1
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Narumi S, Nagasaki K, Kiriya M, Uehara E, Akiba K, Tanase-Nakao K, Shimura K, Abe K, Sugisawa C, Ishii T, Miyako K, Hasegawa Y, Maruo Y, Muroya K, Watanabe N, Nishihara E, Ito Y, Kogai T, Kameyama K, Nakabayashi K, Hata K, Fukami M, Shima H, Kikuchi A, Takayama J, Tamiya G, Hasegawa T. Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities. Nat Genet 2024; 56:869-876. [PMID: 38714868 PMCID: PMC11096107 DOI: 10.1038/s41588-024-01735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024]
Abstract
Insufficient thyroid hormone production in newborns is referred to as congenital hypothyroidism. Multinodular goiter (MNG), characterized by an enlarged thyroid gland with multiple nodules, is usually seen in adults and is recognized as a separate disorder from congenital hypothyroidism. Here we performed a linkage analysis of a family with both nongoitrous congenital hypothyroidism and MNG and identified a signal at 15q26.1. Follow-up analyses with whole-genome sequencing and genetic screening in congenital hypothyroidism and MNG cohorts showed that changes in a noncoding TTTG microsatellite on 15q26.1 were frequently observed in congenital hypothyroidism (137 in 989) and MNG (3 in 33) compared with controls (3 in 38,722). Characterization of the noncoding variants with epigenomic data and in vitro experiments suggested that the microsatellite is located in a thyroid-specific transcriptional repressor, and its activity is disrupted by the variants. Collectively, we presented genetic evidence linking nongoitrous congenital hypothyroidism and MNG, providing unique insights into thyroid abnormalities.
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Affiliation(s)
- Satoshi Narumi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Keisuke Nagasaki
- Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Erika Uehara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhisa Akiba
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiro Shimura
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kiyomi Abe
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Chiho Sugisawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Internal Medicine, Ito Hospital, Tokyo, Japan
| | - Tomohiro Ishii
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenichi Miyako
- Department of Endocrinology and Metabolism, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Yukihiro Hasegawa
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yoshihiro Maruo
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | | | - Eijun Nishihara
- Center for Excellence in Thyroid Care, Kuma Hospital, Kobe, Japan
| | - Yuka Ito
- Department of Genetic Diagnosis and Laboratory Medicine, Dokkyo Medical University, Mibu, Japan
| | - Takahiko Kogai
- Department of Genetic Diagnosis and Laboratory Medicine, Dokkyo Medical University, Mibu, Japan
| | - Kaori Kameyama
- Department of Pathology, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirohito Shima
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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2
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Wormser O, Perez Y, Dolgin V, Kamali B, Tangeman JA, Gradstein L, Yogev Y, Hadar N, Freund O, Drabkin M, Halperin D, Irron I, Grajales-Esquivel E, Del Rio-Tsonis K, Birnbaum RY, Akler G, Birk OS. IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma. NPJ Genom Med 2023; 8:22. [PMID: 37580330 PMCID: PMC10425348 DOI: 10.1038/s41525-023-00364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vadim Dolgin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bahman Kamali
- Medical Advisory Committee, United Mashhadi Jewish Community of America, 54 Steamboat Rd., Great Neck, NY, 11024, USA
| | - Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Hadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ofek Freund
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbar Irron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gidon Akler
- TOVANA Health, Houston, TX, USA.
- Precision Medicine Insights, P.C., Great Neck, NY, USA.
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Genetics Institute, Soroka Medical Center affiliated to Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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3
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Ervilha Pereira P, Schuermans N, Meylemans A, LeBlanc P, Versluys L, Copley KE, Rubien JD, Altheimer C, Peetermans M, Debackere E, Vanakker O, Janssens S, Baets J, Verhoeven K, Lammens M, Symoens S, De Paepe B, Barmada SJ, Shorter J, De Bleecker JL, Bogaert E, Dermaut B. C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD. Acta Neuropathol 2023; 145:793-814. [PMID: 37000196 PMCID: PMC10175433 DOI: 10.1007/s00401-023-02565-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
Neuronal TDP-43-positive inclusions are neuropathological hallmark lesions in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Pathogenic missense variants in TARDBP, the gene encoding TDP-43, can cause ALS and cluster in the C-terminal prion-like domain (PrLD), where they modulate the liquid condensation and aggregation properties of the protein. TDP-43-positive inclusions are also found in rimmed vacuole myopathies, including sporadic inclusion body myositis, but myopathy-causing TDP-43 variants have not been reported. Using genome-wide linkage analysis and whole exome sequencing in an extended five-generation family with an autosomal dominant rimmed vacuole myopathy, we identified a conclusively linked frameshift mutation in TDP-43 producing a C-terminally altered PrLD (TDP-43p.Trp385IlefsTer10) (maximum multipoint LOD-score 3.61). Patient-derived muscle biopsies showed TDP-43-positive sarcoplasmic inclusions, accumulation of autophagosomes and transcriptomes with abnormally spliced sarcomeric genes (including TTN and NEB) and increased expression of muscle regeneration genes. In vitro phase separation assays demonstrated that TDP-43Trp385IlefsTer10 does not form liquid-like condensates and readily forms solid-like fibrils indicating increased aggregation propensity compared to wild-type TDP-43. In Drosophila TDP-43p.Trp385IlefsTer10 behaved as a partial loss-of-function allele as it was able to rescue the TBPH (fly ortholog of TARDBP) neurodevelopmental lethal null phenotype while showing strongly reduced toxic gain-of-function properties upon overexpression. Accordingly, TDP-43p.Trp385IlefsTer10 showed reduced toxicity in a primary rat neuron disease model. Together, these genetic, pathological, in vitro and in vivo results demonstrate that TDP-43p.Trp385IlefsTer10 is an aggregation-prone partial loss-of-function variant that causes autosomal dominant vacuolar myopathy but not ALS/FTD. Our study genetically links TDP-43 proteinopathy to myodegeneration, and reveals a tissue-specific role of the PrLD in directing pathology.
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Affiliation(s)
- Pedro Ervilha Pereira
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Antoon Meylemans
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lauren Versluys
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jack D Rubien
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Myra Peetermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jonathan Baets
- Department of Neurology, Neuromuscular Reference Centre, Antwerp University Hospital, Antwerp, Belgium
- Faculty of Medicine and Health Sciences, Translational Neurosciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kristof Verhoeven
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Neurology, Sint-Jan Hospital Bruges, Brugge, Belgium
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jan L De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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4
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van de Beek I, Glykofridis IE, Oosterwijk JC, van den Akker PC, Diercks GFH, Bolling MC, Waisfisz Q, Mensenkamp AR, Balk JA, Zwart R, Postma AV, Meijers-Heijboer HEJ, van Moorselaar RJA, Wolthuis RMF, Houweling AC. PRDM10 directs FLCN expression in a novel disorder overlapping with Birt-Hogg-Dubé syndrome and familial lipomatosis. Hum Mol Genet 2023; 32:1223-1235. [PMID: 36440963 PMCID: PMC10026250 DOI: 10.1093/hmg/ddac288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 11/05/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder characterized by fibrofolliculomas, pulmonary cysts, pneumothoraces and renal cell carcinomas. Here, we reveal a novel hereditary disorder in a family with skin and mucosal lesions, extensive lipomatosis and renal cell carcinomas. The proband was initially diagnosed with BHD based on the presence of fibrofolliculomas, but no pathogenic germline variant was detected in FLCN, the gene associated with BHD. By whole exome sequencing we identified a heterozygous missense variant (p.(Cys677Tyr)) in a zinc-finger encoding domain of the PRDM10 gene which co-segregated with the phenotype in the family. We show that PRDM10Cys677Tyr loses affinity for a regulatory binding motif in the FLCN promoter, abrogating cellular FLCN mRNA and protein levels. Overexpressing inducible PRDM10Cys677Tyr in renal epithelial cells altered the transcription of multiple genes, showing overlap but also differences with the effects of knocking out FLCN. We propose that PRDM10 controls an extensive gene program and acts as a critical regulator of FLCN gene transcription in human cells. The germline variant PRDM10Cys677Tyr curtails cellular folliculin expression and underlies a distinguishable syndrome characterized by extensive lipomatosis, fibrofolliculomas and renal cell carcinomas.
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Affiliation(s)
- Irma van de Beek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Iris E Glykofridis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Jan C Oosterwijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, Groningen, The Netherlands
| | - Peter C van den Akker
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, Groningen, The Netherlands
| | - Gilles F H Diercks
- University of Groningen, University Medical Center Groningen, Department of Pathology, Hanzeplein 1, Groningen, The Netherlands
| | - Maria C Bolling
- University of Groningen, University Medical Center Groningen, Department of Dermatology, Hanzeplein 1, Groningen, The Netherlands
| | - Quinten Waisfisz
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Arjen R Mensenkamp
- Radboudumc, Department of Human Genetics, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - Jesper A Balk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rob Zwart
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Alex V Postma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hanne E J Meijers-Heijboer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - R Jeroen A van Moorselaar
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Urology and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics and Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Arjan C Houweling
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Human Genetics, De Boelelaan 1117, Amsterdam, The Netherlands
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5
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Limb girdle muscular disease caused by HMGCR mutation and statin myopathy treatable with mevalonolactone. Proc Natl Acad Sci U S A 2023; 120:e2217831120. [PMID: 36745799 PMCID: PMC9963716 DOI: 10.1073/pnas.2217831120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Myopathy is the main adverse effect of the widely prescribed statin drug class. Statins exert their beneficial effect by inhibiting HMG CoA-reductase, the rate-controlling enzyme of the mevalonate pathway. The mechanism of statin myopathy is yet to be resolved, and its treatment is insufficient. Through homozygosity mapping and whole exome sequencing, followed by functional analysis using confocal microscopy and biochemical and biophysical methods, we demonstrate that a distinct form of human limb girdle muscular disease is caused by a pathogenic homozygous loss-of-function missense mutation in HMG CoA reductase (HMGCR), encoding HMG CoA-reductase. We biochemically synthesized and purified mevalonolactone, never administered to human patients before, and establish the safety of its oral administration in mice. We then show that its oral administration is effective in treating a human patient with no significant adverse effects. Furthermore, we demonstrate that oral mevalonolactone resolved statin-induced myopathy in mice. We conclude that HMGCR mutation causes a late-onset severe progressive muscular disease, which shows similar features to statin-induced myopathy. Our findings indicate that mevalonolactone is effective both in the treatment of hereditary HMGCR myopathy and in a murine model of statin myopathy. Further large clinical trials are in place to enable the clinical use of mevalonolactone both in the rare orphan disease and in the more common statin myopathy.
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6
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van de Beek I, Glykofridis IE, Tanck MWT, Luijten MNH, Starink TM, Balk JA, Johannesma PC, Hennekam E, van den Hoff MJB, Gunst QD, Gille JJP, Polstra AM, Postmus PE, van Steensel MAM, Postma AV, Wolthuis RMF, Menko FH, Houweling AC, Waisfisz Q. Familial multiple discoid fibromas is linked to a locus on chromosome 5 including the FNIP1 gene. J Hum Genet 2023; 68:273-279. [PMID: 36599954 DOI: 10.1038/s10038-022-01113-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
Previously, we reported a series of families presenting with trichodiscomas, inherited in an autosomal dominant pattern. The phenotype was named familial multiple discoid fibromas (FMDF). The genetic cause of FMDF remained unknown so far. Trichodiscomas are skin lesions previously reported to be part of the same spectrum as the fibrofolliculoma observed in Birt-Hogg-Dubé syndrome (BHD), an inherited disease caused by pathogenic variants in the FLCN gene. Given the clinical and histological differences with BHD and the exclusion of linkage with the FLCN locus, the phenotype was concluded to be distinct from BHD. We performed extensive clinical evaluations and genetic testing in ten families with FMDF. We identified a FNIP1 frameshift variant in nine families and genealogical studies showed common ancestry for eight families. Using whole exome sequencing, we identified six additional rare variants in the haplotype surrounding FNIP1, including a missense variant in the PDGFRB gene that was found to be present in all tested patients with FMDF. Genome-wide linkage analysis showed that the locus on chromosome 5 including FNIP1 was the only region reaching the maximal possible LOD score. We concluded that FMDF is linked to a haplotype on chromosome 5. Additional evaluations in families with FMDF are required to unravel the exact genetic cause underlying the phenotype. When evaluating patients with multiple trichodisomas without a pathogenic variant in the FLCN gene, further genetic testing is warranted and can include analysis of the haplotype on chromosome 5.
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Affiliation(s)
- Irma van de Beek
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Iris E Glykofridis
- Department of Human Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Michael W T Tanck
- Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Monique N H Luijten
- Department of Dermatology and GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Theo M Starink
- Department of Dermatology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Jesper A Balk
- Department of Human Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Paul C Johannesma
- Department of Surgery, Gelderse Vallei Ziekenhuis, Ede, The Netherlands
| | - Eric Hennekam
- Division of Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinn D Gunst
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Johan J P Gille
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Abeltje M Polstra
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pieter E Postmus
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maurice A M van Steensel
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Singapore Skin Research Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Alex V Postma
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Department of Human Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Fred H Menko
- Family Cancer Clinic, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Arjan C Houweling
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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7
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Young TL, Whisenhunt KN, LaMartina SM, Hewitt AW, Mackey DA, Tompson SW. Sonic Hedgehog Intron Variant Associated With an Unusual Pediatric Cortical Cataract. Invest Ophthalmol Vis Sci 2022; 63:25. [PMID: 35749127 PMCID: PMC9234370 DOI: 10.1167/iovs.63.6.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify the genetic basis of an unusual pediatric cortical cataract demonstrating autosomal dominant inheritance in a large European–Australian pedigree. Methods DNA from four affected individuals were exome sequenced utilizing a NimbleGen SeqCap EZ Exome V3 kit and HiSeq 2500. DNA from 12 affected and four unaffected individuals were genotyped using Human OmniExpress-24 BeadChips. Multipoint linkage and haplotyping were performed (Superlink-Online SNP). DNA from one affected individual and his unaffected father were whole-genome sequenced on a HiSeq X Ten system. Rare small insertions/deletions and single-nucleotide variants (SNVs) were identified in the disease-linked region (Golden Helix SVS). Combined Annotation Dependent Depletion (CADD) analysis predicted variant deleteriousness. Putative enhancer function and variant effects were determined using the Dual-Glo Luciferase Assay system. Results Linkage mapping identified a 6.23-centimorgan support interval at chromosome 7q36. A co-segregating haplotype refined the critical region to 6.03 Mbp containing 21 protein-coding genes. Whole-genome sequencing uncovered 114 noncoding variants from which CADD predicted one was highly deleterious, a novel substitution within intron-1 of the sonic hedgehog signaling molecule (SHH) gene. ENCODE data suggested this site was a putative enhancer, subsequently confirmed by luciferase reporter assays with variant-associated gene overexpression. Conclusions In a large pedigree, we have identified a SHH intron variant that co-segregates with an unusual pediatric cortical cataract phenotype. SHH is important for lens formation, and mutations in its receptor (PTCH1) cause syndromic cataract. Our data implicate increased function of an enhancer important for SHH expression primarily within developing eye tissues.
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Affiliation(s)
- Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Kristina N Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Sarah M LaMartina
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia.,Eye Department, Royal Hobart Hospital, University of Tasmania, Hobart, Tasmania, Australia
| | - David A Mackey
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia.,Eye Department, Royal Hobart Hospital, University of Tasmania, Hobart, Tasmania, Australia
| | - Stuart W Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
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8
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Smits JJ, van Beelen E, Weegerink NJD, Oostrik J, Huygen PLM, Beynon AJ, Lanting CP, Kunst HPM, Schraders M, Kremer H, de Vrieze E, Pennings RJE. A Novel COCH Mutation Affects the vWFA2 Domain and Leads to a Relatively Mild DFNA9 Phenotype. Otol Neurotol 2021; 42:e399-e407. [PMID: 33710989 DOI: 10.1097/mao.0000000000003004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE To study the genotype and phenotype of a Dutch family with autosomal dominantly inherited hearing loss. STUDY DESIGN Genotype-phenotype correlation study. Genetic analysis consisted of linkage analysis, variable number of tandem repeats analysis, and Sanger sequencing. Audiovestibular function was examined. Regression analysis was performed on pure tone audiometry and speech recognition scores and correlated with the age and/or level of hearing loss. SETTING Tertiary referral center. PATIENTS A large Dutch family presenting with sensorineural hearing loss. MAIN OUTCOME MEASURES Identification of the underlying genetic defect of the hearing loss in this family. Results of pure tone and speech audiometry, onset age, progression of hearing loss and vestibular (dys)function. RESULTS A novel mutation in COCH, c.1312C > T p.(Arg438Cys), cosegregates with hearing loss and a variable degree of vestibular (dys)function in this family. The reported mean age of onset of hearing loss is 33 years (range, 18-49 yr). Hearing loss primarily affects higher frequencies and its progression is relatively mild (0.8 dB/yr). Speech perception is remarkably well preserved in affected family members when compared with other DFNA9 families with different COCH mutations. CONCLUSION These findings expand the genotypic and phenotypic spectrum of DFNA9. The c.1312C > T mutation, which affects the vWFA2 domain, causes a relatively mild audiovestibular phenotype when compared with other COCH mutations.
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Affiliation(s)
- Jeroen J Smits
- Department of Otorhinolaryngology, Hearing & Genes
- Donders Institute for Brain, Cognition and Behaviour
| | | | | | - Jaap Oostrik
- Department of Otorhinolaryngology, Hearing & Genes
| | | | | | - Cornelis P Lanting
- Department of Otorhinolaryngology, Hearing & Genes
- Donders Institute for Brain, Cognition and Behaviour
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Hearing & Genes
- Radboud Institute for Health Sciences
| | - Margit Schraders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing & Genes
- Donders Institute for Brain, Cognition and Behaviour
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Hearing & Genes
- Donders Institute for Brain, Cognition and Behaviour
| | - Ronald J E Pennings
- Department of Otorhinolaryngology, Hearing & Genes
- Donders Institute for Brain, Cognition and Behaviour
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9
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Bademci G, Abad C, Cengiz FB, Seyhan S, Incesulu A, Guo S, Fitoz S, Atli EI, Gosstola NC, Demir S, Colbert BM, Seyhan GC, Sineni CJ, Duman D, Gurkan H, Morton CC, Dykxhoorn DM, Walz K, Tekin M. Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development. J Clin Invest 2021; 130:4213-4217. [PMID: 32369452 DOI: 10.1172/jci136951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular mechanisms governing the development of the mammalian cochlea, the hearing organ, remain largely unknown. Through genome sequencing in 3 subjects from 2 families with nonsyndromic cochlear aplasia, we identified homozygous 221-kb and 338-kb deletions in a noncoding region on chromosome 8 with an approximately 200-kb overlapping section. Genomic location of the overlapping deleted region started from approximately 350 kb downstream of GDF6, which codes for growth and differentiation factor 6. Otic lineage cells differentiated from induced pluripotent stem cells derived from an affected individual showed reduced expression of GDF6 compared with control cells. Knockout of Gdf6 in a mouse model resulted in cochlear aplasia, closely resembling the human phenotype. We conclude that GDF6 plays a necessary role in early cochlear development controlled by cis-regulatory elements located within an approximately 500-kb region of the genome in humans and that its disruption leads to deafness due to cochlear aplasia.
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Affiliation(s)
- Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Filiz B Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Serhat Seyhan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Armagan Incesulu
- Department of Otolaryngology, Eskisehir Osmangazi University School of Medicine, Eskisehir, Turkey
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Suat Fitoz
- Department of Diagnostic Radiology, Ankara University School of Medicine, Ankara, Turkey
| | - Emine Ikbal Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Nicholas C Gosstola
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Brett M Colbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Gozde Cosar Seyhan
- Department of Dermatology, Bakirkoy Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Claire J Sineni
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Duygu Duman
- Department of Audiology, Ankara University School of Medicine, Ankara, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Manchester Centre for Audiology and Deafness, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,John T. Macdonald Foundation Department of Human Genetics, and
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,John T. Macdonald Foundation Department of Human Genetics, and
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,John T. Macdonald Foundation Department of Human Genetics, and.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
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10
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Andres EM, Earnest KK, Smith SD, Rice ML, Raza MH. Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:4046-4061. [PMID: 33186502 PMCID: PMC8608229 DOI: 10.1044/2020_jslhr-20-00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218.
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Affiliation(s)
- Erin M. Andres
- Child Language Doctoral Program, University of Kansas, Lawrence
| | | | - Shelley D. Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Mabel L. Rice
- Child Language Doctoral Program, University of Kansas, Lawrence
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11
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Shahraki H, Dorgalaleh A, Fathi M, Tabibian S, Teimourian S, Mollanoori H, Khiabani A, Zaker F. How to Assess Founder Effect in Patients with Congenital Factor XIII Deficiency. Int J Hematol Oncol Stem Cell Res 2020; 14:265-273. [PMID: 33603988 PMCID: PMC7876424 DOI: 10.18502/ijhoscr.v14i4.4480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Congenital factor XIII (FXIII) deficiency is an extremely rare bleeding disorder (RBD) with estimated prevalence of one per 2 million in the general population. The disorder causes different clinical manifestations such as intracranial hemorrhage (ICH), recurrent miscarriage, umbilical cord bleeding, etc. High incidence of the disorder might be due to founder effect. To assess founder effect, haplotype analysis is an important step. For this purpose, suitable and reliable genetic markers such as microsatellites (Hum FXIIIA01 and HumFXIIIA02) and single nucleotide polymorphisms (SNP) are suggested. In the present study we tried to describe evaluation of founder effect in patients with congenital FXIII deficiency via haplotype analysis using suitable genetic markers.
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Affiliation(s)
- Hojat Shahraki
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Akbar Dorgalaleh
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Fathi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences. Tehran- Iran
| | - Shadi Tabibian
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahram Teimourian
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hasan Mollanoori
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Khiabani
- School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Transfusion, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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12
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van Walree ES, Dombrowsky G, Jansen IE, Mirkov MU, Zwart R, Ilgun A, Guo D, Clur SAB, Amin AS, Savage JE, van der Wal AC, Waisfisz Q, Maugeri A, Wilsdon A, Bu'Lock FA, Hurles ME, Dittrich S, Berger F, Audain Martinez E, Christoffels VM, Hitz MP, Milewicz DM, Posthuma D, Meijers-Heijboer H, Postma AV, Mathijssen IB. Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms. Genet Med 2020; 23:103-110. [PMID: 32820247 PMCID: PMC8804301 DOI: 10.1038/s41436-020-00939-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose In this study we aimed to establish the genetic cause of a myriad of cardiovascular defects prevalent in individuals from a genetically isolated population, who were found to share a common ancestor in 1728. Methods Trio genome sequencing was carried out in an index patient with critical congenital heart disease (CHD), family members had either exome or Sanger sequencing. To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370 controls, and the other 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls. Functional consequences of identified variants were evaluated using expression studies. Results We identified a loss-of-function variant in the Notch target transcription factor-encoding gene HEY2. The homozygous state (n=3) causes life-threatening congenital heart defects, while 80% of heterozygous carriers (n=20) had cardiovascular defects, mainly CHD and FTAA of the ascending aorta. We confirm enrichment of rare risk variants in HEY2 functional domains after meta-analysis (meta-SKAT p=0.018). Furthermore, we show that several identified variants lead to dysregulation of repression by HEY2. Conclusion A homozygous germline loss-of-function variant in HEY2 leads to critical CHD. The majority of heterozygotes show a myriad of cardiovascular defects.
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Affiliation(s)
- Eva S van Walree
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands. .,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands.
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Iris E Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Maša Umićević Mirkov
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Rob Zwart
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sally-Ann B Clur
- Department of Pediatric Cardiology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ahmed S Amin
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Allard C van der Wal
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Frances A Bu'Lock
- East Midlands Congenital Heart Centre and University of Leicester, Glenfield Hospital, Leicester, United Kingdom
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sven Dittrich
- Department of Pediatric Cardiology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Felix Berger
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Enrique Audain Martinez
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc-Philip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Dianna M Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniëlle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Alex V Postma
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Inge B Mathijssen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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13
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Li C, Wang N, Schäffer AA, Liu X, Zhao Z, Elliott G, Garrett L, Choi NT, Wang Y, Wang Y, Wang C, Wang J, Chan D, Su P, Cui S, Yang Y, Gao B. Mutations in COMP cause familial carpal tunnel syndrome. Nat Commun 2020; 11:3642. [PMID: 32686688 PMCID: PMC7371736 DOI: 10.1038/s41467-020-17378-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/21/2020] [Indexed: 02/06/2023] Open
Abstract
Carpal tunnel syndrome (CTS) is the most common peripheral nerve entrapment syndrome, affecting a large proportion of the general population. Genetic susceptibility has been implicated in CTS, but the causative genes remain elusive. Here, we report the identification of two mutations in cartilage oligomeric matrix protein (COMP) that segregate with CTS in two large families with or without multiple epiphyseal dysplasia (MED). Both mutations impair the secretion of COMP by tenocytes, but the mutation associated with MED also perturbs its secretion in chondrocytes. Further functional characterization of the CTS-specific mutation reveals similar histological and molecular changes of tendons/ligaments in patients’ biopsies and the mouse models. The mutant COMP fails to oligomerize properly and is trapped in the ER, resulting in ER stress-induced unfolded protein response and cell death, leading to inflammation, progressive fibrosis and cell composition change in tendons/ligaments. The extracellular matrix (ECM) organization is also altered. Our studies uncover a previously unrecognized mechanism in CTS pathogenesis. Familial carpal tunnel syndrome (CTS) is common, but causal genes are not characterized. Here the authors report two CTS-related mutations in two large families that impair secretion of COMP in tenocytes, leading to ER stress-induced unfolded protein response, inflammation and fibrosis in patients and mouse models.
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Affiliation(s)
- Chunyu Li
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Ni Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alejandro A Schäffer
- National Center for Biotechnology Information and National Cancer Institute, National Institutes of Health, Bethesda, MD, US
| | - Xilin Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhuo Zhao
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Gene Elliott
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Lisa Garrett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Nga Ting Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yueshu Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yufa Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Cheng Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peiqiang Su
- Department of Orthopaedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shusen Cui
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
| | - Yingzi Yang
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US. .,Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Harvard University, Boston, MA, US.
| | - Bo Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US.
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14
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Waseem NH, Low S, Shah AZ, Avisetti D, Ostergaard P, Simpson M, Niemiec KA, Martin-Martin B, Aldehlawi H, Usman S, Lee PS, Khawaja AP, Ruddle JB, Shah A, Sackey E, Day A, Jiang Y, Swinfield G, Viswanathan A, Alfano G, Chakarova C, Cordell HJ, Garway-Heath DF, Khaw PT, Bhattacharya SS, Waseem A, Foster PJ. Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma. PLoS Genet 2020; 16:e1008721. [PMID: 32339198 PMCID: PMC7233598 DOI: 10.1371/journal.pgen.1008721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/18/2020] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
Current estimates suggest 50% of glaucoma blindness worldwide is caused by primary angle-closure glaucoma (PACG) but the causative gene is not known. We used genetic linkage and whole genome sequencing to identify Spermatogenesis Associated Protein 13, SPATA13 (NM_001166271; NP_001159743, SPATA13 isoform I), also known as ASEF2 (Adenomatous polyposis coli-stimulated guanine nucleotide exchange factor 2), as the causal gene for PACG in a large seven-generation white British family showing variable expression and incomplete penetrance. The 9 bp deletion, c.1432_1440del; p.478_480del was present in all affected individuals with angle-closure disease. We show ubiquitous expression of this transcript in cell lines derived from human tissues and in iris, retina, retinal pigment and ciliary epithelia, cornea and lens. We also identified eight additional mutations in SPATA13 in a cohort of 189 unrelated PACS/PAC/PACG samples. This gene encodes a 1277 residue protein which localises to the nucleus with partial co-localisation with nuclear speckles. In cells undergoing mitosis SPATA13 isoform I becomes part of the kinetochore complex co-localising with two kinetochore markers, polo like kinase 1 (PLK-1) and centrosome-associated protein E (CENP-E). The 9 bp deletion reported in this study increases the RAC1-dependent guanine nucleotide exchange factors (GEF) activity. The increase in GEF activity was also observed in three other variants identified in this study. Taken together, our data suggest that SPATA13 is involved in the regulation of mitosis and the mutations dysregulate GEF activity affecting homeostasis in tissues where it is highly expressed, influencing PACG pathogenesis.
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Affiliation(s)
- Naushin H. Waseem
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
| | - Sancy Low
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
- Department of Ophthalmology, St. Thomas’ Hospital, Westminster Bridge Road, London, United Kingdom
| | - Amna Z. Shah
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Deepa Avisetti
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Pia Ostergaard
- Medical Genetics Unit, St. George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Michael Simpson
- Genetics and Molecular Medicine, King’s College London, Great Maze Pond, London, United Kingdom
| | - Katarzyna A. Niemiec
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Belen Martin-Martin
- Blizard Advanced Light Microscopy, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Hebah Aldehlawi
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Pak Sang Lee
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Jonathan B. Ruddle
- Department of Ophthalmology, University of Melbourne, Victoria, Australia
| | - Ameet Shah
- Department of Ophthalmology, Royal Free Hospital NHS Foundation Trust, Pond Street, London, United Kingdom
| | - Ege Sackey
- Medical Genetics Unit, St. George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Alexander Day
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
| | - Yuzhen Jiang
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
| | - Geoff Swinfield
- Society of Genealogists, Goswell Road, London, United Kingdom
| | - Ananth Viswanathan
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Giovanna Alfano
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | | | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - David F. Garway-Heath
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Peng T. Khaw
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Shomi S. Bhattacharya
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Paul J. Foster
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
- * E-mail:
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15
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Identification of ADHD risk genes in extended pedigrees by combining linkage analysis and whole-exome sequencing. Mol Psychiatry 2020; 25:2047-2057. [PMID: 30116028 PMCID: PMC7473839 DOI: 10.1038/s41380-018-0210-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 05/01/2018] [Accepted: 06/18/2018] [Indexed: 12/23/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder with a complex genetic background, hampering identification of underlying genetic risk factors. We hypothesized that combining linkage analysis and whole-exome sequencing (WES) in multi-generation pedigrees with multiple affected individuals can point toward novel ADHD genes. Three families with multiple ADHD-affected members (Ntotal = 70) and apparent dominant inheritance pattern were included in this study. Genotyping was performed in 37 family members, and WES was additionally carried out in 10 of those. Linkage analysis was performed using multi-point analysis in Superlink Online SNP 1.1. From prioritized linkage regions with a LOD score ≥ 2, a total of 24 genes harboring rare variants were selected. Those genes were taken forward and were jointly analyzed in gene-set analyses of exome-chip data using the MAGMA software in an independent sample of patients with persistent ADHD and healthy controls (N = 9365). The gene-set including all 24 genes together, and particularly the gene-set from one of the three families (12 genes), were significantly associated with persistent ADHD in this sample. Among the latter, gene-wide analysis for the AAED1 gene reached significance. A rare variant (rs151326868) within AAED1 segregated with ADHD in one of the families. The analytic strategy followed here is an effective approach for identifying novel ADHD risk genes. Additionally, this study suggests that both rare and more frequent variants in multiple genes act together in contributing to ADHD risk, even in individual multi-case families.
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16
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Wünnemann F, Ta-Shma A, Preuss C, Leclerc S, van Vliet PP, Oneglia A, Thibeault M, Nordquist E, Lincoln J, Scharfenberg F, Becker-Pauly C, Hofmann P, Hoff K, Audain E, Kramer HH, Makalowski W, Nir A, Gerety SS, Hurles M, Comes J, Fournier A, Osinska H, Robins J, Pucéat M, Elpeleg O, Hitz MP, Andelfinger G. Loss of ADAMTS19 causes progressive non-syndromic heart valve disease. Nat Genet 2019; 52:40-47. [PMID: 31844321 DOI: 10.1038/s41588-019-0536-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/23/2019] [Indexed: 01/24/2023]
Abstract
Valvular heart disease is observed in approximately 2% of the general population1. Although the initial observation is often localized (for example, to the aortic or mitral valve), disease manifestations are regularly observed in the other valves and patients frequently require surgery. Despite the high frequency of heart valve disease, only a handful of genes have so far been identified as the monogenic causes of disease2-7. Here we identify two consanguineous families, each with two affected family members presenting with progressive heart valve disease early in life. Whole-exome sequencing revealed homozygous, truncating nonsense alleles in ADAMTS19 in all four affected individuals. Homozygous knockout mice for Adamts19 show aortic valve dysfunction, recapitulating aspects of the human phenotype. Expression analysis using a lacZ reporter and single-cell RNA sequencing highlight Adamts19 as a novel marker for valvular interstitial cells; inference of gene regulatory networks in valvular interstitial cells positions Adamts19 in a highly discriminatory network driven by the transcription factor lymphoid enhancer-binding factor 1 downstream of the Wnt signaling pathway. Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance.
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Affiliation(s)
- Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada.,Institute of Bioinformatics, University of Münster, Münster, Germany
| | - Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Monique and Jacques Robo Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Severine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Patrick Piet van Vliet
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada.,LIA (International Associated Laboratory) Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada.,LIA (International Associated Laboratory) INSERM, Marseille, France
| | - Andrea Oneglia
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Emily Nordquist
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Joy Lincoln
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Pediatric Cardiology, Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Franka Scharfenberg
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Christoph Becker-Pauly
- Unit for Degradomics of the Protease Web, Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany.,German Centre for Cardiovascular Research (DZHK), Kiel, Germany
| | - Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany.,German Centre for Cardiovascular Research (DZHK), Kiel, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany.,German Centre for Cardiovascular Research (DZHK), Kiel, Germany
| | | | - Amiram Nir
- Department of Pediatric Cardiology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | | | - Johanna Comes
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Anne Fournier
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Hanna Osinska
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Jeffrey Robins
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Michel Pucéat
- LIA (International Associated Laboratory) Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada.,LIA (International Associated Laboratory) INSERM, Marseille, France.,Université Aix-Marseille, INSERM U-1251, Marseille, France
| | | | - Orly Elpeleg
- Monique and Jacques Robo Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany.,German Centre for Cardiovascular Research (DZHK), Kiel, Germany.,Wellcome Sanger Institute, Cambridge, UK.,Department of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada. .,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada. .,Department of Biochemistry, University of Montreal, Montreal, Quebec, Canada.
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17
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Andres EM, Hafeez H, Yousaf A, Riazuddin S, Rice ML, Basra MAR, Raza MH. A genome-wide analysis in consanguineous families reveals new chromosomal loci in specific language impairment (SLI). Eur J Hum Genet 2019; 27:1274-1285. [PMID: 30976110 DOI: 10.1038/s41431-019-0398-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Language is a uniquely human ability, and failure to attain this ability can have a life-long impact on the affected individuals. This is particularly true for individuals with specific language impairment (SLI), which is defined as an impairment in normal language development in the absence of any other developmental disability. Although SLI displays high heritability, family-based linkage studies have been hampered by an unclear mode of Mendelian segregation, variable disease penetrance, and heterogeneity of diagnostic criteria. We performed genome-wide parametric linkage analysis and homozygosity mapping in 14 consanguineous families from Pakistan segregating SLI. Linkage analysis revealed a multipoint LOD score of 4.18 at chromosome 2q in family PKSLI05 under a recessive mode of inheritance. A second linkage score of 3.85 was observed in family PKSLI12 at a non-overlapping locus on chromosome 2q. Two other suggestive linkage loci were found in family PKSLI05 on 14q and 22q with LOD scores of 2.37 and 2.23, respectively, that were also identified in homozygosity mapping. Reduction to homozygosity was observed on chromosomes 2q, 5p, 8q, 14q, 17q, and 22q. Each homozygosity region occurred in multiple PKSLI families. We report new SLI loci on chromosomes 2 and 8 and confirm suggestive SLI linkage loci on chromosomes 5, 14, 17, and 22 reported previously in the population of Robinson Crusoe Island. These findings indicate that linkage and homozygosity mapping in consanguineous families can improve genetic analyses in SLI and suggest the involvement of additional genes in the causation of this disorder.
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Affiliation(s)
- Erin M Andres
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | - Huma Hafeez
- Institute of Chemistry, University of the Punjab, Lahore, Pakistan
| | - Adnan Yousaf
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.,Department of Biotechnology, International Islamic University, Islamabad, Pakistan
| | | | - Mabel L Rice
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | | | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.
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18
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Dorjbal B, Stinson JR, Ma CA, Weinreich MA, Miraghazadeh B, Hartberger JM, Frey-Jakobs S, Weidinger S, Moebus L, Franke A, Schäffer AA, Bulashevska A, Fuchs S, Ehl S, Limaye S, Arkwright PD, Briggs TA, Langley C, Bethune C, Whyte AF, Alachkar H, Nejentsev S, DiMaggio T, Nelson CG, Stone KD, Nason M, Brittain EH, Oler AJ, Veltri DP, Leahy TR, Conlon N, Poli MC, Borzutzky A, Cohen JI, Davis J, Lambert MP, Romberg N, Sullivan KE, Paris K, Freeman AF, Lucas L, Chandrakasan S, Savic S, Hambleton S, Patel SY, Jordan MB, Theos A, Lebensburger J, Atkinson TP, Torgerson TR, Chinn IK, Milner JD, Grimbacher B, Cook MC, Snow AL. Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease. J Allergy Clin Immunol 2019; 143:1482-1495. [PMID: 30170123 PMCID: PMC6395549 DOI: 10.1016/j.jaci.2018.08.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/02/2018] [Accepted: 08/13/2018] [Indexed: 01/26/2023]
Abstract
BACKGROUND Caspase activation and recruitment domain 11 (CARD11) encodes a scaffold protein in lymphocytes that links antigen receptor engagement with downstream signaling to nuclear factor κB, c-Jun N-terminal kinase, and mechanistic target of rapamycin complex 1. Germline CARD11 mutations cause several distinct primary immune disorders in human subjects, including severe combined immune deficiency (biallelic null mutations), B-cell expansion with nuclear factor κB and T-cell anergy (heterozygous, gain-of-function mutations), and severe atopic disease (loss-of-function, heterozygous, dominant interfering mutations), which has focused attention on CARD11 mutations discovered by using whole-exome sequencing. OBJECTIVES We sought to determine the molecular actions of an extended allelic series of CARD11 and to characterize the expanding range of clinical phenotypes associated with heterozygous CARD11 loss-of-function alleles. METHODS Cell transfections and primary T-cell assays were used to evaluate signaling and function of CARD11 variants. RESULTS Here we report on an expanded cohort of patients harboring novel heterozygous CARD11 mutations that extend beyond atopy to include other immunologic phenotypes not previously associated with CARD11 mutations. In addition to (and sometimes excluding) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phenotypes similar to those observed in signal transducer and activator of transcription 3 loss of function, dedicator of cytokinesis 8 deficiency, common variable immunodeficiency, neutropenia, and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome. Pathogenic variants exhibited dominant negative activity and were largely confined to the CARD or coiled-coil domains of the CARD11 protein. CONCLUSION These results illuminate a broader phenotypic spectrum associated with CARD11 mutations in human subjects and underscore the need for functional studies to demonstrate that rare gene variants encountered in expected and unexpected phenotypes must nonetheless be validated for pathogenic activity.
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Affiliation(s)
- Batsukh Dorjbal
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Jeffrey R Stinson
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Chi A Ma
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael A Weinreich
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Bahar Miraghazadeh
- Department of Immunology, Canberra Hospital, Canberra, Australia; Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Julia M Hartberger
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Frey-Jakobs
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lena Moebus
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Md
| | - Alla Bulashevska
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Fuchs
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Peter D Arkwright
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Tracy A Briggs
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Claire Langley
- Paediatric Allergy and Immunology & the Manchester Center for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Claire Bethune
- Department of Clinical Immunology, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Andrew F Whyte
- Department of Clinical Immunology, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Hana Alachkar
- Immunology, Salford Royal Foundation Trust, Manchester, United Kingdom
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Thomas DiMaggio
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Celeste G Nelson
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kelly D Stone
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Martha Nason
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Erica H Brittain
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Sciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Daniel P Veltri
- Bioinformatics and Computational Sciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - T Ronan Leahy
- Department of Paediatric Immunology and ID, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Niall Conlon
- Department of Immunology, St James's Hospital, Dublin, Ireland
| | - Maria C Poli
- Department of Pediatrics, Baylor College of Medicine, and the Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Arturo Borzutzky
- Department of Pediatrics, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michele P Lambert
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, and the Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa
| | - Kenneth Paris
- Louisiana State University Health Sciences Center and Children's Hospital, New Orleans, La
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Laura Lucas
- Division of Bone Marrow Transplant, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Ga
| | - Shanmuganathan Chandrakasan
- Division of Bone Marrow Transplant, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Ga
| | - Sinisa Savic
- Leeds Institute for Rheumatic and Musculoskeletal Medicine, St James University Hospital, Leeds, United Kingdom
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Smita Y Patel
- Oxford University Hospitals NHS Trust and NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Michael B Jordan
- Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Amy Theos
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Ala
| | - Jeffrey Lebensburger
- Department of Pediatric Hematology Oncology, University of Alabama at Birmingham, Birmingham, Ala
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Troy R Torgerson
- University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Wash
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, and the Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthew C Cook
- Department of Immunology, Canberra Hospital, Canberra, Australia; Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md.
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19
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Puigdevall P, Piccari L, Blanco I, Barberà JA, Geiger D, Badenas C, Milà M, Castelo R, Madrigal I. Genetic linkage analysis of a large family identifies FIGN as a candidate modulator of reduced penetrance in heritable pulmonary arterial hypertension. J Med Genet 2019; 56:481-490. [PMID: 30894412 DOI: 10.1136/jmedgenet-2018-105669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/12/2019] [Accepted: 02/16/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Mapping the genetic component of molecular mechanisms responsible for the reduced penetrance (RP) of rare disorders constitutes one of the most challenging problems in human genetics. Heritable pulmonary arterial hypertension (PAH) is one such disorder characterised by rare mutations mostly occurring in the bone morphogenetic protein receptor type 2 (BMPR2) gene and a wide heterogeneity of penetrance modifier mechanisms. Here, we analyse 32 genotyped individuals from a large Iberian family of 65 members, including 22 carriers of the pathogenic BMPR2 mutation c.1472G>A (p.Arg491Gln), 8 of them diagnosed with PAH by right-heart catheterisation, leading to an RP rate of 36.4%. METHODS We performed a linkage analysis on the genotyping data to search for genetic modifiers of penetrance. Using functional genomics data, we characterised the candidate region identified by linkage analysis. We also predicted the haplotype segregation within the family. RESULTS We identified a candidate chromosome region in 2q24.3, 38 Mb upstream from BMPR2, with significant linkage (LOD=4.09) under a PAH susceptibility model. This region contains common variants associated with vascular aetiology and shows functional evidence that the putative genetic modifier is located in the upstream distal promoter of the fidgetin (FIGN) gene. CONCLUSION Our results suggest that the genetic modifier acts through FIGN transcriptional regulation, whose expression variability would contribute to modulating heritable PAH. This finding may help to advance our understanding of RP in PAH across families sharing the p.Arg491Gln pathogenic mutation in BMPR2.
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Affiliation(s)
- Pau Puigdevall
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lucilla Piccari
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Isabel Blanco
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Joan Albert Barberà
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Dan Geiger
- Faculty of Computer Science, Technion Israel Institute of Technology, Haifa, Israel
| | - Celia Badenas
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Milà
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Robert Castelo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Irene Madrigal
- Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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20
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Homozygous frameshift mutations in FAT1 cause a syndrome characterized by colobomatous-microphthalmia, ptosis, nephropathy and syndactyly. Nat Commun 2019; 10:1180. [PMID: 30862798 PMCID: PMC6414540 DOI: 10.1038/s41467-019-08547-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/09/2019] [Indexed: 01/15/2023] Open
Abstract
A failure in optic fissure fusion during development can lead to blinding malformations of the eye. Here, we report a syndrome characterized by facial dysmorphism, colobomatous microphthalmia, ptosis and syndactyly with or without nephropathy, associated with homozygous frameshift mutations in FAT1. We show that Fat1 knockout mice and zebrafish embryos homozygous for truncating fat1a mutations exhibit completely penetrant coloboma, recapitulating the most consistent developmental defect observed in affected individuals. In human retinal pigment epithelium (RPE) cells, the primary site for the fusion of optic fissure margins, FAT1 is localized at earliest cell-cell junctions, consistent with a role in facilitating optic fissure fusion during vertebrate eye development. Our findings establish FAT1 as a gene with pleiotropic effects in human, in that frameshift mutations cause a severe multi-system disorder whereas recessive missense mutations had been previously associated with isolated glomerulotubular nephropathy. Loss of the cadherin FAT1 has been associated with nephropathy and epithelial cell adhesion defects. Here, the authors report five families with a syndromic form of coloboma associated with homozygous frameshift variants in FAT1 and recapitulate the phenotype in mutant mice and zebrafish.
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21
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SCAPER localizes to primary cilia and its mutation affects cilia length, causing Bardet-Biedl syndrome. Eur J Hum Genet 2019; 27:928-940. [PMID: 30723319 DOI: 10.1038/s41431-019-0347-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/17/2018] [Accepted: 01/04/2019] [Indexed: 01/26/2023] Open
Abstract
Studies of ciliopathies have served in elucidating much of our knowledge of structure and function of primary cilia. We report humans with Bardet-Biedl syndrome who display intellectual disability, retinitis pigmentosa, obesity, short stature and brachydactyly, stemming from a homozyogous truncation mutation in SCAPER, a gene previously associated with mitotic progression. Our findings, based on linkage analysis and exome sequencing studies of two remotely related large consanguineous families, are in line with recent reports of SCAPER variants associated with intellectual disability and retinitis pigmentosa. Using immuno-fluorescence and live cell imaging in NIH/3T3 fibroblasts and SH-SY5Y neuroblastoma cell lines over-expressing SCAPER, we demonstrate that both wild type and mutant SCAPER are expressed in primary cilia and co-localize with tubulin, forming bundles of microtubules. While wild type SCAPER was rarely localized along the ciliary axoneme and basal body, the aberrant protein remained sequestered to the cilia, mostly at the ciliary tip. Notably, longer cilia were demonstrated both in human affected fibroblasts compared to controls, as well as in NIH/3T3 cells transfected with mutant versus wildtype SCAPER. As SCAPER expression is known to peak at late G1 and S phase, overlapping the timing of ciliary resorption, our data suggest a possible role of SCAPER in ciliary dynamics and disassembly, also affecting microtubule-related mitotic progression. Thus, we outline a human ciliopathy syndrome and demonstrate that it is caused by a mutation in SCAPER, affecting primary cilia.
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22
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Wormser O, Gradstein L, Kadar E, Yogev Y, Perez Y, Mashkit E, Elbedour K, Drabkin M, Markus B, Kadir R, Halperin D, Khalaila S, Levy J, Lifshitz T, Manor E, Birk OS. Combined CNV, haplotyping and whole exome sequencing enable identification of two distinct novel EYS mutations causing RP in a single inbred tribe. Am J Med Genet A 2018; 176:2695-2703. [PMID: 30513137 DOI: 10.1002/ajmg.a.40668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/17/2018] [Accepted: 09/28/2018] [Indexed: 11/10/2022]
Abstract
Whole exome sequencing (WES) has become routine in clinical practice, especially in studies of recessive hereditary diseases in inbred consanguineous families, where homozygosity of a founder mutation is assumed. Multiple members of two consanguineous families of a single Bedouin tribe were diagnosed with apparently autosomal recessive/pseudo-dominant retinitis pigmentosa (RP). Affected individuals exhibited severe visual impairment with nyctalopia, marked constriction of visual fields, markedly reduced and delayed responses on electro-retinography (ERG) and eventual loss of central vision. Combined copy-number variant (CNV) analysis, haplotype reconstruction and WES of the kindred identified two distinct novel mutations in EYS (RP25): a p.(W1817*) nonsense mutation (identified through WES) and a large deletion encompassing 9 of the 43 exons, that was missed by WES and was identified through microarray CNV analysis. Segregation analysis of both mutations demonstrated that all affected individuals were either homozygous for one of the mutations, or compound heterozygous for both. The two mutations are predicted to cause loss of function of the encoded protein and were not present in screening of 200 ethnically-matched controls. Our findings of two distinct mutations in the same gene in a single inbred kindred, identified only through combined WES and microarray CNV analysis, highlight the limitations of either CNV or WES alone, as the heterozygous deletion had normal WES read-depth values. Moreover, they demonstrate pitfalls in homozygosity mapping for disease-causing variant identification in inbred communities.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Einat Kadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Elena Mashkit
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Khalil Elbedour
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Kadir
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Soltan Khalaila
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jaime Levy
- Department of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Tova Lifshitz
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Esther Manor
- Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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23
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Bademci G, Abad C, Incesulu A, Rad A, Alper O, Kolb SM, Cengiz FB, Diaz-Horta O, Silan F, Mihci E, Ocak E, Najafi M, Maroofian R, Yilmaz E, Nur BG, Duman D, Guo S, Sant DW, Wang G, Monje PV, Haaf T, Blanton SH, Vona B, Walz K, Tekin M. MPZL2 is a novel gene associated with autosomal recessive nonsyndromic moderate hearing loss. Hum Genet 2018; 137:479-486. [PMID: 29982980 DOI: 10.1007/s00439-018-1901-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023]
Abstract
While recent studies have revealed a substantial portion of the genes underlying human hearing loss, the extensive genetic landscape has not been completely explored. Here, we report a loss-of-function variant (c.72delA) in MPZL2 in three unrelated multiplex families from Turkey and Iran with autosomal recessive nonsyndromic hearing loss. The variant co-segregates with moderate sensorineural hearing loss in all three families. We show a shared haplotype flanking the variant in our families implicating a single founder. While rare in other populations, the allele frequency of the variant is ~ 0.004 in Ashkenazi Jews, suggesting that it may be an important cause of moderate hearing loss in that population. We show that Mpzl2 is expressed in mouse inner ear, and the protein localizes in the auditory inner and outer hair cells, with an asymmetric subcellular localization. We thus present MPZL2 as a novel gene associated with sensorineural hearing loss.
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Affiliation(s)
- Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Armagan Incesulu
- Department of Otorhinolaryngology, Faculty of Medicine, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Abolfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, 009851, Iran
| | - Ozgul Alper
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, 07070, Antalya, Turkey
| | - Susanne M Kolb
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Filiz B Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Oscar Diaz-Horta
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Fatma Silan
- Department of Medical Genetics, Canakkale Onsekiz Mart University School of Medicine, 17100, Canakkale, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University School of Medicine, 07070, Antalya, Turkey
| | - Emre Ocak
- Department of Otolaryngology, Ankara University School of Medicine, 06260, Ankara, Turkey
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL, Nijmegen, The Netherlands
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Elanur Yilmaz
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, 07070, Antalya, Turkey
| | - Banu G Nur
- Department of Pediatric Genetics, Akdeniz University School of Medicine, 07070, Antalya, Turkey
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, 06260, Ankara, Turkey
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - David W Sant
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Paula V Monje
- The Miami Project to Cure Paralysis and the Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre (THRC), Eberhard Karls University Tübingen, 72076, Tübingen, Germany
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. .,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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24
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Wesdorp M, de Koning Gans PAM, Schraders M, Oostrik J, Huynen MA, Venselaar H, Beynon AJ, van Gaalen J, Piai V, Voermans N, van Rossum MM, Hartel BP, Lelieveld SH, Wiel L, Verbist B, Rotteveel LJ, van Dooren MF, Lichtner P, Kunst HPM, Feenstra I, Admiraal RJC, Yntema HG, Hoefsloot LH, Pennings RJE, Kremer H. Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction. Hum Genet 2018; 137:389-400. [PMID: 29754270 PMCID: PMC5973959 DOI: 10.1007/s00439-018-1880-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 03/31/2018] [Indexed: 12/20/2022]
Abstract
Unraveling the causes and pathomechanisms of progressive disorders is essential for the development of therapeutic strategies. Here, we identified heterozygous pathogenic missense variants of LMX1A in two families of Dutch origin with progressive nonsyndromic hearing impairment (HI), using whole exome sequencing. One variant, c.721G > C (p.Val241Leu), occurred de novo and is predicted to affect the homeodomain of LMX1A, which is essential for DNA binding. The second variant, c.290G > C (p.Cys97Ser), predicted to affect a zinc-binding residue of the second LIM domain that is involved in protein–protein interactions. Bi-allelic deleterious variants of Lmx1a are associated with a complex phenotype in mice, including deafness and vestibular defects, due to arrest of inner ear development. Although Lmx1a mouse mutants demonstrate neurological, skeletal, pigmentation and reproductive system abnormalities, no syndromic features were present in the participating subjects of either family. LMX1A has previously been suggested as a candidate gene for intellectual disability, but our data do not support this, as affected subjects displayed normal cognition. Large variability was observed in the age of onset (a)symmetry, severity and progression rate of HI. About half of the affected individuals displayed vestibular dysfunction and experienced symptoms thereof. The late-onset progressive phenotype and the absence of cochleovestibular malformations on computed tomography scans indicate that heterozygous defects of LMX1A do not result in severe developmental abnormalities in humans. We propose that a single LMX1A wild-type copy is sufficient for normal development but insufficient for maintenance of cochleovestibular function. Alternatively, minor cochleovestibular developmental abnormalities could eventually lead to the progressive phenotype seen in the families.
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Affiliation(s)
- Mieke Wesdorp
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pia A M de Koning Gans
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margit Schraders
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andy J Beynon
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vitória Piai
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Psychology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicol Voermans
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michelle M van Rossum
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas P Hartel
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stefan H Lelieveld
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Berit Verbist
- Department of Radiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Helger G Yntema
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Ronald J E Pennings
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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25
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Shalata A, Mahroom M, Milewicz DM, Limin G, Kassum F, Badarna K, Tarabeih N, Assy N, Fell R, Cohen H, Nashashibi M, Livoff A, Azab M, Habib G, Geiger D, Weissbrod O, Nseir W. Fatal thoracic aortic aneurysm and dissection in a large family with a novel MYLK gene mutation: delineation of the clinical phenotype. Orphanet J Rare Dis 2018; 13:41. [PMID: 29544503 PMCID: PMC5856213 DOI: 10.1186/s13023-018-0769-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Background Thoracic and abdominal aortic aneurysms and dissection often develop in hypertensive elderly patients. At higher risk are smokers and those who have a family history of aortic aneurysms. In most affected families, the aortic aneurysms and dissection is inherited in an autosomal dominant manner with decreased penetrance and variable expressivity. Mutations at two chromosomal loci, TAA1 at 11q23 and the TAA2 at 5q13–14, and eight genes, MYLK, MYH11, TGFBR2, TGFBR1, ACTA2, SMAD3, TGFB2, and MAT2A, have been identified as being responsible for the disease in 23% of affected families. Results Herein, we inform on the clinical, genetic and pathological characteristics of nine living and deceased members of a large consanguineous Arab family with thoracic aortic aneurysm and dissection who carry a missense mutation c.4471G > T (Ala1491Ser), in exon 27 of MYLK gene. We show a reduced kinase activity of the Ala1491Ser protein compared to wildtype protein. This mutation is expressed as aortic aneurysm and dissection in one of two distinct phenotypes. A severe fatal and early onset symptom in homozygous or mild late onset in heterozygous genotypes. Conclusions We found that MYLK gene Ala1491Ser mutation affect the kinase activity and clinically, it presents with vascular aneurysms and dissection. We describe a distinct genotype phenotype correlation where; heterozygous patients have mild late onset and incomplete penetrance disease compared with the early onset severe and generally fatal outcome in homozygous patients.
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Affiliation(s)
- Adel Shalata
- Simon Winter Institute for Human Genetics, B'nai Zion Medical Center, P.O.B 4940, 31048, Haifa, Israel. .,Genetic Unit, Ziv Medical Center, Safed, Israel. .,Ginatuna Association, Sakhnin, Israel.
| | - Mohammad Mahroom
- Simon Winter Institute for Human Genetics, B'nai Zion Medical Center, P.O.B 4940, 31048, Haifa, Israel.,Genetic Unit, Ziv Medical Center, Safed, Israel.,Ginatuna Association, Sakhnin, Israel
| | - Dianna M Milewicz
- Department of Internal Medicine, McGoven Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Gong Limin
- Department of Internal Medicine, McGoven Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | | | | | | | - Nimmer Assy
- Department of Internal Medicine, Western Galilee Medical Center, Nahariya, Israel
| | - Rona Fell
- Research Unit, Western Galilee Medical Center, Nahariya, Israel
| | - Hector Cohen
- Department of Pathology, Western Galilee Medical Center, Nahariya, Israel
| | - Munir Nashashibi
- Department of Pathology, Laniado hospital, Netanya, Israel.,Faculty of medicine, Technion, Haifa, Israel
| | - Alejandro Livoff
- Department of Pathology, Western Galilee Medical Center, Nahariya, Israel
| | | | - George Habib
- Faculty of medicine, Technion, Haifa, Israel.,Rheumatology unit, Laniado hospital, Netanya, Israel
| | - Dan Geiger
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - Omer Weissbrod
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - William Nseir
- Department of Internal Medicine, EMMS Nazareth Hospital, Nazareth, Israel
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26
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Yogev Y, Perez Y, Noyman I, Madegem AA, Flusser H, Shorer Z, Cohen E, Kachko L, Michaelovsky A, Birk R, Koifman A, Drabkin M, Wormser O, Halperin D, Kadir R, Birk OS. Progressive hereditary spastic paraplegia caused by a homozygous KY mutation. Eur J Hum Genet 2017; 25:966-972. [PMID: 28488683 DOI: 10.1038/ejhg.2017.85] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 12/19/2022] Open
Abstract
Twelve individuals of consanguineous Bedouin kindred presented with autosomal recessive progressive spastic paraplegia evident as of age 0-24 months, with spasticity of lower limbs, hyperreflexia, toe walking and equinus deformity. Kyphoscolisois was evident in older patients. Most had atrophy of the lateral aspects of the tongue and few had intellectual disability. Nerve conduction velocity, electromyography and head and spinal cord magnetic resonance imaging were normal in tested subjects. Muscle biopsy showed occasional central nuclei and fiber size variability with small angular fibers. Genome-wide linkage analysis identified a 6.7Mbp disease-associated locus on chromosome 3q21.3-3q22.2 (LOD score 9.02; D3S1290). Whole-exome sequencing identified a single homozygous variant within this locus, c.51_52ins(28); p.(V18fs56*) in KY, segregating in the family as expected and not found in 190 Bedouin controls. High KY transcript levels were demonstrated in muscular organs with lower expression in the CNS. The phenotype is reminiscent of kyphoscoliosis seen in Ky null mice. Two recent studies done independently and parallel to ours describe somewhat similar phenotypes in one and two patients with KY mutations. KY encodes a tranglutaminase-like peptidase, which interacts with muscle cytoskeletal proteins and is part of a Z-band protein complex, suggesting the disease mechanism may resemble myofibrillar myopathy. However, the mixed myopathic-neurologic features caused by human and mouse Ky mutations are difficult to explain by loss of KY sarcomere stabilizing function alone. KY transcription in CNS tissues may imply that it also has a role in neuromotor function, in line with the irregularity of neuromuscular junction in Ky null mutant mice.
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Affiliation(s)
- Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Iris Noyman
- Department of Pediatric Neurology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anwar Abu Madegem
- Department of Pediatrics, Beer Sheva, Clalit Health Services, Israel
| | - Hagit Flusser
- Zussman Child Development Center, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zamir Shorer
- Department of Pediatric Neurology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eugene Cohen
- Department of Orthopaedics, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Leonid Kachko
- Department of Pathology, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Analia Michaelovsky
- Zussman Child Development Center, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ruth Birk
- Department of Nutrition, Faculty of Health Sciences, Ariel University, Ariel, Israel
| | - Arie Koifman
- Genetics Institute, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Rotem Kadir
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel.,Genetics Institute, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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27
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Preuss C, Capredon M, Wünnemann F, Chetaille P, Prince A, Godard B, Leclerc S, Sobreira N, Ling H, Awadalla P, Thibeault M, Khairy P, Samuels ME, Andelfinger G. Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease. PLoS Genet 2016; 12:e1006335. [PMID: 27760138 PMCID: PMC5070860 DOI: 10.1371/journal.pgen.1006335] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 11/23/2022] Open
Abstract
Left-ventricular outflow tract obstructions (LVOTO) encompass a wide spectrum of phenotypically heterogeneous heart malformations which frequently cluster in families. We performed family based whole-exome and targeted re-sequencing on 182 individuals from 51 families with multiple affected members. Central to our approach is the family unit which serves as a reference to identify causal genotype-phenotype correlations. Screening a multitude of 10 overlapping phenotypes revealed disease associated and co-segregating variants in 12 families. These rare or novel protein altering mutations cluster predominantly in genes (NOTCH1, ARHGAP31, MAML1, SMARCA4, JARID2, JAG1) along the Notch signaling cascade. This is in line with a significant enrichment (Wilcoxon, p< 0.05) of variants with a higher pathogenicity in the Notch signaling pathway in patients compared to controls. The significant enrichment of novel protein truncating and missense mutations in NOTCH1 highlights the allelic and phenotypic heterogeneity in our pediatric cohort. We identified novel co-segregating pathogenic mutations in NOTCH1 associated with left and right-sided cardiac malformations in three independent families with a total of 15 affected individuals. In summary, our results suggest that a small but highly pathogenic fraction of family specific mutations along the Notch cascade are a common cause of LVOTO. Left-ventricular outflow tract obstructions comprise a group of developmental heart disorders that are genetically and phenotypically heterogeneous, with no single gene accounting for the majority of cases. In order to identify mutations contributing to disease, we selected patients from 51 families with a history of congenital cardiac malformations. We interrogated the entire coding sequences of 106 patients and identified a small but highly pathogenic fraction of mutations that are likely to contribute to disease in 12 families (23.5%). Furthermore, we present a strategy for identifying candidate mutations based on familial segregation in a genetically heterogeneous disorder.
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Affiliation(s)
- Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Melanie Capredon
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Faculty of Biology, University of Muenster, Muenster, Germany
| | - Philippe Chetaille
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Québec, Canada
| | - Andrea Prince
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Beatrice Godard
- Omics-Ethics Research Group, Research Institute of Public Health, Université de Montréal, Montréal Québec, Canada
| | - Severine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Nara Sobreira
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hua Ling
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Paul Khairy
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | | | - Mark E. Samuels
- Centre de Recherche CHU Sainte Justine, Université de Montreal, Montréal, Québec, Canada
- Department of Medicine, Université de Montreal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
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28
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Kim YJ, Seymen F, Koruyucu M, Kasimoglu Y, Gencay K, Shin TJ, Hyun HK, Lee ZH, Kim JW. Unexpected identification of a recurrent mutation in the DLX3 gene causing amelogenesis imperfecta. Oral Dis 2016; 22:297-302. [PMID: 26762616 DOI: 10.1111/odi.12439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To identify the molecular genetic aetiology of a family with autosomal dominant amelogenesis imperfecta (AI). SUBJECTS AND METHODS DNA samples were collected from a six-generation family, and the candidate gene approach was used to screen for the enamelin (ENAM) gene. Whole-exome sequencing and linkage analysis with SNP array data identified linked regions, and candidate gene screening was performed. RESULTS Mutational analysis revealed a mutation (c.561_562delCT and p.Tyr188Glnfs*13) in the DLX3 gene. After finding a recurrent DLX3 mutation, the clinical phenotype of the family members was re-examined. The proband's mother had pulp elongation in the third molars. The proband had not hair phenotype, but her cousin had curly hair at birth. CONCLUSIONS In this study, we identified a recurrent 2-bp deletional DLX3 mutation in a new family. The clinical phenotype was the mildest one associated with the DLX3 mutations. These results will advance the understanding of the functional role of DLX3 in developmental processes.
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Affiliation(s)
- Y-J Kim
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - F Seymen
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - M Koruyucu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Y Kasimoglu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - K Gencay
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - T J Shin
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - H-K Hyun
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - Z H Lee
- Department of Cell and Developmental Biology & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - J-W Kim
- Department of Pediatric Dentistry & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea.,Department of Molecular Genetics & Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
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29
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Lal D, Neubauer BA, Toliat MR, Altmüller J, Thiele H, Nürnberg P, Kamrath C, Schänzer A, Sander T, Hahn A, Nothnagel M. Increased Probability of Co-Occurrence of Two Rare Diseases in Consanguineous Families and Resolution of a Complex Phenotype by Next Generation Sequencing. PLoS One 2016; 11:e0146040. [PMID: 26789268 PMCID: PMC4720433 DOI: 10.1371/journal.pone.0146040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/11/2015] [Indexed: 12/11/2022] Open
Abstract
Massively parallel sequencing of whole genomes and exomes has facilitated a direct assessment of causative genetic variation, now enabling the identification of genetic factors involved in rare diseases (RD) with Mendelian inheritance patterns on an almost routine basis. Here, we describe the illustrative case of a single consanguineous family where this strategy suffered from the difficulty to distinguish between two etiologically distinct disorders, namely the co-occurrence of hereditary hypophosphatemic rickets (HRR) and congenital myopathies (CM), by their phenotypic manifestation alone. We used parametric linkage analysis, homozygosity mapping and whole exome-sequencing to identify mutations underlying HRR and CM. We also present an approximate approach for assessing the probability of co-occurrence of two unlinked recessive RD in a single family as a function of the degree of consanguinity and the frequency of the disease-causing alleles. Linkage analysis and homozygosity mapping yielded elusive results when assuming a single RD, but whole-exome sequencing helped to identify two mutations in two genes, namely SLC34A3 and SEPN1, that segregated independently in this family and that have previously been linked to two etiologically different diseases. We assess the increase in chance co-occurrence of rare diseases due to consanguinity, i.e. under circumstances that generally favor linkage mapping of recessive disease, and show that this probability can increase by several orders of magnitudes. We conclude that such potential co-occurrence represents an underestimated risk when analyzing rare or undefined diseases in consanguineous families and should be given more consideration in the clinical and genetic evaluation.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- * E-mail: (DL); (MN)
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Mohammad R. Toliat
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Clemens Kamrath
- Department of Pediatrics, University Medical Faculty Giessen, 35392, Giessen, Germany
| | - Anne Schänzer
- Institute of Neuropathology University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Andreas Hahn
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- * E-mail: (DL); (MN)
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30
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Nato AQ, Chapman NH, Sohi HK, Nguyen HD, Brkanac Z, Wijsman EM. PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers. Bioinformatics 2015; 31:3790-8. [PMID: 26231429 PMCID: PMC4668752 DOI: 10.1093/bioinformatics/btv444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/07/2015] [Accepted: 07/25/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often start with a dense marker panel, a subset of which may be used for linkage analysis to reduce computational burden and to limit linkage disequilibrium between single-nucleotide polymorphisms (SNPs). Programs attempting to select markers for linkage panels exist but lack flexibility. RESULTS We developed a pedigree-based analysis pipeline (PBAP) suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which can handle analyses for small and large pedigrees, typically human, and results can be used with other programs and for downstream analyses. We evaluate and illustrate its features with two real datasets. AVAILABILITY AND IMPLEMENTATION PBAP scripts may be downloaded from http://faculty.washington.edu/wijsman/software.shtml. CONTACT wijsman@uw.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Hiep D Nguyen
- Division of Medical Genetics, Department of Medicine
| | | | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, Department of Biostatistics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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31
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Perez Y, Kadir R, Volodarsky M, Noyman I, Flusser H, Shorer Z, Gradstein L, Birnbaum RY, Birk OS. UNC80 mutation causes a syndrome of hypotonia, severe intellectual disability, dyskinesia and dysmorphism, similar to that caused by mutations in its interacting cation channel NALCN. J Med Genet 2015; 53:397-402. [PMID: 26545877 DOI: 10.1136/jmedgenet-2015-103352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/17/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND A syndrome of profound hypotonia, intellectual disability, intrauterine growth retardation with subsequent failure to thrive, dyskinesia and epilepsy was diagnosed in Bedouin Israeli families. Mild dysmorphism was evident: plagiocephaly, broad forehead with prominent nose, smooth philtrum and congenital esotropia. We set out to decipher the molecular basis of this syndrome. METHODS Genome-wide linkage analysis and fine mapping were done. Whole exome sequencing data were filtered for candidate variants within locus. Validation and segregation of the mutation was assayed via Sanger sequencing. UNC80 expression pattern was analysed through reverse transcription PCR. RESULTS Homozygosity mapping followed by fine mapping identified a 7.5 Mb disease-associated locus (logarithm of odds score 3.5) on chromosome 2. Whole exome and Sanger sequencing identified a single homozygous nonsense mutation within this locus, segregating within the families as expected for recessive heredity and not found in a homozygous state in 150 Bedouin controls: c.151C>T, p.(R51*) in UNC80. CONCLUSIONS The syndrome described is caused by a mutation in UNC80, truncating most of the 3258 amino acids highly conserved encoded protein, that has no known motifs. UNC80 bridges between UNC79 and the cation channel NALCN, enabling NALCN's role in basal Na(+) leak conductance in neurons, essential for neuronal function. The phenotype caused by the UNC80 mutation resembles that previously described for homozygous NALCN mutations.
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Affiliation(s)
- Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rotem Kadir
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michael Volodarsky
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Iris Noyman
- Pediatric Neurology Unit, Division of Pediatrics, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Hagit Flusser
- Zussman Child Development Center, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zamir Shorer
- Pediatric Neurology Unit, Division of Pediatrics, Faculty of Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Faculty of Health Sciences, Soroka Medical Center and Clalit Health Services, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel Genetics Institute, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva, Israel
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32
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Zazo Seco C, Serrão de Castro L, van Nierop J, Morín M, Jhangiani S, Verver E, Schraders M, Maiwald N, Wesdorp M, Venselaar H, Spruijt L, Oostrik J, Schoots J, van Reeuwijk J, Lelieveld S, Huygen P, Insenser M, Admiraal R, Pennings R, Hoefsloot L, Arias-Vásquez A, de Ligt J, Yntema H, Jansen J, Muzny D, Huls G, van Rossum M, Lupski J, Moreno-Pelayo M, Kunst H, Kremer H, Kremer H. Allelic Mutations of KITLG, Encoding KIT Ligand, Cause Asymmetric and Unilateral Hearing Loss and Waardenburg Syndrome Type 2. Am J Hum Genet 2015; 97:647-60. [PMID: 26522471 DOI: 10.1016/j.ajhg.2015.09.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/24/2015] [Indexed: 01/04/2023] Open
Abstract
Linkage analysis combined with whole-exome sequencing in a large family with congenital and stable non-syndromic unilateral and asymmetric hearing loss (NS-UHL/AHL) revealed a heterozygous truncating mutation, c.286_303delinsT (p.Ser96Ter), in KITLG. This mutation co-segregated with NS-UHL/AHL as a dominant trait with reduced penetrance. By screening a panel of probands with NS-UHL/AHL, we found an additional mutation, c.200_202del (p.His67_Cys68delinsArg). In vitro studies revealed that the p.His67_Cys68delinsArg transmembrane isoform of KITLG is not detectable at the cell membrane, supporting pathogenicity. KITLG encodes a ligand for the KIT receptor. Also, KITLG-KIT signaling and MITF are suggested to mutually interact in melanocyte development. Because mutations in MITF are causative of Waardenburg syndrome type 2 (WS2), we screened KITLG in suspected WS2-affected probands. A heterozygous missense mutation, c.310C>G (p.Leu104Val), that segregated with WS2 was identified in a small family. In vitro studies revealed that the p.Leu104Val transmembrane isoform of KITLG is located at the cell membrane, as is wild-type KITLG. However, in culture media of transfected cells, the p.Leu104Val soluble isoform of KITLG was reduced, and no soluble p.His67_Cys68delinsArg and p.Ser96Ter KITLG could be detected. These data suggest that mutations in KITLG associated with NS-UHL/AHL have a loss-of-function effect. We speculate that the mechanism of the mutation underlying WS2 and leading to membrane incorporation and reduced secretion of KITLG occurs via a dominant-negative or gain-of-function effect. Our study unveils different phenotypes associated with KITLG, previously associated with pigmentation abnormalities, and will thereby improve the genetic counseling given to individuals with KITLG variants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hannie Kremer
- Hearing & Genes Division, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands; The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands.
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33
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Ahram DF, Grozdanic SD, Kecova H, Henkes A, Collin RWJ, Kuehn MH. Variants in Nebulin (NEB) Are Linked to the Development of Familial Primary Angle Closure Glaucoma in Basset Hounds. PLoS One 2015; 10:e0126660. [PMID: 25938837 PMCID: PMC4418656 DOI: 10.1371/journal.pone.0126660] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 04/06/2015] [Indexed: 12/12/2022] Open
Abstract
Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip genotyping was carried out in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1 and a locus was mapped to chromosome 19q with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and is syntenic to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, non-synonymous variant in the gene Nebulin (NEB) was found to segregate with PACG which alters a phylogenetically conserved Lysine residue. The association of this variants with PACG was confirmed in a secondary cohort of unrelated Basset Hounds (p = 3.4 × 10-4, OR = 15.3 for homozygosity). Nebulin, a protein that promotes the contractile function of sarcomeres, was found to be prominently expressed in the ciliary muscles of the anterior segment. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG.
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Affiliation(s)
- Dina F. Ahram
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA, United States of America
| | | | - Helga Kecova
- Animal Eye Consultants of Iowa, North Liberty, IA, United States of America
| | - Arjen Henkes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Markus H. Kuehn
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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34
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Kerns SL, Guevara-Aguirre J, Andrew S, Geng J, Guevara C, Guevara-Aguirre M, Guo M, Oddoux C, Shen Y, Zurita A, Rosenfeld RG, Ostrer H, Hwa V, Dauber A. A novel variant in CDKN1C is associated with intrauterine growth restriction, short stature, and early-adulthood-onset diabetes. J Clin Endocrinol Metab 2014; 99:E2117-22. [PMID: 25057881 PMCID: PMC4184067 DOI: 10.1210/jc.2014-1949] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CONTEXT CDKN1C, a cyclin-dependent kinase inhibitor and negative regulator of cellular proliferation, is paternally imprinted and has been shown to regulate β-cell proliferation. CDKN1C mutations are associated with growth disorders, including Beckwith-Wiedemann syndrome and IMAGe syndrome. OBJECTIVE To investigate the genetic basis for a familial disorder characterized by intrauterine growth restriction, short stature, and early-adulthood-onset diabetes. DESIGN, SETTING, AND PARTICIPANTS Genomic DNA samples (15 affected and 26 unaffected from a six-generation pedigree) were analyzed by genome-wide single nucleotide polymorphism arrays, whole exome and Sanger sequencing, and multiplex ligation-dependent probe amplification. MAIN OUTCOME MEASURE(S) Subjects were assessed for height, weight, adrenal gland size, ACTH, diabetes status, and testis volume. Linkage and sequence analyses were performed, and the identified genetic variant was functionally evaluated in reconstitution studies. RESULTS The pedigree followed a paternally imprinted pattern of inheritance, and genetic linkage analysis identified a single significant 2.6-megabase locus on chromosome 11p15, within the imprinting center region 2. Multiplex ligation-dependent probe amplification did not detect copy number variants or methylation abnormalities. Whole exome sequencing revealed a single novel variant in the proliferating cell nuclear antigen-binding region of CDKN1C (c.842G>T, p.R281I) that co-segregated with affected status and, unlike variants found in IMAGe, did not entirely abrogate proliferating cell nuclear antigen binding. Clinical assessments revealed that affected individuals had low testicular volume but normal adrenal function. CONCLUSIONS We report a novel CDKN1C mutation associated with features of IMAGe syndrome, but without adrenal insufficiency or metaphyseal dysplasia, and characterized by early-adulthood-onset diabetes. Our data expand the range of phenotypes observed with CDKN1C defects and suggest that CDKN1C mutations may represent a novel monogenic form of diabetes.
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