BC, Page LC, Stefanovic-Racic M, Barr SL, Rasmussen BB, Moro T, Paddon-Jones D, Volpi E, Spratt H, Musi N, Espinoza S, Patel D, Serra M, Gelfond J, Burns A, Bamman MM, Buford TW, Cutter GR, Bodine SC, Esser K, Farrar RP, Goodyear LJ, Hirshman MF, Albertson BG, Qian WJ, Piehowski P, Gritsenko MA, Monore ME, Petyuk VA, McDermott JE, Hansen JN, Hutchison C, Moore S, Gaul DA, Clish CB, Avila-Pacheco J, Dennis C, Kellis M, Carr S, Jean-Beltran PM, Keshishian H, Mani D, Clauser K, Krug K, Mundorff C, Pearce C, Ivanova AA, Ortlund EA, Maner-Smith K, Uppal K, Zhang T, Sealfon SC, Zaslavsky E, Nair V, Li S, Jain N, Ge Y, Sun Y, Nudelman G, Ruf-zamojski F, Smith G, Pincas N, Rubenstein A, Anne Amper M, Seenarine N, Lappalainen T, Lanza IR, Sreekumaran Nair K, Klaus K, Montgomery SB, Smith KS, Gay NR, Zhao B, Hung CJ, Zebarjadi N, Balliu B, Fresard L, Burant CF, Li JZ, Kachman M, Soni T, Raskind AB, Gerszten R, Robbins J, Ilkayeva O, Muehlbauer MJ, Newgard CB, Ashley EA, Wheeler MT, Jimenez-Morales D, Raja A, Dalton KP, Zhen J, Suk Kim Y, Christle JW, Marwaha S, Chin ET, Hershman SG, Hastie T, Tibshirani R, Rivas MA. Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell 2020; 181:1464-1474. [DOI: 10.1016/j.cell.2020.06.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
|
7
|
Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
Collapse
|
8
|
Davis J, Fresard L, Knowles D, Pala M, Bustamante C, Battle A, Montgomery S. An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants. Am J Hum Genet 2016; 98:216-24. [PMID: 26749306 DOI: 10.1016/j.ajhg.2015.11.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022] Open
Abstract
Methods for multiple-testing correction in local expression quantitative trait locus (cis-eQTL) studies are a trade-off between statistical power and computational efficiency. Bonferroni correction, though computationally trivial, is overly conservative and fails to account for linkage disequilibrium between variants. Permutation-based methods are more powerful, though computationally far more intensive. We present an alternative correction method called eigenMT, which runs over 500 times faster than permutations and has adjusted p values that closely approximate empirical ones. To achieve this speed while also maintaining the accuracy of permutation-based methods, we estimate the effective number of independent variants tested for association with a particular gene, termed Meff, by using the eigenvalue decomposition of the genotype correlation matrix. We employ a regularized estimator of the correlation matrix to ensure Meff is robust and yields adjusted p values that closely approximate p values from permutations. Finally, using a common genotype matrix, we show that eigenMT can be applied with even greater efficiency to studies across tissues or conditions. Our method provides a simpler, more efficient approach to multiple-testing correction than existing methods and fits within existing pipelines for eQTL discovery.
Collapse
|