1
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Malik F, Furtado LV, Eldomery MK, Shi Z, Koo SC. Pediatric NCOA3-rearranged low-grade fibroblastic tumor with nuclear beta-catenin immunoreactivity. Genes Chromosomes Cancer 2024; 63:e23223. [PMID: 38340030 DOI: 10.1002/gcc.23223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/27/2023] [Accepted: 12/25/2023] [Indexed: 02/12/2024] Open
Affiliation(s)
- Faizan Malik
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mohammad K Eldomery
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zonggao Shi
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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2
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Scollon S, Eldomery MK, Reuther J, Lin FY, Potter SL, Desrosiers L, McClain KL, Smith V, Su JMF, Venkatramani R, Hu J, Korchina V, Zarrin-Khameh N, Gibbs RA, Muzny DM, Eng C, Roy A, Parsons DW, Plon SE. Clinical and molecular features of pediatric cancer patients with Lynch syndrome. Pediatr Blood Cancer 2022; 69:e29859. [PMID: 35713195 PMCID: PMC9529793 DOI: 10.1002/pbc.29859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND The association of childhood cancer with Lynch syndrome is not established compared with the significant pediatric cancer risk in recessive constitutional mismatch repair deficiency syndrome (CMMRD). PROCEDURE We describe the clinical features, germline analysis, and tumor genomic profiling of patients with Lynch syndrome among patients enrolled in pediatric cancer genomic studies. RESULTS There were six of 773 (0.8%) pediatric patients with solid tumors identified with Lynch syndrome, defined as a germline heterozygous pathogenic variant in one of the mismatch repair (MMR) genes (three with MSH6, two with MLH1, and one with MSH2). Tumor analysis demonstrated evidence for somatic second hits and/or increased tumor mutation burden in three of four patients with available tumor with potential implications for therapy and identification of at-risk family members. Only one patient met current guidelines for pediatric cancer genetics evaluation at the time of tumor diagnosis. CONCLUSION Approximately 1% of children with cancer have Lynch syndrome, which is missed with current referral guidelines, suggesting the importance of adding MMR genes to tumor and hereditary pediatric cancer panels. Tumor analysis may provide the first suggestion of an underlying cancer predisposition syndrome and is useful in distinguishing between Lynch syndrome and CMMRD.
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Affiliation(s)
- Sarah Scollon
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Mohammad K. Eldomery
- Department of Pathology, Texas Children’s Hospital, Houston, TX
- Department of Pathology & Immunology, Baylor College of Medicine, TX
| | - Jacquelyn Reuther
- Department of Pathology, Texas Children’s Hospital, Houston, TX
- Department of Pathology & Immunology, Baylor College of Medicine, TX
| | - Frank Y Lin
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Samara L Potter
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Lauren Desrosiers
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Kenneth L McClain
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Valeria Smith
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Jack Meng-Fen Su
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Rajkumar Venkatramani
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | | | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Angshumoy Roy
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
- Department of Pathology, Texas Children’s Hospital, Houston, TX
- Department of Pathology & Immunology, Baylor College of Medicine, TX
| | - D. Williams Parsons
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
- Department of Pathology, Texas Children’s Hospital, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sharon E Plon
- Department of Pediatrics, Texas Children’s Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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3
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Penon-Portmann M, Eldomery MK, Potocki L, Marafi D, Posey JE, Coban-Akdemir Z, Harel T, Grochowski CM, Loucks H, Devine WP, Van Ziffle J, Doherty D, Lupski JR, Shieh JT. De novo heterozygous variants in SLC30A7 are a candidate cause for Joubert syndrome. Am J Med Genet A 2022; 188:2360-2366. [PMID: 35751429 PMCID: PMC9756141 DOI: 10.1002/ajmg.a.62872] [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: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/08/2022]
Abstract
Joubert syndrome (JS), a well-established ciliopathy, is characterized by the distinctive molar tooth sign on brain MRI, ataxia, and neurodevelopmental features. Other manifestations can include polydactyly, accessory frenula, renal, or liver disease. Here, we report individuals meeting criteria for JS with de novo heterozygous variants in SLC30A7 (Chr1p21.2). The first individual is a female with history of unilateral postaxial polydactyly, classic molar tooth sign on MRI, macrocephaly, ataxia, ocular motor apraxia, neurodevelopmental delay, and precocious puberty. Exome sequencing detected a de novo heterozygous missense variant in SLC30A7: NM_133496.5: c.407 T > C, (p.Val136Ala). The second individual had bilateral postaxial polydactyly, molar tooth sign, macrocephaly, developmental delay, and an extra oral frenulum. A de novo deletion-insertion variant in SLC30A7, c.490_491delinsAG (p.His164Ser) was found. Both de novo variants affect highly conserved residues. Variants were not identified in known Joubert genes for either case. SLC30A7 has not yet been associated with a human phenotype. The SLC30 family of zinc transporters, like SLC30A7, permit cellular efflux of zinc, and although it is expressed in the brain its functions remain unknown. Published data from proteomic studies support SLC30A7 interaction with TCTN3, another protein associated with JS. The potential involvement of such genes in primary cilia suggest a role in Sonic Hedgehog signaling. SLC30A7 is a candidate JS-associated gene. Future work could be directed toward further characterization of SLC30A7 variants and understanding its function.
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Affiliation(s)
- Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Hailey Loucks
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Walter Patrick Devine
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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4
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Thoe J, Ducis K, Eldomery MK, Marshall M, Ferguson M, Vortmeyer AO, Raskin JS, Coven SL. Pineal teratoma with nephroblastic component in a newborn male: Case report and review of the literature. J Clin Neurosci 2020; 80:207-214. [PMID: 33099347 DOI: 10.1016/j.jocn.2020.07.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/19/2020] [Indexed: 11/19/2022]
Abstract
Neonatal germ cell tumors are rare and comprise both benign and malignant neoplasms. Teratoma with nephroblastoma is a malignant subset defined pathologically by the presence of nephroblastoma and teratoma elements. Although teratoma with nephroblastoma is most often found in the kidney, 24 of 59 reported cases are associated with extrarenal locations, such as the mediastinum or retroperitoneum. To our knowledge, this is the first patient in the literature with intracranial/pineal teratoma with nephroblastoma, which was managed with staged transcranial approaches resulting in gross total resection and no adjuvant therapy (surveillance observation imaging). We further augmented the patient's management by comprehensive genomic profiling of the tumor to better understand the molecular biology and explore options for targeted therapy.
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Affiliation(s)
- Jessica Thoe
- Section of Pediatric Hematology/Oncology, Riley Hospital for Children, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Katrina Ducis
- Section of Pediatric Neurosurgery, Riley Hospital for Children, Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Mohammad K Eldomery
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Mark Marshall
- Department of Precision Medicine, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Michael Ferguson
- Section of Pediatric Hematology/Oncology, Riley Hospital for Children, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Alexander O Vortmeyer
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Jeffrey S Raskin
- Section of Pediatric Neurosurgery, Riley Hospital for Children, Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Scott L Coven
- Section of Pediatric Hematology/Oncology, Riley Hospital for Children, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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5
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Al-Obaidy KI, Eble JN, Nassiri M, Cheng L, Eldomery MK, Williamson SR, Sakr WA, Gupta N, Hassan O, Idrees MT, Grignon DJ. Recurrent KRAS mutations in papillary renal neoplasm with reverse polarity. Mod Pathol 2020; 33:1157-1164. [PMID: 31534204 DOI: 10.1038/s41379-019-0362-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022]
Abstract
We recently proposed that an epithelial renal tumor "papillary renal neoplasm with reverse polarity" represents a distinct entity. It constituted 4% of previously diagnosed papillary renal cell carcinoma at the participating institutions. Histologically, it is characterized by papillary or tubulopapillary architecture covered by a single layer of eosinophilic cells with finely granular cytoplasm and apically located nuclei. It is characteristically positive for GATA3 and L1CAM and lack vimentin and, to a lesser extent, α-methylacyl-CoA-racemase (AMACR/p504s) immunostaining. To investigate the molecular pathogenesis of these tumors, we performed targeted next-generation sequencing on ten previously reported papillary renal neoplasms with reverse polarity, followed by a targeted polymerase chain reaction analysis for KRAS mutations in a control series of 30 type 1 and 2 papillary renal cell carcinomas. KRAS missense mutations were identified in eight of ten papillary renal neoplasms with reverse polarity. These mutations were clustered in exon 2-codon 12: c.35 G > T (n = 6) or c.34 G > C (n = 2) resulting in p.Gly12Val and p.Gly12Arg alterations, respectively. One of the wild-type tumors had BRAF c.1798_1799delGTinsAG (p.Val600Arg) mutation. No KRAS mutations were identified in any of the 30 control tumors. In summary, this study supports our proposal that papillary renal neoplasm with reverse polarity is an entity distinct from papillary renal cell carcinoma and the only renal cell neoplasm to consistently harbor KRAS mutations.
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Affiliation(s)
- Khaleel I Al-Obaidy
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Mehdi Nassiri
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mohammad K Eldomery
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sean R Williamson
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Wael A Sakr
- Department of Pathology and Laboratory Medicine, Wayne State University/Harper University Hospital, Detroit, MI, USA
| | - Nilesh Gupta
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Oudai Hassan
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Muhammad T Idrees
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David J Grignon
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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6
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Wang X, Posey JE, Rosenfeld JA, Bacino CA, Scaglia F, Immken L, Harris JM, Hickey SE, Mosher TM, Slavotinek A, Zhang J, Beuten J, Leduc MS, He W, Vetrini F, Walkiewicz MA, Bi W, Xiao R, Liu P, Shao Y, Gezdirici A, Gulec EY, Jiang Y, Darilek SA, Hansen AW, Khayat MM, Pehlivan D, Piard J, Muzny DM, Hanchard N, Belmont JW, Van Maldergem L, Gibbs RA, Eldomery MK, Akdemir ZC, Adesina AM, Chen S, Lee YC, Lee B, Lupski JR, Eng CM, Xia F, Yang Y, Graham BH, Moretti P. Phenotypic expansion in DDX3X - a common cause of intellectual disability in females. Ann Clin Transl Neurol 2018; 5:1277-1285. [PMID: 30349862 PMCID: PMC6186933 DOI: 10.1002/acn3.622] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/21/2018] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
De novo variants in DDX3X account for 1–3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty‐seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique DDX3X variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late‐onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with DDX3X disorders.
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Affiliation(s)
- Xia Wang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Jennifer E Posey
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Jill A Rosenfeld
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Carlos A Bacino
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Fernando Scaglia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | | | | | - Scott E Hickey
- Clinical Pediatrics The Ohio State University Columbus Ohio.,Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Theresa M Mosher
- Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Anne Slavotinek
- Department of Pediatrics Division of Genetics University of California San Francisco California
| | | | | | - Magalie S Leduc
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | | | | | - Magdalena A Walkiewicz
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Weimin Bi
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Rui Xiao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Pengfei Liu
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yunru Shao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Alper Gezdirici
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Elif Y Gulec
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Yunyun Jiang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Sandra A Darilek
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adam W Hansen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Michael M Khayat
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Davut Pehlivan
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Section of Neurology Department of Pediatrics Baylor College of Medicine Houston Texas
| | - Juliette Piard
- Centre de Génétique Humaine Université de Franche-Comté Besançon France
| | - Donna M Muzny
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Neil Hanchard
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - John W Belmont
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Richard A Gibbs
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | | | - Zeynep C Akdemir
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adekunle M Adesina
- Texas Children's Hospital Houston Texas.,Pathology Baylor College of Medicine Houston Texas
| | - Shan Chen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Yi-Chien Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Brendan Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - James R Lupski
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Christine M Eng
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Fan Xia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yaping Yang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Brett H Graham
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana
| | - Paolo Moretti
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Neurology Baylor College of Medicine and Michael E. DeBakey VA Medical Center Houston Texas.,Neurology University of Utah and George E. Wahlen VA Medical Center Salt Lake City Utah
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7
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Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet 2018; 102:985-994. [PMID: 29656860 DOI: 10.1016/j.ajhg.2018.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 11/13/2017] [Accepted: 02/27/2018] [Indexed: 11/30/2022] Open
Abstract
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.
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Affiliation(s)
| | | | - Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ning Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deepti Domingo
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Alan F Rope
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Asbjørg Stray-Pedersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah R Crews
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Vernon R Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Katherine Agre
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Magdalena Walkiewicz
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | | | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Sakkubai Naidu
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Sonal Mahida
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Derek Lim
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Stefania Giusto
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Emanuela Stracuzzi
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Corrado Romano
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | | | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle WA, 98195, USA
| | - Sébastien Küry
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mathilde Nizon
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Alison Gardner
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Jolanda Schieving
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Marjolijn J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jozef Gecz
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Holly A F Stessman
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Linyan Meng
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
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8
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Lessel D, Schob C, Küry S, Reijnders MR, Harel T, Eldomery MK, Coban-Akdemir Z, Denecke J, Edvardson S, Colin E, Stegmann AP, Gerkes EH, Tessarech M, Bonneau D, Barth M, Besnard T, Cogné B, Revah-Politi A, Strom TM, Rosenfeld JA, Yang Y, Posey JE, Immken L, Oundjian N, Helbig KL, Meeks N, Zegar K, Morton J, the DDD study, Schieving JH, Claasen A, Huentelman M, Narayanan V, Ramsey K, Brunner HG, Elpeleg O, Mercier S, Bézieau S, Kubisch C, Kleefstra T, Kindler S, Lupski JR, Kreienkamp HJ, Kreienkamp HJ. De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder. Am J Hum Genet 2018; 102:196. [PMID: 29304375 DOI: 10.1016/j.ajhg.2017.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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9
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Gambin T, Akdemir ZC, Yuan B, Gu S, Chiang T, Carvalho CMB, Shaw C, Jhangiani S, Boone PM, Eldomery MK, Karaca E, Bayram Y, Stray-Pedersen A, Muzny D, Charng WL, Bahrambeigi V, Belmont JW, Boerwinkle E, Beaudet AL, Gibbs RA, Lupski JR. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res 2017; 45:1633-1648. [PMID: 27980096 PMCID: PMC5389578 DOI: 10.1093/nar/gkw1237] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/29/2016] [Indexed: 11/14/2022] Open
Abstract
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, Norway
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
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10
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Luo X, Rosenfeld JA, Yamamoto S, Harel T, Zuo Z, Hall M, Wierenga KJ, Pastore MT, Bartholomew D, Delgado MR, Rotenberg J, Lewis RA, Emrick L, Bacino CA, Eldomery MK, Coban Akdemir Z, Xia F, Yang Y, Lalani SR, Lotze T, Lupski JR, Lee B, Bellen HJ, Wangler MF. Clinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially. PLoS Genet 2017; 13:e1006905. [PMID: 28742085 PMCID: PMC5557584 DOI: 10.1371/journal.pgen.1006905] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/15/2017] [Accepted: 07/03/2017] [Indexed: 01/04/2023] Open
Abstract
Dominant mutations in CACNA1A, encoding the α-1A subunit of the neuronal P/Q type voltage-dependent Ca2+ channel, can cause diverse neurological phenotypes. Rare cases of markedly severe early onset developmental delay and congenital ataxia can be due to de novo CACNA1A missense alleles, with variants affecting the S4 transmembrane segments of the channel, some of which are reported to be loss-of-function. Exome sequencing in five individuals with severe early onset ataxia identified one novel variant (p.R1673P), in a girl with global developmental delay and progressive cerebellar atrophy, and a recurrent, de novo p.R1664Q variant, in four individuals with global developmental delay, hypotonia, and ophthalmologic abnormalities. Given the severity of these phenotypes we explored their functional impact in Drosophila. We previously generated null and partial loss-of-function alleles of cac, the homolog of CACNA1A in Drosophila. Here, we created transgenic wild type and mutant genomic rescue constructs with the two noted conserved point mutations. The p.R1673P mutant failed to rescue cac lethality, displayed a gain-of-function phenotype in electroretinograms (ERG) recorded from mutant clones, and evolved a neurodegenerative phenotype in aging flies, based on ERGs and transmission electron microscopy. In contrast, the p.R1664Q variant exhibited loss of function and failed to develop a neurodegenerative phenotype. Hence, the novel R1673P allele produces neurodegenerative phenotypes in flies and human, likely due to a toxic gain of function.
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Affiliation(s)
- Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States of America
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Melissa Hall
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Klaas J. Wierenga
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Matthew T. Pastore
- Nationwide Children’s Hospital & The Ohio State University, Columbus, OH, United States of America
| | - Dennis Bartholomew
- Nationwide Children’s Hospital & The Ohio State University, Columbus, OH, United States of America
| | - Mauricio R. Delgado
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center andTexas Scottish Rite Hospital, Dallas, TX, United States of America
| | | | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
- Texas Children’s Hospital, Houston, TX, United States of America
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Timothy Lotze
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
- Texas Children’s Hospital, Houston, TX, United States of America
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States of America
- Howard Hughes Medical Institute, Houston TX, United States of America
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States of America
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11
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- 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
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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Harms FL, Girisha KM, Hardigan AA, Kortüm F, Shukla A, Alawi M, Dalal A, Brady L, Tarnopolsky M, Bird LM, Ceulemans S, Bebin M, Bowling KM, Hiatt SM, Lose EJ, Primiano M, Chung WK, Juusola J, Akdemir ZC, Bainbridge M, Charng WL, Drummond-Borg M, Eldomery MK, El-Hattab AW, Saleh MAM, Bézieau S, Cogné B, Isidor B, Küry S, Lupski JR, Myers RM, Cooper GM, Kutsche K. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. Am J Hum Genet 2017; 100:117-127. [PMID: 28017373 PMCID: PMC5223027 DOI: 10.1016/j.ajhg.2016.11.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022] Open
Abstract
From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.
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Affiliation(s)
- Frederike Leonie Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India
| | - Malik Alawi
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Bioinformatics, University of Hamburg, 20246 Hamburg, Germany; Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20246 Hamburg, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, 500001 Hyderabad, Telangana, India
| | - Lauren Brady
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92123, USA; Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Sophia Ceulemans
- Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL35294, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Edward J Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michelle Primiano
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | | | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, 15258 Al-Ain, United Arab Emirates
| | - Mohammed A M Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, 11564 Riyadh, Saudi Arabia
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France; INSERM UMR-S 957, 44035 Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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13
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Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AG, Skogen V, Osnes LTN, Kulseth MA, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MS, Bezrodnik L, Lugo Reyes SO, Espinosa Rosales FJ, Guerrero-Cursaru ND, Pedroza LA, Poli CM, Franco JL, Trujillo Vargas CM, Aldave Becerra JC, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MM, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, Hanson IC, Zhang VW, Wong LJ, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2017; 139:232-245. [PMID: 27577878 PMCID: PMC5222743 DOI: 10.1016/j.jaci.2016.05.042] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/10/2016] [Accepted: 05/13/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.
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Affiliation(s)
- Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway.
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Ivan K Chinn
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Zeynep H Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | | | - Lisa R Forbes
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Shen Gu
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Bo Yuan
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sarah K Nicholas
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Lenora M Noroski
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Filiz O Seeborg
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carla M Davis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Debra L Canter
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Timothy J Vece
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Harshal A Abhyankar
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Philip M Boone
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine R Beck
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Wojciech Wiszniewski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Børre Fevang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir E Tjønnfjord
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Ingvild Nordøy
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Silje F Jørgensen
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vegard Skogen
- Department of Infectious Diseases, Medical Clinic, University Hospital of North-Norway, Tromsø, Norway
| | - Liv T N Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ann Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine E Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil R Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Nicholas L Rider
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Javier Chinen
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Eric A Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Tex
| | - Maria Soledad Caldirola
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Bezrodnik
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Saul Oswaldo Lugo Reyes
- Immunodeficiencies Research Unit, National Institute of Pediatrics, Coyoacan, Mexico City, Mexico
| | | | | | | | - Cecilia M Poli
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Hospital Roberto del Rio, Universidad de Chile, Santiago, Chile
| | - Jose L Franco
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Claudia M Trujillo Vargas
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Nicola Wright
- Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Andrew C Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Jordan Abbott
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunological Diseases, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC
| | - Diana K Bayer
- Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Alice Y Chan
- Department of Pediatrics, University of California, San Francisco, Calif
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), and Vita-Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- University Department of Pediatrics, DPUO, Bambino Gesù Children's Hospital, and Tor Vergata University, Rome, Italy
| | - Eva Holmberg
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Ender Karaca
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Gözde Yesil
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul, Turkey
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Selcuk University Medical Faculty, Alaeddin Keykubat Kampusu, Konya, Turkey
| | - Yavuz Bayram
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mehmed Musa Atik
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad K Eldomery
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, Department of Paediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Alison A Bertuch
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex
| | - I Celine Hanson
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Victor W Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Eric Boerwinkle
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Human Genetics Center, University of Texas School of Public Health, Houston, Tex
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - William T Shearer
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jordan S Orange
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex.
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex.
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14
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Eldomery MK, Akdemir ZC, Vögtle FN, Charng WL, Mulica P, Rosenfeld JA, Gambin T, Gu S, Burrage LC, Al Shamsi A, Penney S, Jhangiani SN, Zimmerman HH, Muzny DM, Wang X, Tang J, Medikonda R, Ramachandran PV, Wong LJ, Boerwinkle E, Gibbs RA, Eng CM, Lalani SR, Hertecant J, Rodenburg RJ, Abdul-Rahman OA, Yang Y, Xia F, Wang MC, Lupski JR, Meisinger C, Sutton VR. MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. Genome Med 2016; 8:106. [PMID: 27799064 PMCID: PMC5088683 DOI: 10.1186/s13073-016-0360-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. METHODS Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC), developmental delay (DD), seizures, and severe hypotonia. Proposed pathogenic variants were confirmed by Sanger sequencing or array comparative genomic hybridization. Functional analysis of the identified MIP variants was performed using the model organism Saccharomyces cerevisiae as the protein and its functions are highly conserved from yeast to human. RESULTS Biallelic single nucleotide variants (SNVs) or copy number variants (CNVs) in MIPEP, which encodes MIP, were present in all four probands, three of whom had infantile/childhood death. Two patients had compound heterozygous SNVs (p.L582R/p.L71Q and p.E602*/p.L306F) and one patient from a consanguineous family had a homozygous SNV (p.K343E). The fourth patient, identified through the GeneMatcher tool, a part of the Matchmaker Exchange Project, was found to have inherited a paternal SNV (p.H512D) and a maternal CNV (1.4-Mb deletion of 13q12.12) that includes MIPEP. All amino acids affected in the patients' missense variants are highly conserved from yeast to human and therefore S. cerevisiae was employed for functional analysis (for p.L71Q, p.L306F, and p.K343E). The mutations p.L339F (human p.L306F) and p.K376E (human p.K343E) resulted in a severe decrease of Oct1 protease activity and accumulation of non-processed Oct1 substrates and consequently impaired viability under respiratory growth conditions. The p.L83Q (human p.L71Q) failed to localize to the mitochondria. CONCLUSIONS Our findings reveal for the first time the role of the mitochondrial intermediate peptidase in human disease. Loss of MIP function results in a syndrome which consists of LVNC, DD, seizures, hypotonia, and cataracts. Our approach highlights the power of data exchange and the importance of an interrelationship between clinical and research efforts for disease gene discovery.
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Affiliation(s)
- Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Patrycja Mulica
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Aisha Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Holly H Zimmerman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jia Tang
- Medical Genetics Center, Jiang Men Maternity and Childhealth Care Hospital, Jiang Men, 529000, China
| | - Ravi Medikonda
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Prasanna V Ramachandran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al Ain, 15258, United Arab Emirates
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, RadboudUMC, 6500HB, Nijmegen, Netherlands
| | - Omar A Abdul-Rahman
- Department of Pediatrics, University of Mississippi Medical Center, 2500N State St, Jackson, MS, 39216, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ and BIOSS Centre for Biological Signalling Studies and Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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15
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Harel T, Yoon WH, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RA, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet 2016; 99:831-845. [PMID: 27640307 DOI: 10.1016/j.ajhg.2016.08.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [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: 06/06/2016] [Accepted: 08/04/2016] [Indexed: 12/22/2022] Open
Abstract
ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane protein implicated in mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. We identified a recurrent de novo ATAD3A c.1582C>T (p.Arg528Trp) variant by whole-exome sequencing (WES) in five unrelated individuals with a core phenotype of global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. We also describe two families with biallelic variants in ATAD3A, including a homozygous variant in two siblings, and biallelic ATAD3A deletions mediated by nonallelic homologous recombination (NAHR) between ATAD3A and gene family members ATAD3B and ATAD3C. Tissue-specific overexpression of borR534W, the Drosophila mutation homologous to the human c.1582C>T (p.Arg528Trp) variant, resulted in a dramatic decrease in mitochondrial content, aberrant mitochondrial morphology, and increased autophagy. Homozygous null bor larvae showed a significant decrease of mitochondria, while overexpression of borWT resulted in larger, elongated mitochondria. Finally, fibroblasts of an affected individual exhibited increased mitophagy. We conclude that the p.Arg528Trp variant functions through a dominant-negative mechanism that results in small mitochondria that trigger mitophagy, resulting in a reduction in mitochondrial content. ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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16
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Vetrini F, D'Alessandro LCA, Akdemir ZC, Braxton A, Azamian MS, Eldomery MK, Miller K, Kois C, Sack V, Shur N, Rijhsinghani A, Chandarana J, Ding Y, Holtzman J, Jhangiani SN, Muzny DM, Gibbs RA, Eng CM, Hanchard NA, Harel T, Rosenfeld JA, Belmont JW, Lupski JR, Yang Y. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. Am J Hum Genet 2016; 99:886-893. [PMID: 27616478 DOI: 10.1016/j.ajhg.2016.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023] Open
Abstract
Disruption of the establishment of left-right (L-R) asymmetry leads to situs anomalies ranging from situs inversus totalis (SIT) to situs ambiguus (heterotaxy). The genetic causes of laterality defects in humans are highly heterogeneous. Via whole-exome sequencing (WES), we identified homozygous mutations in PKD1L1 from three affected individuals in two unrelated families. PKD1L1 encodes a polycystin-1-like protein and its loss of function is known to cause laterality defects in mouse and medaka fish models. Family 1 had one fetus and one deceased child with heterotaxy and complex congenital heart malformations. WES identified a homozygous splicing mutation, c.6473+2_6473+3delTG, which disrupts the invariant splice donor site in intron 42, in both affected individuals. In the second family, a homozygous c.5072G>C (p.Cys1691Ser) missense mutation was detected in an individual with SIT and congenital heart disease. The p.Cys1691Ser substitution affects a highly conserved cysteine residue and is predicted by molecular modeling to disrupt a disulfide bridge essential for the proper folding of the G protein-coupled receptor proteolytic site (GPS) motif. Damaging effects associated with substitutions of this conserved cysteine residue in the GPS motif have also been reported in other genes, namely GPR56, BAI3, and PKD1 in human and lat-1 in C. elegans, further supporting the likely pathogenicity of p.Cys1691Ser in PKD1L1. The identification of bi-allelic PKD1L1 mutations recapitulates previous findings regarding phenotypic consequences of loss of function of the orthologous genes in mice and medaka fish and further expands our understanding of genetic contributions to laterality defects in humans.
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Affiliation(s)
| | - Lisa C A D'Alessandro
- Division of Cardiology, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia Braxton
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid S Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Judy Holtzman
- Genetics Department, Kaiser Permanente Medical Group, San Jose, CA 95123, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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17
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Lodder EM, De Nittis P, Koopman CD, Wiszniewski W, Moura de Souza CF, Lahrouchi N, Guex N, Napolioni V, Tessadori F, Beekman L, Nannenberg EA, Boualla L, Blom NA, de Graaff W, Kamermans M, Cocciadiferro D, Malerba N, Mandriani B, Coban Akdemir ZH, Fish RJ, Eldomery MK, Ratbi I, Wilde AAM, de Boer T, Simonds WF, Neerman-Arbez M, Sutton VR, Kok F, Lupski JR, Reymond A, Bezzina CR, Bakkers J, Merla G. GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability. Am J Hum Genet 2016; 99:786. [PMID: 27588455 DOI: 10.1016/j.ajhg.2016.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Harel T, Yesil G, Bayram Y, Coban-Akdemir Z, Charng WL, Karaca E, Al Asmari A, Eldomery MK, Hunter JV, Jhangiani SN, Rosenfeld JA, Pehlivan D, El-Hattab AW, Saleh MA, LeDuc CA, Muzny D, Boerwinkle E, Gibbs RA, Chung WK, Yang Y, Belmont JW, Lupski JR. Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy. Am J Hum Genet 2016; 98:562-570. [PMID: 26942288 DOI: 10.1016/j.ajhg.2016.01.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/19/2016] [Indexed: 01/08/2023] Open
Abstract
The paradigm of a single gene associated with one specific phenotype and mode of inheritance has been repeatedly challenged. Genotype-phenotype correlations can often be traced to different mutation types, localization of the variants in distinct protein domains, or the trigger of or escape from nonsense-mediated decay. Using whole-exome sequencing, we identified homozygous variants in EMC1 that segregated with a phenotype of developmental delay, hypotonia, scoliosis, and cerebellar atrophy in three families. In addition, a de novo heterozygous EMC1 variant was seen in an individual with a similar clinical and MRI imaging phenotype. EMC1 encodes a member of the endoplasmic reticulum (ER)-membrane protein complex (EMC), an evolutionarily conserved complex that has been proposed to have multiple roles in ER-associated degradation, ER-mitochondria tethering, and proper assembly of multi-pass transmembrane proteins. Perturbations of protein folding and organelle crosstalk have been implicated in neurodegenerative processes including cerebellar atrophy. We propose EMC1 as a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum.
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Affiliation(s)
- Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul 34093, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill V Hunter
- Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain 15258, United Arab Emirates
| | - Mohammed A Saleh
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Charles A LeDuc
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston TX 77030, USA
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19
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Burrage LC, Charng WL, Eldomery MK, Willer JR, Davis EE, Lugtenberg D, Zhu W, Leduc MS, Akdemir ZC, Azamian M, Zapata G, Hernandez PP, Schoots J, de Munnik SA, Roepman R, Pearring JN, Jhangiani S, Katsanis N, Vissers LELM, Brunner HG, Beaudet AL, Rosenfeld JA, Muzny DM, Gibbs RA, Eng CM, Xia F, Lalani SR, Lupski JR, Bongers EMHF, Yang Y. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet 2015; 97:904-13. [PMID: 26637980 PMCID: PMC4678788 DOI: 10.1016/j.ajhg.2015.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/05/2015] [Indexed: 12/21/2022] Open
Abstract
Meier-Gorlin syndrome (MGS) is a genetically heterogeneous primordial dwarfism syndrome known to be caused by biallelic loss-of-function mutations in one of five genes encoding pre-replication complex proteins: ORC1, ORC4, ORC6, CDT1, and CDC6. Mutations in these genes cause disruption of the origin of DNA replication initiation. To date, only an autosomal-recessive inheritance pattern has been described in individuals with this disorder, with a molecular etiology established in about three-fourths of cases. Here, we report three subjects with MGS and de novo heterozygous mutations in the 5' end of GMNN, encoding the DNA replication inhibitor geminin. We identified two truncating mutations in exon 2 (the 1(st) coding exon), c.16A>T (p.Lys6(∗)) and c.35_38delTCAA (p.Ile12Lysfs(∗)4), and one missense mutation, c.50A>G (p.Lys17Arg), affecting the second-to-last nucleotide of exon 2 and possibly RNA splicing. Geminin is present during the S, G2, and M phases of the cell cycle and is degraded during the metaphase-anaphase transition by the anaphase-promoting complex (APC), which recognizes the destruction box sequence near the 5' end of the geminin protein. All three GMNN mutations identified alter sites 5' to residue Met28 of the protein, which is located within the destruction box. We present data supporting a gain-of-function mechanism, in which the GMNN mutations result in proteins lacking the destruction box and hence increased protein stability and prolonged inhibition of replication leading to autosomal-dominant MGS.
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Affiliation(s)
- Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Wenmiao Zhu
- Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia P Hernandez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeroen Schoots
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Jillian N Pearring
- Department of Ophthalmology, Duke University Medical Center, Durham, NC 27701, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands.
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX 77030, USA.
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