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Li J, Wang Q, Yang A, Zhang J. Monoallelic missense variants in MAB21L1 cause a novel autosomal dominant microphthalmia. Ophthalmic Genet 2024:1-7. [PMID: 39016008 DOI: 10.1080/13816810.2024.2378029] [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: 03/23/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
PURPOSE The biallelic variant of MAB21L1 has previously been documented in conjunction with the autosomal recessive cerebellar, ocular, craniofacial, and genital syndrome (COFG). The purpose of this study was to investigate the gene-disease association of MAB21L1 and the newly discovered autosomal dominant (AD) microphthalmia. METHODS We report the presence of an exceptionally rare missense variant in a single allele of the Arg51 codon of MAB21L1 among four individuals from a single family diagnosed with microphthalmia, which suggesting an autosomal dominant inheritance pattern. Subsequently, based on comprehensive literature review, we identified another 13 families that have reported cases of autosomal dominant microphthalmos. RESULTS Genotype-phenotype analysis revealed that patients with a single allele missense variant in MAB21L1 exhibited solely eye abnormalities. This starkly diverged from the clinical presentation of COFG, typified by the concurrent occurrence of ocular and extraocular symptoms stemming from the biallelic variant in MAB21L1. Our findings revealed that the heterozygous pathogenic variant in MAB21L1 resulted in the emergence of autosomal dominant microphthalmia. By combining these genetic and experimental evidence, the clinical validity of MAB21L1 and the emerging autosomal dominant microphthalmia can be regarded as moderate. CONCLUSION In summary, there is sufficient convincing evidence to prove that MAB21L1 is a novel pathogenic gene responsible for autosomal dominant microphthalmia, thus offering valuable insights for precise diagnosis and targeted therapeutic interventions in cases of microphthalmia.
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Affiliation(s)
- Jinli Li
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qin Wang
- Department of Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining City, Shandong, China
| | - Aijun Yang
- Department of Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining City, Shandong, China
| | - Junyu Zhang
- Reproductive Medicine Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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2
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Harkin J, Peña KH, Gomes C, Hernandez M, Lavekar SS, So K, Lentsch K, Feder EM, Morrow S, Huang KC, Tutrow KD, Morris A, Zhang C, Meyer JS. A highly reproducible and efficient method for retinal organoid differentiation from human pluripotent stem cells. Proc Natl Acad Sci U S A 2024; 121:e2317285121. [PMID: 38870053 PMCID: PMC11194494 DOI: 10.1073/pnas.2317285121] [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: 10/09/2023] [Accepted: 05/15/2024] [Indexed: 06/15/2024] Open
Abstract
Human pluripotent stem cell (hPSC)-derived retinal organoids are three-dimensional cellular aggregates that differentiate and self-organize to closely mimic the spatial and temporal patterning of the developing human retina. Retinal organoid models serve as reliable tools for studying human retinogenesis, yet limitations in the efficiency and reproducibility of current retinal organoid differentiation protocols have reduced the use of these models for more high-throughput applications such as disease modeling and drug screening. To address these shortcomings, the current study aimed to standardize prior differentiation protocols to yield a highly reproducible and efficient method for generating retinal organoids. Results demonstrated that through regulation of organoid size and shape using quick reaggregation methods, retinal organoids were highly reproducible compared to more traditional methods. Additionally, the timed activation of BMP signaling within developing cells generated pure populations of retinal organoids at 100% efficiency from multiple widely used cell lines, with the default forebrain fate resulting from the inhibition of BMP signaling. Furthermore, given the ability to direct retinal or forebrain fates at complete purity, mRNA-seq analyses were then utilized to identify some of the earliest transcriptional changes that occur during the specification of these two lineages from a common progenitor. These improved methods also yielded retinal organoids with expedited differentiation timelines when compared to traditional methods. Taken together, the results of this study demonstrate the development of a highly reproducible and minimally variable method for generating retinal organoids suitable for analyzing the earliest stages of human retinal cell fate specification.
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Affiliation(s)
- Jade Harkin
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN46202
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
| | - Kiersten H. Peña
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN46202
| | - Cátia Gomes
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
| | - Melody Hernandez
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
| | - Sailee S. Lavekar
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN46202
| | - Kaman So
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
| | - Kelly Lentsch
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN46202
| | - Elyse M. Feder
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN46202
| | - Sarah Morrow
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
| | - Kang-Chieh Huang
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN46202
| | - Kaylee D. Tutrow
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
| | - Ann Morris
- Department of Biology, University of Kentucky, Lexington, KY40506
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
| | - Jason S. Meyer
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN46202
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN46202
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Harding P, Gore S, Malka S, Rajkumar J, Oluonye N, Moosajee M. Real-world clinical and molecular management of 50 prospective patients with microphthalmia, anophthalmia and/or ocular coloboma. Br J Ophthalmol 2023; 107:1925-1935. [PMID: 36192130 DOI: 10.1136/bjo-2022-321991] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/22/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND/AIMS Microphthalmia, anophthalmia and coloboma (MAC) are clinically and genetically heterogenous rare developmental eye conditions, which contribute to a significant proportion of childhood blindness worldwide. Clear understanding of MAC aetiology and comorbidities is essential to providing patients with appropriate care. However, current management is unstandardised and molecular diagnostic rates remain low, particularly in those with unilateral presentation. To further understanding of clinical and genetic management of patients with MAC, we charted their real-world experience to ascertain optimal management pathways and yield from molecular analysis. METHODS A prospective cohort study of consecutive patients with MAC referred to the ocular genetics service at Moorfields Eye Hospital between 2017-2020. RESULTS Clinical analysis of 50 MAC patients (15 microphthalmia; 2 anophthalmia; 11 coloboma; and 22 mixed) from 44 unrelated families found 44% had additional ocular features (complex) and 34% had systemic involvement, most frequently intellectual/developmental delay (8/17). Molecular analysis of 39 families using targeted gene panels, whole genome sequencing and microarray comparative genomic hybridisation identified genetic causes in, 28% including novel variants in six known MAC genes (SOX2, KMT2D, MAB21L2, ALDH1A3, BCOR and FOXE3), and a molecular diagnostic rate of 33% for both bilateral and unilateral cohorts. New phenotypic associations were found for FOXE3 (bilateral sensorineural hearing loss) and MAB21L2 (unilateral microphthalmia). CONCLUSION This study highlights the importance of thorough clinical and molecular phenotyping of MAC patients to provide appropriate multidisciplinary care. Routine genetic testing for both unilateral and bilateral cases in the clinic may increase diagnostic rates in the future, helping elucidate genotype-phenotype correlations and informing genetic counselling.
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Affiliation(s)
- Philippa Harding
- Institute of Ophthalmology, University College London, London, UK
| | - Sri Gore
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital For Children NHS Trust, London, UK
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Ngozi Oluonye
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital For Children NHS Trust, London, UK
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital For Children NHS Trust, London, UK
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Li Y, Slavik KM, Toyoda HC, Morehouse BR, de Oliveira Mann CC, Elek A, Levy S, Wang Z, Mears KS, Liu J, Kashin D, Guo X, Mass T, Sebé-Pedrós A, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell 2023; 186:3261-3276.e20. [PMID: 37379839 PMCID: PMC10527820 DOI: 10.1016/j.cell.2023.05.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and in vivo analysis in coral and oyster animals, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hunter C Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shani Levy
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Kepler S Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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5
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Trieschmann G, Wilhelm C, Berweck S, Zech M. De novo retinoic acid receptor beta (RARB) variant associated with microphthalmia and dystonia. Eur J Med Genet 2023; 66:104802. [PMID: 37321544 DOI: 10.1016/j.ejmg.2023.104802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Definition of the individual genotypes that cause a Mendelian phenotype is of great importance both to clinical diagnostics and disease characterization. Heterozygous de novo gain-of-function missense variants in RARB are associated with syndromic microphthalmia 12 (MCOPS12), a developmental disorder characterized by eye malformations and variable involvement of other organs. A subset of patients were described with poorly delineated movement disorders. Additionally, RARB bi-allelic loss-of-function variants, inherited from asymptomatic heterozygous carrier parents, have been found in a recessive family with four MCOPS12-affected members. PATIENT/METHODS We used trio whole-exome sequencing to explore the molecular basis of disease in an individual with congenital eye abnormality and movement disorder. All patients with reported RARB variants were reviewed. RESULTS We report on identification of a heterozygous de novo RARB nonsense variant in a girl with microphthalmia and progressive generalized dystonia. Public database entries indicate that the de novo variant is recurrently present in clinically affected subjects but a literature report has not yet been available. CONCLUSIONS We provide the first detailed evidence for a role of dominant RARB truncating alterations in congenital eye-brain disease, expanding the spectrum of MCOPS12-associated mutations. Considered together with the published family with bi-allelic variants, the data suggest manifestation and non-manifestation of disease in relation to almost identical RARB loss-of-function variations, an apparent paradox that is seen in a growing number of human genetic conditions associated with both recessive and dominant inheritance patterns.
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Affiliation(s)
- Gesa Trieschmann
- Specialist Centre for Paediatric Neurology, Neurorehabilitation and Epileptology, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | | | - Steffen Berweck
- Specialist Centre for Paediatric Neurology, Neurorehabilitation and Epileptology, Schoen Clinic Vogtareuth, Vogtareuth, Germany; LMU Hospital, Department of Pediatrics-Dr. von Hauner Childrens's Hospital, Division of Pediatric Neurology and Developmental Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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Seese SE, Muheisen S, Gath N, Gross JM, Semina EV. Identification of HSPA8 as an interacting partner of MAB21L2 and an important factor in eye development. Dev Dyn 2023; 252:510-526. [PMID: 36576422 PMCID: PMC10947772 DOI: 10.1002/dvdy.560] [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: 06/19/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Pathogenic variants in human MAB21L2 result in microphthalmia, anophthalmia, and coloboma. The exact molecular function of MAB21L2 is currently unknown. We conducted a series of yeast two-hybrid (Y2H) experiments to determine protein interactomes of normal human and zebrafish MAB21L2/mab21l2 as well as human disease-associated variant MAB21L2-p.(Arg51Gly) using human adult retina and zebrafish embryo libraries. RESULTS These screens identified klhl31, tnpo1, TNPO2/tnpo2, KLC2/klc2, and SPTBN1/sptbn1 as co-factors of MAB21L2/mab21l2. Several factors, including hspa8 and hspa5, were found to interact with MAB21L2-p.Arg51Gly but not wild-type MAB21L2/mab21l2 in Y2H screens. Further analyses via 1-by-1 Y2H assays, co-immunoprecipitation, and mass spectrometry revealed that both normal and variant MAB21L2 interact with HSPA5 and HSPA8. In situ hybridization detected co-expression of hspa5 and hspa8 with mab21l2 during eye development in zebrafish. Examination of zebrafish mutant hspa8hi138Tg identified reduced hspa8 expression associated with severe ocular developmental defects, including small eye, coloboma, and anterior segment dysgenesis. To investigate the effects of hspa8 deficiency on the mab21l2Arg51_Phe52del allele, corresponding zebrafish double mutants were generated and found to be more severely affected than single mutant lines. CONCLUSION This study identifies heat shock proteins as interacting partners of MAB21L2/mab21l2 and suggests a role for this interaction in vertebrate eye development.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Natalie Gath
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M. Gross
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Elena V. Semina
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
- Children’s Research Institute, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
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7
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Wang P, Wu P, Wang J, Zeng Y, Jiang Y, Wang Y, Li S, Xiao X, Zhang Q. Missense Mutations in MAB21L1: Causation of Novel Autosomal Dominant Ocular BAMD Syndrome. Invest Ophthalmol Vis Sci 2023; 64:19. [PMID: 36892533 PMCID: PMC10010443 DOI: 10.1167/iovs.64.3.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Purpose Biallelic MAB21L1 variants have been reported to cause autosomal recessive cerebellar, ocular, craniofacial, and genital syndrome (COFG), whereas only five heterozygous pathogenic variants have been suspected to cause autosomal dominant (AD) microphthalmia and aniridia in eight families. This study aimed to report an AD ocular syndrome (blepharophimosis plus anterior segment and macular dysgenesis [BAMD]) syndrome based on clinical and genetic findings from patients with monoallelic MAB21L1 pathogenic variants in our cohort and reported cases. Methods Potential pathogenic variants in MAB21L1 were detected from a large in-house exome sequencing dataset. Ocular phenotypes of the patients with potential pathogenic variants in MAB21L1 were summarized, and the genotype-phenotype correlation was analyzed through a comprehensive literature review. Results Three heterozygous missense variants in MAB21L1, predicted to be damaging, were detected in 5 unrelated families, including c.152G>T in 2, c.152G>A in 2, and c.155T>G in one. All were absent from gnomAD. The variants were de novo in two families, transmitted from affected parents to offspring in two families, and with an unknown origin in the other family, demonstrating strong evidence of AD inheritance. All patients revealed similar BAMD phenotypes, including blepharophimosis, anterior segment dysgenesis, and macular dysgenesis. Genotype-phenotype analysis suggested that patients with monoallelic MAB21L1 missense variants had only ocular anomalies (BAMD), whereas patients with biallelic variants presented both ocular and extraocular symptoms. Conclusions Heterozygous pathogenic variants in MAB21L1 account for a new AD BAMD syndrome, which is completely different from COFG caused by homozygous variants in MAB21L1. Nucleotide c.152 is likely a mutation hot spot, and the encoded residue of p.Arg51 might be critical for MAB21L1.
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Affiliation(s)
- Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Pengsen Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yiyan Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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8
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Li Y, Slavik KM, Morehouse BR, de Oliveira Mann CC, Mears K, Liu J, Kashin D, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in animal innate immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529553. [PMID: 36865129 PMCID: PMC9980059 DOI: 10.1101/2023.02.22.529553] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
cGAS (cyclic GMP-AMP synthase) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates the protein STING and downstream immunity. Here we discover cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in animal innate immunity. Building on recent analysis in Drosophila , we use a bioinformatic approach to identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screen of 140 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of alternative nucleotide signals including isomers of cGAMP and cUMP-AMP. Using structural biology, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Together our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M. Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R. Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Kepler Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Lead Contact
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9
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Ge F, Li C, Iqbal S, Muhammad A, Li F, Thafar MA, Yan Z, Worachartcheewan A, Xu X, Song J, Yu DJ. VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Brief Bioinform 2023; 24:6931725. [PMID: 36528806 DOI: 10.1093/bib/bbac535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
Determining the pathogenicity and functional impact (i.e. gain-of-function; GOF or loss-of-function; LOF) of a variant is vital for unraveling the genetic level mechanisms of human diseases. To provide a 'one-stop' framework for the accurate identification of pathogenicity and functional impact of variants, we developed a two-stage deep-learning-based computational solution, termed VPatho, which was trained using a total of 9619 pathogenic GOF/LOF and 138 026 neutral variants curated from various databases. A total number of 138 variant-level, 262 protein-level and 103 genome-level features were extracted for constructing the models of VPatho. The development of VPatho consists of two stages: (i) a random under-sampling multi-scale residual neural network (ResNet) with a newly defined weighted-loss function (RUS-Wg-MSResNet) was proposed to predict variants' pathogenicity on the gnomAD_NV + GOF/LOF dataset; and (ii) an XGBOD model was constructed to predict the functional impact of the given variants. Benchmarking experiments demonstrated that RUS-Wg-MSResNet achieved the highest prediction performance with the weights calculated based on the ratios of neutral versus pathogenic variants. Independent tests showed that both RUS-Wg-MSResNet and XGBOD achieved outstanding performance. Moreover, assessed using variants from the CAGI6 competition, RUS-Wg-MSResNet achieved superior performance compared to state-of-the-art predictors. The fine-trained XGBOD models were further used to blind test the whole LOF data downloaded from gnomAD and accordingly, we identified 31 nonLOF variants that were previously labeled as LOF/uncertain variants. As an implementation of the developed approach, a webserver of VPatho is made publicly available at http://csbio.njust.edu.cn/bioinf/vpatho/ to facilitate community-wide efforts for profiling and prioritizing the query variants with respect to their pathogenicity and functional impact.
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Affiliation(s)
- Fang Ge
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.,School of Computer Science and Information Engineering, Bengbu University, 1866 Caoshan Road, Bengbu, 233030, China
| | - Chen Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shahid Iqbal
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Arif Muhammad
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.,College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Maha A Thafar
- Department of Computer Science, College of Computers and Information Technology, Taif University, P.O.Box 110099, Taif 21944, Saudi Arabia
| | - Zihao Yan
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Apilak Worachartcheewan
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Xiaofeng Xu
- School of Computer and Information, Anhui Polytechnic University, Beijingzhong Road, Wuhu 241000, China
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
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10
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Meng F, Li X, Zhang J, Gao Z, Yang X, Liu Z, Liu Y, Guo T, Wang L, Yang L, Wang Z. Single amino acid variation in MAB21L1 is dominantly associated with congenital eye defects. J Med Genet 2022:jmg-2022-108506. [DOI: 10.1136/jmg-2022-108506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
BackgroundDiagnosis of a genetic disease and determination of the causative molecular lesion rely on the availability of the disease-associated pedigrees. Microphthalmia is a congenital eye defect due to an insufficiently developed visual system; its prevalence is 1–3 in 10 000 live births.ObjectiveWe analysed a pedigree exhibiting autosomal dominant inheritance of microphthalmia to determine the genetic lesion; used AlphaFold2 to predict the changes in the protein’s 3-Dimensional structure; and compared wild-type and variant proteins in cultured cells or Drosophila model was used to explore the cellular or developmental function of the encoded product.ResultsWe identified a novel missense variation, F52L, in MAB21L1 that is absent in population databases and present exclusively in the individuals diagnosed with microphthalmia in this pedigree. Common structural changes were predicted for the disease-associated variants clustered at amino acids 49–52, and these variant products were also predominantly trapped in the cytoplasm of cultured human lens epithelia. To recapitulate its dominant effect in development, we expressed the Drosophila homologue corresponding to MAB21L1F52Land caused malformation of sensory organs.ConclusionMutations at the residues 49–52 of MAB21L1 compromise eye development. We recommend includingMAB21L1in the genetic testing panel for congenital eye disorders.
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11
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Hall HN, Bengani H, Hufnagel RB, Damante G, Ansari M, Marsh JA, Grimes GR, von Kriegsheim A, Moore D, McKie L, Rahmat J, Mio C, Blyth M, Keng WT, Islam L, McEntargart M, Mannens MM, Heyningen VV, Rainger J, Brooks BP, FitzPatrick DR. Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia. PLoS One 2022; 17:e0268149. [PMID: 36413568 PMCID: PMC9681113 DOI: 10.1371/journal.pone.0268149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Classical aniridia is a congenital and progressive panocular disorder almost exclusively caused by heterozygous loss-of-function variants at the PAX6 locus. We report nine individuals from five families with severe aniridia and/or microphthalmia (with no detectable PAX6 mutation) with ultrarare monoallelic missense variants altering the Arg51 codon of MAB21L1. These mutations occurred de novo in 3/5 families, with the remaining families being compatible with autosomal dominant inheritance. Mice engineered to carry the p.Arg51Leu change showed a highly-penetrant optic disc anomaly in heterozygous animals with severe microphthalmia in homozygotes. Substitutions of the same codon (Arg51) in MAB21L2, a close homolog of MAB21L1, cause severe ocular and skeletal malformations in humans and mice. The predicted nucleotidyltransferase function of MAB21L1 could not be demonstrated using purified protein with a variety of nucleotide substrates and oligonucleotide activators. Induced expression of GFP-tagged wildtype and mutant MAB21L1 in human cells caused only modest transcriptional changes. Mass spectrometry of immunoprecipitated protein revealed that both mutant and wildtype MAB21L1 associate with transcription factors that are known regulators of PAX6 (MEIS1, MEIS2 and PBX1) and with poly(A) RNA binding proteins. Arg51 substitutions reduce the association of wild-type MAB21L1 with TBL1XR1, a component of the NCoR complex. We found limited evidence for mutation-specific interactions with MSI2/Musashi-2, an RNA-binding proteins with effects on many different developmental pathways. Given that biallelic loss-of-function variants in MAB21L1 result in a milder eye phenotype we suggest that Arg51-altering monoallelic variants most plausibly perturb eye development via a gain-of-function mechanism.
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Affiliation(s)
- Hildegard Nikki Hall
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert B. Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David Moore
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, United Kingdom
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jamalia Rahmat
- Ophthalmology Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Catia Mio
- Department of Medicine, University of Udine, Udine, Italy
| | - Moira Blyth
- University of Leeds, St. James’s University Hospital, Leeds, United Kingdom
| | - Wee Teik Keng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Lily Islam
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, England
| | - Meriel McEntargart
- Medical Genetics, St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Marcel M. Mannens
- Genome Diagnostics laboratory, Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Veronica Van Heyningen
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Joe Rainger
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian P. Brooks
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - David R. FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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12
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van Heyningen V. A Journey Through Genetics to Biology. Annu Rev Genomics Hum Genet 2022; 23:1-27. [PMID: 35567277 DOI: 10.1146/annurev-genom-010622-095109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but building biological insight was my main goal. The project trajectory was hugely influenced by the evolutionarily conserved nature of the implicated genes and by the pace of progress in genetic technologies. The rich detail of clinical observations, particularly in eye disease, makes humans an excellent model, especially when complemented by the use of multiple other animal species for experimental validation. The contributions of collaborators and rivals also influenced our approach. We are very fortunate to work in this era of unprecedented progress in genetics and genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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13
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Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol 2022; 32:289-303.e6. [PMID: 34793695 PMCID: PMC8792248 DOI: 10.1016/j.cub.2021.10.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/26/2023]
Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Pushpanathan Muthuirulan
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stanley J Neufeld
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Mai P Tran
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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14
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Yamada R, Oguri A, Fujiki K, Shirahige K, Hirate Y, Kanai-Azuma M, Takezoe H, Akimoto Y, Takahashi N, Kanai Y. MAB21L1 modulates gene expression and DNA metabolic processes in the lens placode. Dis Model Mech 2021; 14:dmm049251. [PMID: 34779479 PMCID: PMC8713989 DOI: 10.1242/dmm.049251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Mutations in human MAB21L1 cause aberrations in lens ectoderm morphogenesis and lead to congenital cerebellar, ocular, craniofacial and genital (COFG) syndrome. Murine Mab21l1-null mutations cause severe cell-autonomous defects in lens formation, leading to microphthalmia; therefore, Mab21l1-null mice are used as a mouse model for COFG syndrome. In this study, we investigated the early-onset single-cell-level phenotypes of murine Mab21l1-null lens ectoderms using electron microscopy and single-cell RNA sequencing (scRNA-seq). Electron microscopy and immunohistochemical analyses indicated endoplasmic reticulum stress at the 24- to 26-somite stage in Mab21l1-null lens placodes. scRNA-seq analysis revealed that 131 genes were downregulated and 148 were upregulated in Mab21l1-null lens ectoderms relative to the wild type. We successfully identified 21 lens-specific genes that were downregulated in Mab21l1-null cells, including three key genes involved in lens formation: Pitx3, Maf and Sfrp2. Moreover, gene ontology analysis of the 279 differentially expressed genes indicated enrichment in housekeeping genes associated with DNA/nucleotide metabolism prior to cell death. These findings suggest that MAB21L1 acts as a nuclear factor that modulates not only lens-specific gene expression but also DNA/nucleotide metabolic processes during lens placode formation.
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Affiliation(s)
- Ryuichi Yamada
- Department of Veterinary Anatomy, the University of Tokyo, Tokyo 113-8657, Japan
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
- RNA Company Limited, Tokyo 144-0051, Japan
| | - Akira Oguri
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
| | - Katsunori Fujiki
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | - Yoshikazu Hirate
- Department of Experimental Animal Model for Human Disease, Center for Experimental Animals, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masami Kanai-Azuma
- Department of Experimental Animal Model for Human Disease, Center for Experimental Animals, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | | | - Yoshihiro Akimoto
- Department of Anatomy, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Naoki Takahashi
- Department of Applied Biological Chemistry, the University of Tokyo, Tokyo 113-8657, Japan
- RNA Company Limited, Tokyo 144-0051, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, the University of Tokyo, Tokyo 113-8657, Japan
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15
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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16
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Seese SE, Deml B, Muheisen S, Sorokina E, Semina EV. Genetic disruption of zebrafish mab21l1 reveals a conserved role in eye development and affected pathways. Dev Dyn 2021; 250:1056-1073. [PMID: 33570754 PMCID: PMC8349561 DOI: 10.1002/dvdy.312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The male-abnormal 21 like (MAB21L) genes are important in human ocular development. Homozygous loss of MAB21L1 leads to corneal dystrophy in all affected individuals along with cataracts and buphthalmos in some. The molecular function and downstream pathways of MAB21L factors are largely undefined. RESULTS We generated the first mab21l1 zebrafish mutant carrying a putative loss-of-function allele, c.107delA p.(Lys36Argfs*7). At the final stages of embryonic development, homozygous mab21l1c.107delA fish displayed enlarged anterior chambers and corneal thinning which progressed with age. Additional studies revealed increased cell death in the mutant corneas, transformation of the cornea into a skin-like epithelium, and progressive lens degeneration with development of fibrous masses in the anterior chamber. RNA-seq of wild-type and mutant ocular transcriptomes revealed significant changes in expression of several genes, including irf1a and b, stat1, elf3, krt17, tlr9, and loxa associated with immunity and/or corneal function. Abnormal expression of lysyl oxidases have been previously linked with corneal thinning, fibrosis, and lens defects in mammals, suggesting a role for loxa misexpression in the progressive mab21l1c.107delA eye phenotype. CONCLUSIONS Zebrafish mab21l1 is essential for normal corneal development, similar to human MAB21L1. The identified molecular changes in mab21l1c.107delA mutants provide the first clues about possible affected pathways.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brett Deml
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- PreventionGenetics, Marshfield, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena Sorokina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V. Semina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
- Children's Research Institute, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
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17
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Seese SE, Reis LM, Deml B, Griffith C, Reich A, Jamieson RV, Semina EV. Identification of missense MAB21L1 variants in microphthalmia and aniridia. Hum Mutat 2021; 42:877-890. [PMID: 33973683 PMCID: PMC8238893 DOI: 10.1002/humu.24218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/29/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Microphthalmia, coloboma, and aniridia are congenital ocular phenotypes with a strong genetic component but often unknown cause. We present a likely causative novel variant in MAB21L1, c.152G>T p.(Arg51Leu), in two family members with microphthalmia and aniridia, as well as novel or rare compound heterozygous variants of uncertain significance, c.184C>T p.(Arg62Cys)/c.-68T>C, and c.658G>C p.(Gly220Arg)/c.*529A>G, in two additional probands with microphthalmia, coloboma and/or cataracts. All variants were predicted as damaging by in silico programs. In vitro studies of coding variants revealed normal subcellular localization but variable stability for the corresponding mutant proteins. In vivo complementation assays using the zebrafish mab21l2 Q48Sfs*5 loss-of-function line demonstrated that though overexpression of wild-type MAB21L1 messenger RNA (mRNA) compensated for the loss of mab21l2, none of the coding variant mRNAs produced a statistically significant rescue, with p.(Arg51Leu) showing the highest degree of functional deficiency. Dominant variants in a close homolog of MAB21L1, MAB21L2, have been associated with microphthalmia and/or coloboma and repeatedly involved the same Arg51 residue, further supporting its pathogenicity. The possible role of p.(Arg62Cys) and p.(Gly220Arg) in microphthalmia is similarly supported by the observed functional defects, with or without an additional impact from noncoding MAB21L1 variants identified in each patient. This study suggests a broader spectrum of MAB21L1-associated disease.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Department of Cell Biology, Neurobiology, and AnatomyThe Medical College of WisconsinMilwaukeeWisconsinUSA
| | - Linda M. Reis
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
| | - Brett Deml
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Present address:
PreventionGeneticsMarshfieldWisconsinUSA
| | | | | | - Robyn V. Jamieson
- Eye Genetics Research Unit, Sydney Children's Hospitals Network and Children's Medical Research InstituteUniversity of SydneySydneyNew South WalesAustralia
| | - Elena V. Semina
- Department of Pediatrics and Children's Research Institute, Medical College of WisconsinChildren's of WisconsinMilwaukeeWIUSA
- Department of Cell Biology, Neurobiology, and AnatomyThe Medical College of WisconsinMilwaukeeWisconsinUSA
- Department of Ophthalmology and Visual SciencesMedical College of WisconsinMilwaukeeWisconsinUSA
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18
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Kroll F, Powell GT, Ghosh M, Gestri G, Antinucci P, Hearn TJ, Tunbak H, Lim S, Dennis HW, Fernandez JM, Whitmore D, Dreosti E, Wilson SW, Hoffman EJ, Rihel J. A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes. eLife 2021; 10:e59683. [PMID: 33416493 PMCID: PMC7793621 DOI: 10.7554/elife.59683] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
Hundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week.
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Affiliation(s)
- François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gareth T Powell
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Paride Antinucci
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Timothy J Hearn
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Hande Tunbak
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Sumi Lim
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Harvey W Dennis
- School of Biological Sciences, Faculty of Science, University of BristolBristolUnited Kingdom
| | | | - David Whitmore
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
- Department of Molecular and Cell Biology, James Cook UniversityTownsvilleAustralia
| | - Elena Dreosti
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Ellen J Hoffman
- Child Study Center, Yale School of MedicineNew HavenUnited States
- Department of Neuroscience, Yale School of MedicineNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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19
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Casslén B, Jugård Y, Taha Najim R, Odersjö M, Topa A, Andersson Grönlund M. Visual function and quality of life in children and adolescents with anophthalmia and microphthalmia treated with ocular prosthesis. Acta Ophthalmol 2020; 98:662-670. [PMID: 32356375 DOI: 10.1111/aos.14424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE To evaluate health-related quality of life (HR-QoL), vision-related (VR-)QoL and perceptual visual dysfunction (PVD) among individuals with anophthalmia (A) and microphthalmia (M) treated with ocular prosthesis. METHODS The study comprised 15 individuals (mean age 6.6 years; range 1.7-14.1) with unilateral A or M. Three validated instruments measuring HR-QoL and VR-QoL were used: The Pediatric QoL Inventory (PedsQL), consisting of physical and psychosocial self-report and parent-proxy report (2-18 years); Children's Visual Function Questionnaire (CVFQ); and Effects of Youngsters' Eyesight on Quality of Life (EYE-Q). Perceptual visual dysfunctions (PVDs) were assessed by history taking according to a specific protocol. RESULTS A/M children and their parents showed low HR-QoL scores (PedsQL total score: 66.3; 69.6) compared with controls (83.0; 87.61) (p = 0.0035 and <0.0001, respectively, unpaired t-test). No differences were found between A/M children and parents, but parents tended to underestimate their children's emotional state. A/M children with subnormal visual acuity (VA) for age scored lower in physical health compared with A/M children with normal VA (p = 0.03, Mann-Whitney U-test). No significant VR-QoL differences between A/M children and references or between A/M children with subnormal or normal VA for age were found. More A/M children than controls exhibited PVDs in ≥1 area (7/11 versus 4/118; p < 0.0001, Fisher's exact test). CONCLUSION A/M individuals show poor HR-QoL and increased PVDs. No difference in QoL was found between children and parents, though the children tended to score lower in emotional well-being. A/M children with subnormal VA showed lower physical health score. These problems indicate the necessity of a thorough multidisciplinary assessment and follow-up of children with A/M.
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Affiliation(s)
- Beatrice Casslén
- Department of Clinical Neuroscience Institute of Neuroscience and Physiology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Ylva Jugård
- Department of Ophthalmology Södra Älvsborg Hospital Region Västra Götaland Borås Sweden
| | - Rezhna Taha Najim
- Department of Clinical Neuroscience Institute of Neuroscience and Physiology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Marie Odersjö
- Department of Otolaryngology Sahlgrenska University Hospital Region Västra Götaland Gothenburg Sweden
| | - Alexandra Topa
- Department of Clinical Genetics and Genomics Sahlgrenska University Hospital Region Västra Götaland Gothenburg Sweden
- Department of Laboratory Medicine Institute of Biomedicine Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Marita Andersson Grönlund
- Department of Clinical Neuroscience Institute of Neuroscience and Physiology Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
- Department of Ophthalmology Sahlgrenska University Hospital Region Västra Götaland Mölndal Sweden
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20
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Aubert-Mucca M, Pernin-Grandjean J, Marchasson S, Gaston V, Habib C, Meunier I, Sigaudy S, Kaplan J, Roche O, Denis D, Bitoun P, Haye D, Verloes A, Calvas P, Chassaing N, Plaisancié J. Confirmation of FZD5 implication in a cohort of 50 patients with ocular coloboma. Eur J Hum Genet 2020; 29:131-140. [PMID: 32737437 DOI: 10.1038/s41431-020-0695-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 11/09/2022] Open
Abstract
Defects in optic fissure closure can lead to congenital ocular coloboma. This ocular malformation, often associated with microphthalmia, is described in various clinical forms with different inheritance patterns and genetic heterogeneity. In recent times, the identification of an increased number of genes involved in numerous cellular functions has led to a better understanding in optic fissure closure mechanisms. Nevertheless, most of these genes are also involved in wider eye growth defects such as micro-anophthalmia, questioning the mechanisms controlling both extension and severity of optic fissure closure defects. However, some genes, such as FZD5, have only been so far identified in isolated coloboma. Thus, to estimate the frequency of implication of different ocular genes, we screened a cohort of 50 patients affected by ocular coloboma by using targeted sequencing of 119 genes involved in ocular development. This analysis revealed seven heterozygous (likely) pathogenic variants in RARB, MAB21L2, RBP4, TFAP2A, and FZD5. Surprisingly, three out of the seven variants detected herein were novel disease-causing variants in FZD5 identified in three unrelated families with dominant inheritance. Although molecular diagnosis rate remains relatively low in patients with ocular coloboma (14% (7/50) in this work), these results, however, highlight the importance of genetic screening, especially of FZD5, in such patients. Indeed, in our series, FZD5 variants represent half of the genetic causes, constituting 6% (3/50) of the patients who benefited from a molecular diagnosis. Our findings support the involvement of FZD5 in ocular coloboma and provide clues for screening this gene during current diagnostic procedures.
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Affiliation(s)
- Marion Aubert-Mucca
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | | | | | - Veronique Gaston
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Christophe Habib
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Isabelle Meunier
- Centre de Référence des Maladies Sensorielles Génétiques, Hôpital Gui de Chauliac, Institut de Neurosciences de Montpellier, INSERM U1051, Université de Montpellier, Montpellier, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, AP-HM, CHU Timone Enfants, Marseille, France
| | - Josseline Kaplan
- Laboratoire de Génétique Ophtalmologique, INSERM U1163 Institut Imagine, Paris, France
| | - Olivier Roche
- Département d'Ophtalmologie, IHU Necker-Enfants-Malades, Université Paris-Descartes, Paris, France
| | - Danièle Denis
- Institut de Neurosciences de la Timone (INT), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), Marseille, France
| | - Pierre Bitoun
- Département d'Ophtalmologie, SIDVA 91, Juvisy-sur-Orge, France
| | - Damien Haye
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Alain Verloes
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Patrick Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, UDEAR, Equipe 4, Université Toulouse III, Toulouse, France.,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, UDEAR, Equipe 4, Université Toulouse III, Toulouse, France.,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France
| | - Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France. .,INSERM U1056, UDEAR, Equipe 4, Université Toulouse III, Toulouse, France. .,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, CHU Toulouse, Toulouse, France.
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21
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Eintracht J, Corton M, FitzPatrick D, Moosajee M. CUGC for syndromic microphthalmia including next-generation sequencing-based approaches. Eur J Hum Genet 2020; 28:679-690. [PMID: 31896778 PMCID: PMC7171178 DOI: 10.1038/s41431-019-0565-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 01/29/2023] Open
Affiliation(s)
| | - Marta Corton
- Department of Genetics, IIS-University Hospital Fundación Jiménez Díaz-CIBERER, Madrid, Spain
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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22
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Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Am J Hum Genet 2020; 106:234-245. [PMID: 31928709 DOI: 10.1016/j.ajhg.2019.12.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
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Affiliation(s)
- David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Petracovici
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chongsheng He
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China
| | | | | | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Sofia Douzgou
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Boris Keren
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Marie-Christine Nougues
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | | | - Julien Buratti
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Dustin Baldridge
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA
| | | | | | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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23
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George A, Cogliati T, Brooks BP. Genetics of syndromic ocular coloboma: CHARGE and COACH syndromes. Exp Eye Res 2020; 193:107940. [PMID: 32032630 DOI: 10.1016/j.exer.2020.107940] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Optic fissure closure defects result in uveal coloboma, a potentially blinding condition affecting between 0.5 and 2.6 per 10,000 births that may cause up to 10% of childhood blindness. Uveal coloboma is on a phenotypic continuum with microphthalmia (small eye) and anophthalmia (primordial/no ocular tissue), the so-called MAC spectrum. This review gives a brief overview of the developmental biology behind coloboma and its clinical presentation/spectrum. Special attention will be given to two prominent, syndromic forms of coloboma, namely, CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies/deafness) and COACH (Cerebellar vermis hypoplasia, Oligophrenia, Ataxia, Coloboma, and Hepatic fibrosis) syndromes. Approaches employed to identify genes involved in optic fissure closure in animal models and recent advances in live imaging of zebrafish eye development are also discussed.
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Affiliation(s)
- Aman George
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Tiziana Cogliati
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA.
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24
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Mitani T, Punetha J, Akalin I, Pehlivan D, Dawidziuk M, Coban Akdemir Z, Yilmaz S, Aslan E, Hunter JV, Hijazi H, Grochowski CM, Jhangiani SN, Karaca E, Fatih JM, Iwanowski P, Gambin T, Wlasienko P, Goszczanska-Ciuchta A, Bekiesinska-Figatowska M, Hosseini M, Arzhangi S, Najmabadi H, Rosenfeld JA, Du H, Marafi D, Blaser S, Teitelbaum R, Silver R, Posey JE, Ropers HH, Gibbs RA, Wiszniewski W, Lupski JR, Chitayat D, Kahrizi K, Gawlinski P, Gawlinski P. Bi-allelic Pathogenic Variants in TUBGCP2 Cause Microcephaly and Lissencephaly Spectrum Disorders. Am J Hum Genet 2019; 105:1005-1015. [PMID: 31630790 DOI: 10.1016/j.ajhg.2019.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/13/2019] [Indexed: 10/25/2022] Open
Abstract
Lissencephaly comprises a spectrum of malformations of cortical development. This spectrum includes agyria, pachygyria, and subcortical band heterotopia; each represents anatomical malformations of brain cortical development caused by neuronal migration defects. The molecular etiologies of neuronal migration anomalies are highly enriched for genes encoding microtubules and microtubule-associated proteins, and this enrichment highlights the critical role for these genes in cortical growth and gyrification. Using exome sequencing and family based rare variant analyses, we identified a homozygous variant (c.997C>T [p.Arg333Cys]) in TUBGCP2, encoding gamma-tubulin complex protein 2 (GCP2), in two individuals from a consanguineous family; both individuals presented with microcephaly and developmental delay. GCP2 forms the multiprotein γ-tubulin ring complex (γ-TuRC) together with γ-tubulin and other GCPs to regulate the assembly of microtubules. By querying clinical exome sequencing cases and through GeneMatcher-facilitated collaborations, we found three additional families with bi-allelic variation and similarly affected phenotypes including a homozygous variant (c.1843G>C [p.Ala615Pro]) in two families and compound heterozygous variants consisting of one missense variant (c.889C>T [p.Arg297Cys]) and one splice variant (c.2025-2A>G) in another family. Brain imaging from all five affected individuals revealed varying degrees of cortical malformations including pachygyria and subcortical band heterotopia, presumably caused by disruption of neuronal migration. Our data demonstrate that pathogenic variants in TUBGCP2 cause an autosomal recessive neurodevelopmental trait consisting of a neuronal migration disorder, and our data implicate GCP2 as a core component of γ-TuRC in neuronal migrating cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland.
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25
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Valensi M, Goldman G, Marchant D, Van Den Berghe L, Jonet L, Daruich A, Robert MP, Krejci E, Klein C, Mascarelli F, Versaux-Botteri C, Moulin A, Putterman M, Guimiot F, Molina T, Terris B, Brémond-Gignac D, Behar-Cohen F, Abitbol MM. Sostdc1 is expressed in all major compartments of developing and adult mammalian eyes. Graefes Arch Clin Exp Ophthalmol 2019; 257:2401-2427. [PMID: 31529323 DOI: 10.1007/s00417-019-04462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 01/16/2023] Open
Abstract
PURPOSE This study was conducted in order to study Sostdc1 expression in rat and human developing and adult eyes. METHODS Using the yeast signal sequence trap screening method, we identified the Sostdc1 cDNA encoding a protein secreted by the adult rat retinal pigment epithelium. We determined by in situ hybridization, RT-PCR, immunohistochemistry, and western blot analysis Sostdc1 gene and protein expression in developing and postnatal rat ocular tissue sections. We also investigated Sostdc1 immunohistolocalization in developing and adult human ocular tissues. RESULTS We demonstrated a prominent Sostdc1 gene expression in the developing rat central nervous system (CNS) and eyes at early developmental stages from E10.5 days postconception (dpc) to E13 dpc. Specific Sostdc1 immunostaining was also detected in most adult cells of rat ocular tissue sections. We also identified the rat ocular embryonic compartments characterized by a specific Sostdc1 immunohistostaining and specific Pax6, Sox2, Otx2, and Vsx2 immunohistostaining from embryonic stages E10.5 to E13 dpc. Furthermore, we determined the localization of SOSTDC1 immunoreactivity in ocular tissue sections of developing and adult human eyes. Indeed, we detected SOSTDC1 immunostaining in developing and adult human retinal pigment epithelium (RPE) and neural retina (NR) as well as in several developing and adult human ocular compartments, including the walls of choroidal and scleral vessels. Of utmost importance, we observed a strong SOSTDC1 expression in a pathological ocular specimen of type 2 Peters' anomaly complicated by retinal neovascularization as well in the walls ofother pathological extra-ocular vessels. CONCLUSION: As rat Sostdc1 and human SOSTDC1 are dual antagonists of the Wnt/β-catenin and BMP signaling pathways, these results underscore the potential crucial roles of these pathways and their antagonists, such as Sostdc1 and SOSTDC1, in developing and adult mammalian normal eyes as well as in syndromic and nonsyndromic congenital eye diseases.
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Affiliation(s)
- Maud Valensi
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Gabrielle Goldman
- APHP, Service de Pathologie de L'Hôpital Cochin-Hôtel-Dieu, Université Paris Descartes, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Dominique Marchant
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- Sorbonne Paris Cité, UFR SMBH, Laboratoire Hypoxie et poumons, Université Paris 13, EA 2363, 93017, Bobigny, France
| | - Loïc Van Den Berghe
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- Inserm UMR 1037, CRCT (Cancer Research Center of Toulouse), 31037, Toulouse, France
| | - Laurent Jonet
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Alejandra Daruich
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
| | - Matthieu P Robert
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
- COGnition and Action Group, UMR 8257, CNRS, Université Paris Descartes, Paris, France
| | - Eric Krejci
- COGnition and Action Group, UMR 8257, CNRS, Université Paris Descartes, Paris, France
| | - Christophe Klein
- Centre d'Imagerie Cellulaire et de Cytométrie (CICC), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6, Université Paris Descartes - Paris 5, UMR_S 1138, 75006, Paris, France
| | - Frédéric Mascarelli
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Claudine Versaux-Botteri
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
| | - Alexandre Moulin
- Département de Pathologie, Hôpital Ophtalmique Jules-Gonin , 15, avenue de France, 1004, Lausanne, Switzerland
| | - Marc Putterman
- APHP, Service de Pathologie de l'Hôpital Universitaire Necker-Enfants-Malades, Université Paris Descartes, 149 rue de Sèvres, 75015, Paris, France
| | - Fabien Guimiot
- Unité Fonctionnelle de Foeto-Pathologie, Hôpital Universitaire Robert Debré, 48 Boulevard Serrurier, 75019, Paris, France
| | - Thierry Molina
- APHP, Service de Pathologie de l'Hôpital Universitaire Necker-Enfants-Malades, Université Paris Descartes, 149 rue de Sèvres, 75015, Paris, France
| | - Benoît Terris
- APHP, Service de Pathologie de L'Hôpital Cochin-Hôtel-Dieu, Université Paris Descartes, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Dominique Brémond-Gignac
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France
| | - Francine Behar-Cohen
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France
- AP-HP, Service d'Ophtalmologie, Hôpital Universitaire Cochin-Hôtel-Dieu, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Marc M Abitbol
- Centre de Recherches des Cordeliers, UMR_S INSERM 1138, Equipe 17, Université Paris Descartes, 15 rue de l'école de médecine, 75006, Paris, France.
- AP-HP, Hôpital Universitaire Necker-Enfants-Malades, Service d'Ophtalmologie, 149 rue de Sèvres, 75015, Paris, France.
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Harding P, Moosajee M. The Molecular Basis of Human Anophthalmia and Microphthalmia. J Dev Biol 2019; 7:jdb7030016. [PMID: 31416264 PMCID: PMC6787759 DOI: 10.3390/jdb7030016] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Human eye development is coordinated through an extensive network of genetic signalling pathways. Disruption of key regulatory genes in the early stages of eye development can result in aborted eye formation, resulting in an absent eye (anophthalmia) or a small underdeveloped eye (microphthalmia) phenotype. Anophthalmia and microphthalmia (AM) are part of the same clinical spectrum and have high genetic heterogeneity, with >90 identified associated genes. By understanding the roles of these genes in development, including their temporal expression, the phenotypic variation associated with AM can be better understood, improving diagnosis and management. This review describes the genetic and structural basis of eye development, focusing on the function of key genes known to be associated with AM. In addition, we highlight some promising avenues of research involving multiomic approaches and disease modelling with induced pluripotent stem cell (iPSC) technology, which will aid in developing novel therapies.
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Affiliation(s)
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
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27
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Karaca E, Posey JE, Bostwick B, Liu P, Gezdirici A, Yesil G, Coban Akdemir Z, Bayram Y, Harms FL, Meinecke P, Alawi M, Bacino CA, Sutton VR, Kortüm F, Lupski JR. Biallelic and De Novo Variants in DONSON Reveal a Clinical Spectrum of Cell Cycle-opathies with Microcephaly, Dwarfism and Skeletal Abnormalities. Am J Med Genet A 2019; 179:2056-2066. [PMID: 31407851 DOI: 10.1002/ajmg.a.61315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/10/2019] [Accepted: 07/14/2019] [Indexed: 01/30/2023]
Abstract
Co-occurrence of primordial dwarfism and microcephaly together with particular skeletal findings are seen in a wide range of Mendelian syndromes including microcephaly micromelia syndrome (MMS, OMIM 251230), microcephaly, short stature, and limb abnormalities (MISSLA, OMIM 617604), and microcephalic primordial dwarfisms (MPDs). Genes associated with these syndromes encode proteins that have crucial roles in DNA replication or in other critical steps of the cell cycle that link DNA replication to cell division. We identified four unrelated families with five affected individuals having biallelic or de novo variants in DONSON presenting with a core phenotype of severe short stature (z score < -3 SD), additional skeletal abnormalities, and microcephaly. Two apparently unrelated families with identical homozygous c.631C > T p.(Arg211Cys) variant had clinical features typical of Meier-Gorlin syndrome (MGS), while two siblings with compound heterozygous c.346delG p.(Asp116Ile*62) and c.1349A > G p.(Lys450Arg) variants presented with Seckel-like phenotype. We also identified a de novo c.683G > T p.(Trp228Leu) variant in DONSON in a patient with prominent micrognathia, short stature and hypoplastic femur and tibia, clinically diagnosed with Femoral-Facial syndrome (FFS, OMIM 134780). Biallelic variants in DONSON have been recently described in individuals with microcephalic dwarfism. These studies also demonstrated that DONSON has an essential conserved role in the cell cycle. Here we describe novel biallelic and de novo variants that are associated with MGS, Seckel-like phenotype and FFS, the last of which has not been associated with any disease gene to date.
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Affiliation(s)
- Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Center for Bioinformatics, University of Hamburg, Hamburg, Germany.,Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
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28
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Jolly A, Bayram Y, Turan S, Aycan Z, Tos T, Abali ZY, Hacihamdioglu B, Coban Akdemir ZH, Hijazi H, Bas S, Atay Z, Guran T, Abali S, Bas F, Darendeliler F, Colombo R, Barakat TS, Rinne T, White JJ, Yesil G, Gezdirici A, Gulec EY, Karaca E, Pehlivan D, Jhangiani SN, Muzny DM, Poyrazoglu S, Bereket A, Gibbs RA, Posey JE, Lupski JR. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease. J Clin Endocrinol Metab 2019; 104:3049-3067. [PMID: 31042289 PMCID: PMC6563799 DOI: 10.1210/jc.2019-00248] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
Abstract
CONTEXT Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait. OBJECTIVE To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI. DESIGN, SETTING, AND PARTICIPANTS We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity. RESULTS This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds. CONCLUSIONS ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zehra Aycan
- Department of Pediatric Endocrinology, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Zehra Yavas Abali
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | | | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serpil Bas
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zeynep Atay
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Saygin Abali
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Firdevs Bas
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Darendeliler
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Roberto Colombo
- Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
- Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli University Hospital, Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sukran Poyrazoglu
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Abdullah Bereket
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
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29
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Paine I, Posey JE, Grochowski CM, Jhangiani SN, Rosenheck S, Kleyner R, Marmorale T, Yoon M, Wang K, Robison R, Cappuccio G, Pinelli M, Magli A, Coban Akdemir Z, Hui J, Yeung WL, Wong BKY, Ortega L, Bekheirnia MR, Bierhals T, Hempel M, Johannsen J, Santer R, Aktas D, Alikasifoglu M, Bozdogan S, Aydin H, Karaca E, Bayram Y, Ityel H, Dorschner M, White JJ, Wilichowski E, Wortmann SB, Casella EB, Kitajima JP, Kok F, Monteiro F, Muzny DM, Bamshad M, Gibbs RA, Sutton VR, Van Esch H, Brunetti-Pierri N, Hildebrandt F, Brautbar A, Van den Veyver IB, Glass I, Lessel D, Lyon GJ, Lupski JR. Paralog Studies Augment Gene Discovery: DDX and DHX Genes. Am J Hum Genet 2019; 105:302-316. [PMID: 31256877 PMCID: PMC6698803 DOI: 10.1016/j.ajhg.2019.06.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Members of a paralogous gene family in which variation in one gene is known to cause disease are eight times more likely to also be associated with human disease. Recent studies have elucidated DHX30 and DDX3X as genes for which pathogenic variant alleles are involved in neurodevelopmental disorders. We hypothesized that variants in paralogous genes encoding members of the DExD/H-box RNA helicase superfamily might also underlie developmental delay and/or intellectual disability (DD and/or ID) disease phenotypes. Here we describe 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes. In addition, these individuals exhibit a variety of other tissue and organ system involvement including ocular, outer ear, hearing, cardiac, and kidney tissues. Five individuals with homozygous (one), compound-heterozygous (two), or de novo (two) missense variants in DHX37 were identified by exome sequencing. We identified ten total individuals with missense variants in three other DDX/DHX paralogs: DHX16 (four individuals), DDX54 (three individuals), and DHX34 (three individuals). Most identified variants are rare, predicted to be damaging, and occur at conserved amino acid residues. Taken together, these 15 individuals implicate the DExD/H-box helicases in both dominantly and recessively inherited neurodevelopmental phenotypes and highlight the potential for more than one disease mechanism underlying these disorders.
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Affiliation(s)
- Ingrid Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Rosenheck
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Taylor Marmorale
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Reid Robison
- Utah Foundation for Biomedical Research, Salt Lake City, UT 84107, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Michele Pinelli
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Adriano Magli
- Department of Pediatric Ophthalmology, University of Salerno, 84081 Baronissi SA, Italy
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joannie Hui
- Department of Pediatrics, Prince of Wales Hospital, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai Lan Yeung
- Department of Pediatrics and Adolescent Medicine, Alice Ho Miu Ling Nethersole Hospital, Hong Kong SAR, China
| | - Bibiana K Y Wong
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lucia Ortega
- Medical Genetics Department, Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Section of Pediatric Renal, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics, Texas Children's Hospital, Houston, TX 76104, USA
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Dilek Aktas
- DAMAGEN Genetic Diagnostic Center, 06690 Ankara, Turkey
| | | | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, 01330 Adana, Turkey
| | - Hatip Aydin
- Department of Medical Genetics, Medical Faculty of Namik Kemal University, Tekirdag 59100, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yavuz Bayram
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Hadas Ityel
- Division of Nephrology, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Dorschner
- Center for Precision Diagnostics, University of Washington, Seattle, WA 98195, USA
| | - Janson J White
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Ekkehard Wilichowski
- Department of Pediatrics and Pediatric Neurology, Georg-August-Universität Göttingen, 37075 Göttingen, Germany
| | - Saskia B Wortmann
- Institute of Human Genetics, Technical University München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum Munchen, 85764 Neuherberg, Germany; University Children's Hospital, Paracelsus Medical University, 5020 Salsburg, Austria
| | - Erasmo B Casella
- Children's Institute, Hospital das Clinicas, University of Sao Paulo, 05405-000 Sao Paulo, Brazil
| | | | - Fernando Kok
- Mendelics Genomic Analysis, 04013-000 Sao Paulo, Brazil; Department of Neurology, University of Sao Paulo School of Medicine, 01246-903 Sao Paulo, Brazil
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples "Federico II," 80131 Napoli, Italy; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ariel Brautbar
- Medical Genetics Department, Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ian Glass
- Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, NY 11724, USA; Utah Foundation for Biomedical Research, Salt Lake City, UT 84107, USA; Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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30
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Pehlivan D, Bayram Y, Gunes N, Coban Akdemir Z, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EY, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HM, Radhakrishnan P, Erdem HB, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KM, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet 2019; 105:132-150. [PMID: 31230720 PMCID: PMC6612529 DOI: 10.1016/j.ajhg.2019.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 01/29/2023] Open
Abstract
Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.
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Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Burcu Tabakci
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey
| | - Yavuz Sahin
- Department of Medical Genetics, Necip Fazıl City Hospital, Kahramanmaras 46050, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul 34093, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Ocak
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatice Mutlu Albayrak
- Department of Pediatrics, Division of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55270, Turkey
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Ibrahim Sahin
- Department of Medical Genetics, University of Erzurum, School of Medicine, Erzurum 25240, Turkey
| | - Timur Yildirim
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Ilhan A Bayhan
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Aysegul Bursali
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Zafer Yuksel
- Medical Genetics Clinic, Mersin Women and Children Hospital, Mersin 33330, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Onur Yildiz
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, University of Health Sciences, Van Training and Research Hospital, Van 65130, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri 38080, Turkey
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin 10, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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31
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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32
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Hardy H, Prendergast JG, Patel A, Dutta S, Trejo-Reveles V, Kroeger H, Yung AR, Goodrich LV, Brooks B, Sowden JC, Rainger J. Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential mediator of epithelial fusion. eLife 2019; 8:43877. [PMID: 31162046 PMCID: PMC6606025 DOI: 10.7554/elife.43877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/03/2019] [Indexed: 12/13/2022] Open
Abstract
Epithelial fusion underlies many vital organogenic processes during embryogenesis. Disruptions to these cause a significant number of human birth defects, including ocular coloboma. We provide robust spatial-temporal staging and unique anatomical detail of optic fissure closure (OFC) in the embryonic chick, including evidence for roles of apoptosis and epithelial remodelling. We performed complementary transcriptomic profiling and show that Netrin-1 (NTN1) is precisely expressed in the chick fissure margin during fusion but is immediately downregulated after fusion. We further provide a combination of protein localisation and phenotypic evidence in chick, humans, mice and zebrafish that Netrin-1 has an evolutionarily conserved and essential requirement for OFC, and is likely to have an important role in palate fusion. Our data suggest that NTN1 is a strong candidate locus for human coloboma and other multi-system developmental fusion defects, and show that chick OFC is a powerful model for epithelial fusion research. Our bodies are made of many different groups of cells, which are arranged into tissues that perform specific roles. As tissues form in the embryo they must adopt precise three-dimensional structures, depending on their position in the body. In many cases this involves two edges of tissue fusing together to prevent gaps being present in the final structure. In individuals with a condition called ocular coloboma some of the tissues in the eyes fail to merge together correctly, leading to wide gaps that can severely affect vision. There are currently no treatments available for ocular coloboma and in over 70% of patients the cause of the defect is not known. Identifying new genes that control how tissues fuse may help researchers to find what causes this condition and multiple other tissue fusion defects, and establish whether these may be preventable in the future. Much of what is currently known about how tissues fuse has come from studying mice and zebrafish embryos. Although the extensive genetic tools available in these ‘models’ have proved very useful, both offer only a limited time window for observing tissues as they fuse, and the regions involved are very small. Chick embryos, on the other hand, are much larger than mouse or zebrafish embryos and are easier to access from within their eggs. This led Hardy et al. to investigate whether the developing chick eye could be a more useful model for studying the precise details of how tissues merge. Examining chick embryos revealed that tissues in the base of their eyes fuse between five and eight days after the egg had been fertilised, a comparatively long time compared to existing models. Also, many of the genes that Hardy et al. found switched on in chick eyes as the tissues merged had previously been identified as being essential for tissue fusion in humans. However, several new genes were also shown to be involved in the fusing process. For example, Netrin-1 was important for tissues to fuse in the eyes as well as in other regions of the developing embryo. These findings demonstrate that the chick eye is an excellent new model system to study how tissues fuse in animals. Furthermore, the genes identified by Hardy et al. may help researchers to identify the genetic causes of ocular coloboma and other tissue fusion defects in humans.
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Affiliation(s)
- Holly Hardy
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - James Gd Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Aara Patel
- Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Sunit Dutta
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, United States
| | - Violeta Trejo-Reveles
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Hannah Kroeger
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Andrea R Yung
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Brian Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, United States
| | - Jane C Sowden
- Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Joe Rainger
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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33
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Gath N, Gross JM. Zebrafish mab21l2 mutants possess severe defects in optic cup morphogenesis, lens and cornea development. Dev Dyn 2019; 248:514-529. [PMID: 31037784 DOI: 10.1002/dvdy.44] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mutations in MAB21L2 result in severe ocular defects including microphthalmia, anophthalmia, coloboma, microcornea, and cataracts. The molecular and cellular underpinnings of these defects are unknown, as is the normal cellular function of MAB21L2. Zebrafish mab21l2 au10 mutants possess ocular defects resembling those in humans with MAB21L2 mutations, providing an excellent model to characterize mab21l2 functions during eye development. RESULTS mab21l2 -/- mutants possessed a host of ocular defects including microphthalmia and colobomas as well as small, disorganized lenses and cornea dysgenesis. Decreased proliferation, increased cell death, and defects in marker gene expression were detected in the lens. Cell death in the optic stalk was elevated in mab21l2 -/- mutants and the basement membrane between the edges of the choroid fissure failed to break down. Neuronal differentiation in the retina was normal, however. mab21l2 -/- mutant corneas were disorganized, possessed an increased number of cells, some of which proliferated ectopically, and failed to differentiate the corneal stroma. CONCLUSIONS mab21l2 function is required for morphogenesis and cell survival in the lens and optic cup, and basement membrane breakdown in the choroid fissure. mab21l2 function also regulates proliferation in the lens and cornea; in its absence, the lens is small and mispatterned, and corneal morphogenesis and patterning are also disrupted.
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Affiliation(s)
- Natalie Gath
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jeffrey M Gross
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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34
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An update on the genetics of ocular coloboma. Hum Genet 2019; 138:865-880. [PMID: 31073883 DOI: 10.1007/s00439-019-02019-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Ocular coloboma is an uncommon, but often severe, sight-threatening condition that can be identified from birth. This congenital anomaly is thought to be caused by maldevelopment of optic fissure closure during early eye morphogenesis. It has been causally linked to both inherited (genetic) and environmental influences. In particular, as a consequence of work to identify genetic causes of coloboma, new molecular pathways that control optic fissure closure have now been identified. Many more regulatory mechanisms still await better understanding to inform on the development of potential therapies for patients with this malformation. This review provides an update of known coloboma genes, the pathways they influence and how best to manage the condition. In the age of precision medicine, determining the underlying genetic cause in any given patient is of high importance.
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35
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Sghari S, Gunhaga L. Temporal Requirement of Mab21l2 During Eye Development in Chick Reveals Stage-Dependent Functions for Retinogenesis. Invest Ophthalmol Vis Sci 2019; 59:3869-3878. [PMID: 30073347 DOI: 10.1167/iovs.18-24236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Different missense mutations in the single exon gene Mab21l2 have been identified in unrelated families with various bilateral eye malformations, including microphthalmia, anophthalmia, and coloboma, but the molecular function of Mab21l2 during eye development still remains largely unknown. Methods We have established an in vivo Mab21l2-deficient eye development model in chick, by using a Mab21l2 RNA interference construct that we electroporated in ovo in prospective retinal cells. In addition, we designed a Mab21l2 gain-of-function electroporation vector. Mab21l2-modulated retinas were analyzed on consecutive sections in terms of morphology, and molecular markers for apoptosis, cell proliferation, and retinogenesis. Results Our Mab21l2-deficient chick model mimics human ocular phenotypes. When Mab21l2 is downregulated prior to optic vesicle formation, the embryos develop anophthalmia, and Mab21l2 inhibition by optic cup stages results in a microphthalmic colobomatous phenotype. Our results show that inhibition of Mab21l2 affects cell proliferation, cell cycle exit, and the expression of Atoh7/Ath5, NeuroD4/Ath3, Isl1, Pax6, AP-2α, and Prox1. In addition, Mab21l2 overexpression hampers cell cycle exit and differentiation of retinal progenitor cells (RPCs). Conclusions Our results highlight the importance of a regulated temporal expression of Mab21l2 during eye development: At early stages, Mab21l2 is required to maintain RPC proliferation and expansion of cell number; before retinogenesis, a decrease in Mab21l2 expression in proliferating RPCs is required for cell cycle exit and differentiation; during retinogenesis, Mab21l2 is chronologically upregulated in RGCs, followed by differentiated horizontal and amacrine cells and cone photoreceptor cells.
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Affiliation(s)
- Soufien Sghari
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Lena Gunhaga
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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36
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Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
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37
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Genetics of anophthalmia and microphthalmia. Part 1: Non-syndromic anophthalmia/microphthalmia. Hum Genet 2019; 138:799-830. [PMID: 30762128 DOI: 10.1007/s00439-019-01977-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.
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38
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Blackburn PR, Chacon-Camacho OF, Ortiz-González XR, Reyes M, Lopez-Uriarte GA, Zarei S, Bhoj EJ, Perez-Solorzano S, Vaubel RA, Murphree MI, Nava J, Cortes-Gonzalez V, Parisi JE, Villanueva-Mendoza C, Tirado-Torres IG, Li D, Klee EW, Pichurin PN, Zenteno JC. Extension of the mutational and clinical spectrum of SOX2 related disorders: Description of six new cases and a novel association with suprasellar teratoma. Am J Med Genet A 2018; 176:2710-2719. [PMID: 30450772 DOI: 10.1002/ajmg.a.40644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 01/05/2023]
Abstract
SOX2 is a transcription factor that is essential for maintenance of pluripotency and has several conserved roles in early embryonic development. Heterozygous loss-of-function variants in SOX2 are identified in approximately 40% of all cases of bilateral anophthalmia/micropthalmia (A/M). Increasingly SOX2 mutation-positive patients without major eye findings, but with a range of other developmental disorders including autism, mild to moderate intellectual disability with or without structural brain changes, esophageal atresia, urogenital anomalies, and endocrinopathy are being reported, suggesting that the clinical phenotype associated with SOX2 loss is much broader than previously appreciated. In this report we describe six new cases, four of which carry novel pathogenic SOX2 variants. Four cases presented with bilateral anophthalmia in addition to extraocular involvement. Another individual presented with only unilateral anophthalmia. One individual did not have any eye findings but presented with a suprasellar teratoma in infancy and was found to have the recurrent c.70del20 mutation in SOX2 (c.70_89del, p.Asn24Argfs*65). This is this first time this tumor type has been reported in the context of a de novo SOX2 mutation. Notably, individuals with hypothalamic hamartomas and slow-growing hypothalamo-pituitary tumors have been reported previously, but it is still unclear how SOX2 loss contributes to their formation.
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Affiliation(s)
- Patrick R Blackburn
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Health Sciences Research, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Oscar F Chacon-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Xilma R Ortiz-González
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mariana Reyes
- Department of Genetics, Hospital "Dr. Luis Sánchez Bulnes", Asociación para Evitar la Ceguera en México, Mexico City, Mexico
| | - Graciela A Lopez-Uriarte
- Genetics Department, University Hospital "Dr. José Eleuterio González" and Medical School, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Shabnam Zarei
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sofia Perez-Solorzano
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Rachael A Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jessica Nava
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Vianney Cortes-Gonzalez
- Department of Genetics, Hospital "Dr. Luis Sánchez Bulnes", Asociación para Evitar la Ceguera en México, Mexico City, Mexico
| | - Joseph E Parisi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Cristina Villanueva-Mendoza
- Department of Genetics, Hospital "Dr. Luis Sánchez Bulnes", Asociación para Evitar la Ceguera en México, Mexico City, Mexico
| | - Iris G Tirado-Torres
- Genetics Department, University Hospital "Dr. José Eleuterio González" and Medical School, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Health Sciences Research, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Juan C Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
- Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
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39
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Tsang SW, Guo Y, Chan LH, Huang Y, Chow KL. Generation and characterization of pathogenic Mab21l2(R51C) mouse model. Genesis 2018; 56:e23261. [PMID: 30375740 DOI: 10.1002/dvg.23261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
MAB21L2(R51C) is one of the five documented MAB21L2 mutations in human patients with bilateral eye malformations identified via whole exome sequencing. In addition to the eye abnormality, patients with MAB21L2 R51C/+ mutation also have skeletal dysplasia and intellectual disability. To evaluate the pathology of this mutant allele systematically in understanding the functional role of MAB21L2 in human development, we introduce the R51C mutation into the mouse genome by CRISPR/Cas9 system to generate a mouse model for detailed characterization. The Mab21l2 R51C/+ mice have eyeless phenotype and skeletal abnormalities. Micro-computed tomography (micro-CT) analysis showed the Mab21l2 R51C/+ mice have no eye balls but with two abnormal tissues underneath the brain. Histological analysis revealed that the early eye development in the mutant embryos is interrupted. In addition, Mab21l2 R51C/+ mice also have joint fusion phenotype; the humerus is fused with radius, whereas femur is fused with tibia. Limbs in the mutant animals are distinctly shorter than the wild type; and deltoid tuberosities in humeri are absent in these Mab21l2 R51C/+ mice. In summary, we showed that our Mab21l2 R51C/+ mutant mice have recapitulated the pathological features in eye and bone of human patients. Further analyses of the mutant phenotype with molecular markers will provide insight on how MAB21L2 guides the optic differentiation and skeletogenesis, revealing specific underlying pathogenic mechanism of the MAB21L2(R51C) mutation.
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Affiliation(s)
- Shun-Wa Tsang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yanjiang Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Long-Hei Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yingyu Huang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - King L Chow
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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40
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Rad A, Altunoglu U, Miller R, Maroofian R, James KN, Çağlayan AO, Najafi M, Stanley V, Boustany RM, Yeşil G, Sahebzamani A, Ercan-Sencicek G, Saeidi K, Wu K, Bauer P, Bakey Z, Gleeson JG, Hauser N, Gunel M, Kayserili H, Schmidts M. MAB21L1 loss of function causes a syndromic neurodevelopmental disorder with distinctive cerebellar, ocular, cranio facial and genital features (COFG syndrome). J Med Genet 2018; 56:332-339. [PMID: 30487245 PMCID: PMC6581149 DOI: 10.1136/jmedgenet-2018-105623] [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: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Putative nucleotidyltransferase MAB21L1 is a member of an evolutionarily well-conserved family of the male abnormal 21 (MAB21)-like proteins. Little is known about the biochemical function of the protein; however, prior studies have shown essential roles for several aspects of embryonic development including the eye, midbrain, neural tube and reproductive organs. OBJECTIVE A homozygous truncating variant in MAB21L1 has recently been described in a male affected by intellectual disability, scrotal agenesis, ophthalmological anomalies, cerebellar hypoplasia and facial dysmorphism. We employed a combination of exome sequencing and homozygosity mapping to identify the underlying genetic cause in subjects with similar phenotypic features descending from five unrelated consanguineous families. RESULTS We identified four homozygous MAB21L1 loss of function variants (p.Glu281fs*20, p.Arg287Glufs*14 p.Tyr280* and p.Ser93Serfs*48) and one missense variant (p.Gln233Pro) in 10 affected individuals from 5 consanguineous families with a distinctive autosomal recessive neurodevelopmental syndrome. Cardinal features of this syndrome include a characteristic facial gestalt, corneal dystrophy, hairy nipples, underdeveloped labioscrotal folds and scrotum/scrotal agenesis as well as cerebellar hypoplasia with ataxia and variable microcephaly. CONCLUSION This report defines an ultrarare but clinically recognisable Cerebello-Oculo-Facio-Genital syndrome associated with recessive MAB21L1 variants. Additionally, our findings further support the critical role of MAB21L1 in cerebellum, lens, genitalia and as craniofacial morphogenesis.
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Affiliation(s)
- Abolfazl Rad
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey
| | - Rebecca Miller
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's, University of London, London, UK
| | - Kiely N James
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA.,Medical Genetics Department, Bilim University School of Medicine, İstanbul, Turkey
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Rose-Mary Boustany
- Department of Pediatrics and Adolescent Medicine, Neurogenetics Program and Division of Pediatric Neurology, American University of Beirut Medical Center Special Kids Clinic, Beirut, Lebanon.,Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Gözde Yeşil
- Medical Genetics Department, Bezmi Alem University School of Medicine, Istanbul, Turkey
| | - Afsaneh Sahebzamani
- Paediatric and Genetic Counselling Center, Kerman Welfare Organization, Kerman, Iran
| | - Gülhan Ercan-Sencicek
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kolsoum Saeidi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Department of Medical Genetics, Kerman University of Medical Sciences, Kerman, Iran
| | - Kaman Wu
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Zeineb Bakey
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, California, USA
| | - Natalie Hauser
- Inova Cardiovascular Genomics Clinic, Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - Murat Gunel
- Department of Neurosurgery, Program on Neurogenetics, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Hulya Kayserili
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine (KUSoM), İstanbul, Turkey
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Nijmegen, The Netherlands.,Pediatrics Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
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41
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Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC. Quantifying the contribution of recessive coding variation to developmental disorders. Science 2018; 362:1161-1164. [PMID: 30409806 DOI: 10.1126/science.aar6731] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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Affiliation(s)
- Hilary C Martin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Great Ormond Street Hospital for Children, National Health Service (NHS) Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Rebecca McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Mark Sanderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James D Stephenson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carla P Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juliet Handsaker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mari Niemi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Joanna Kaplanis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth J Radford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - John Dean
- Department of Genetics, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Rachel Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Alice Hulbert
- Cheshire and Merseyside Clinical Genetic Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - Katie Johnson
- Department of Clinical Genetics, City Hospital Campus, Hucknall Road, Nottingham NG5 1PB, UK
| | - Dhavendra Kumar
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew Bassett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Research, Innovation, Learning and Development (RILD), Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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42
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Slavotinek A. Genetics of anophthalmia and microphthalmia. Part 2: Syndromes associated with anophthalmia-microphthalmia. Hum Genet 2018; 138:831-846. [PMID: 30374660 DOI: 10.1007/s00439-018-1949-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 10/20/2018] [Indexed: 12/12/2022]
Abstract
As new genes for A/M are identified in the genomic era, the number of syndromes associated with A/M has greatly expanded. In this review, we provide a brief synopsis of the clinical presentation and molecular genetic etiology of previously characterized pathways involved in A/M, including the Sex-determining region Y-box 2 (SOX2), Orthodenticle Homeobox 2 (OTX2) and Paired box protein-6 (PAX6) genes, and the Stimulated by retinoic acid gene 6 homolog (STRA6), Aldehyde Dehydrogenase 1 Family Member A3 (ALDH1A3), and RA Receptor Beta (RARβ) genes that are involved in retinoic acid synthesis. Less common genetic causes of A/M, including genes involved in BMP signaling [Bone Morphogenetic Protein 4 (BMP4), Bone Morphogenetic Protein 7 (BMP7) and SPARC-related modular calcium-binding protein 1 (SMOC1)], genes involved in the mitochondrial respiratory chain complex [Holocytochrome c-type synthase (HCCS), Cytochrome C Oxidase Subunit 7B (COX7B), and NADH:Ubiquinone Oxidoreductase subunit B11 (NDUFB11)], the BCL-6 corepressor gene (BCOR), Yes-Associated Protein 1 (YAP1) and Transcription Factor AP-2 Alpha (TFAP2α), are more briefly discussed. We also review several recently described genes and pathways associated with A/M, including Smoothened (SMO) that is involved in Sonic hedgehog (SHH) signaling, Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) and Solute carrier family 25 member 24 (SLC25A24), emphasizing phenotype-genotype correlations and shared pathways where relevant.
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Affiliation(s)
- Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco Room RH384C, 1550 4th St, San Francisco, CA, 94143-2711, USA.
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43
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Ocular Manifestations of a Novel Proximal 19p13.3 Microdeletion. Case Rep Genet 2018; 2018:2492437. [PMID: 29854496 PMCID: PMC5952563 DOI: 10.1155/2018/2492437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/19/2018] [Accepted: 03/26/2018] [Indexed: 11/17/2022] Open
Abstract
Microdeletions at 19p13.3 are rarely reported in the medical literature with significant phenotypic variability. Among the reported cases, common clinical manifestations have included developmental delay, facial dysmorphism, and hypotonia. Herein we described a child with a de novo 19p13.3 microdeletion, proximal to the reported cases of 19p13.3 microdeletion/duplication, with ocular manifestations of bilateral ocular colobomata complicated with microphthalmos and cataract, associated with short stature. This case highlights the phenotypic heterogeneity of deletions in the 19p13.3 region.
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44
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Mutation of IPO13 causes recessive ocular coloboma, microphthalmia, and cataract. Exp Mol Med 2018; 50:1-11. [PMID: 29700284 PMCID: PMC5938035 DOI: 10.1038/s12276-018-0079-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 11/12/2022] Open
Abstract
Ocular coloboma is a developmental structural defect of the eye that often occurs as complex ocular anomalies. However, its genetic etiology remains largely unexplored. Here we report the identification of mutation (c.331C>T, p.R111C) in the IPO13 gene in a consanguineous family with ocular coloboma, microphthalmia, and cataract by a combination of whole-exome sequencing and homozygosity mapping. IPO13 encodes an importin-B family protein and has been proven to be associated with the pathogenesis of coloboma and microphthalmia. We found that Ipo13 was expressed in the cornea, sclera, lens, and retina in mice. Additionally, the mRNA expression level of Ipo13 decreased significantly in the patient compared with its expression in a healthy individual. Morpholino-oligonucleotide-induced knockdown of ipo13 in zebrafish caused dose-dependent microphthalmia and coloboma, which is highly similar to the ocular phenotypes in the patient. Moreover, both visual motor response and optokinetic response were impaired severely. Notably, these ocular phenotypes in ipo13-deficient zebrafish could be rescued remarkably by full-length ipo13 mRNA, suggesting that the phenotypes observed in zebrafish were due to insufficient ipo13 function. Altogether, our findings demonstrate, for the first time, a new role of IPO13 in eye morphogenesis and that loss of function of IPO13 could lead to ocular coloboma, microphthalmia, and cataract in humans and zebrafish. In-depth genomic analysis of the family of a young man with severe visual impairment reveals a new gene involved in eye development. Ocular coloboma encompasses various hereditary disorders in which the eyes form improperly. Many of the underlying genetic factors remain unidentified. Researchers led by Zi-Bing Jin at Wenzhou Medical University in China sequenced the genes of 28-year-old man with a recessive form of ocular coloboma. By comparing these genetic data against equivalent genome sequences from his healthy parents, Jin’s team identified a gene called IPO13 as the culprit. IPO13 has not been linked to human disease before, but the researchers demonstrated that switching off IPO13 expression in zebrafish embryos gave rise to underdeveloped eyes with defects in the iris and cornea. These findings give clinicians another potential indicator for early diagnosis of ocular coloboma.
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45
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Phenotypic expansion illuminates multilocus pathogenic variation. Genet Med 2018; 20:1528-1537. [PMID: 29790871 PMCID: PMC6450542 DOI: 10.1038/gim.2018.33] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022] Open
Abstract
Purpose: Multilocus variation, pathogenic variants in two or more disease
genes, can potentially explain the underlying genetic basis for apparent
phenotypic expansion in cases for which the observed clinical features
extend beyond those reported in association with a “known”
disease gene. Methods: Analyses focused on 106 patients, 19 for which apparent phenotypic
expansion was previously attributed to variation at known disease genes. We
performed a retrospective computational re-analysis of whole exome
sequencing data using stringent Variant Call File filtering criteria to
determine whether molecular diagnoses involving additional disease loci
might explain the observed expanded phenotypes. Results: Multilocus variation was identified in 31.6% (6/19) of families with
phenotypic expansion and 2.3% (2/87) without phenotypic expansion.
Intrafamilial clinical variability within 2 families was explained by
multilocus variation identified in the more severely affected sibling. Conclusions: Our findings underscore the role of multiple rare variants at
different loci in the etiology of genetically and clinically heterogeneous
cohorts. Intrafamilial phenotypic and genotypic variability allowed a
dissection of genotype-phenotype relationships in 2 families. Our data
emphasize the critical role of the clinician in diagnostic genomic analyses
and demonstrate that apparent phenotypic expansion may represent blended
phenotypes resulting from pathogenic variation at more than one locus.
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46
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Patel N, Khan AO, Alsahli S, Abdel-Salam G, Nowilaty SR, Mansour AM, Nabil A, Al-Owain M, Sogati S, Salih MA, Kamal AM, Alsharif H, Alsaif HS, Alzahrani SS, Abdulwahab F, Ibrahim N, Hashem M, Faquih T, Shah ZA, Abouelhoda M, Monies D, Dasouki M, Shaheen R, Wakil SM, Aldahmesh MA, Alkuraya FS. Genetic investigation of 93 families with microphthalmia or posterior microphthalmos. Clin Genet 2018; 93:1210-1222. [PMID: 29450879 DOI: 10.1111/cge.13239] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/12/2018] [Accepted: 02/12/2018] [Indexed: 01/24/2023]
Abstract
Microphthalmia is a developmental eye defect that is highly variable in severity and in its potential for systemic association. Despite the discovery of many disease genes in microphthalmia, at least 50% of patients remain undiagnosed genetically. Here, we describe a cohort of 147 patients (93 families) from our highly consanguineous population with various forms of microphthalmia (including the distinct entity of posterior microphthalmos) that were investigated using a next-generation sequencing multi-gene panel (i-panel) as well as whole exome sequencing and molecular karyotyping. A potentially causal mutation was identified in the majority of the cohort with microphthalmia (61%) and posterior microphthalmos (82%). The identified mutations (55 point mutations, 15 of which are novel) spanned 24 known disease genes, some of which have not or only very rarely been linked to microphthalmia (PAX6, SLC18A2, DSC3 and CNKSR1). Our study has also identified interesting candidate variants in 2 genes that have not been linked to human diseases (MYO10 and ZNF219), which we present here as novel candidates for microphthalmia. In addition to revealing novel phenotypic aspects of microphthalmia, this study expands its allelic and locus heterogeneity and highlights the need for expanded testing of patients with this condition.
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Affiliation(s)
- N Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - A O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - S Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | | | - S R Nowilaty
- Vitreo-retinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - A M Mansour
- Department of Ophthalmology, American University of Beirut, Beirut, Lebanon
| | - A Nabil
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - S Sogati
- Department of Medical Genetics, King Fahad General Hospital, Jeddah, Saudi Arabia
| | - M A Salih
- Division of Pediatrics Neurology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - A M Kamal
- Department of Ophthalmology, Cairo University, Cairo, Egypt
| | - H Alsharif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - H S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - S S Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - F Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - N Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - M Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - T Faquih
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Z A Shah
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - M Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - D Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - M Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - R Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - S M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - M A Aldahmesh
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - F S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.,Saudi Human Genome Project, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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47
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Genes and pathways in optic fissure closure. Semin Cell Dev Biol 2017; 91:55-65. [PMID: 29198497 DOI: 10.1016/j.semcdb.2017.10.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/29/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
Embryonic development of the vertebrate eye begins with the formation of an optic vesicle which folds inwards to form a double-layered optic cup with a fissure on the ventral surface, known as the optic fissure. Closure of the optic fissure is essential for subsequent growth and development of the eye. A defect in this process can leave a gap in the iris, retina or optic nerve, known as a coloboma, which can lead to severe visual impairment. This review brings together current information about genes and pathways regulating fissure closure from human coloboma patients and animal models. It focuses especially on current understanding of the morphological changes and processes of epithelial remodelling occurring at the fissure margins.
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48
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Nguyen D, Yamada R, Yoshimitsu N, Oguri A, Kojima T, Takahashi N. Involvement of the Mab21l1 gene in calvarial osteogenesis. Differentiation 2017; 98:70-78. [PMID: 29156428 DOI: 10.1016/j.diff.2017.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/19/2017] [Accepted: 11/08/2017] [Indexed: 01/09/2023]
Abstract
The Mab-21 gene family is crucial for animal development. A deficiency in the Mab-21 genes associates with several defects, including skeletal malformation in mice and humans. In this study, we observed that mice lacking Mab21l1 displayed an unclosed fontanelle, suggesting impaired calvarial bone development. Cells isolated from the calvaria of these mice showed a greater osteoblast differentiation potential as evidenced by the abundance of mineralized bone nodules and higher expression levels of osteogenic markers than wild-type cells. Mab21l1-/- osteoblasts also expressed higher levels of adipocyte genes and interferon-regulated genes at early stages of osteogenesis. Rankl/Opg expression levels were also higher in Mab21l1-/- osteoblasts than in wild-type cells. These data suggest that Mab21l1 is involved in either the regulation of mesenchymal cell proliferation and differentiation or the balance between bone formation and resorption. An alteration in these regulatory machineries, therefore, may lead to insufficient bone formation, causing the bone phenotype in Mab21l1-/- mice.
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Affiliation(s)
- Dan Nguyen
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryuichi Yamada
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan; RNA Company Limited, 7-25-7, Nishikamata, Ota-ku, Tokyo 114-8661, Japan
| | - Nodoka Yoshimitsu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Oguri
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Kojima
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan; RNA Company Limited, 7-25-7, Nishikamata, Ota-ku, Tokyo 114-8661, Japan
| | - Naoki Takahashi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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49
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Cvekl A, Zhang X. Signaling and Gene Regulatory Networks in Mammalian Lens Development. Trends Genet 2017; 33:677-702. [PMID: 28867048 DOI: 10.1016/j.tig.2017.08.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 11/16/2022]
Abstract
Ocular lens development represents an advantageous system in which to study regulatory mechanisms governing cell fate decisions, extracellular signaling, cell and tissue organization, and the underlying gene regulatory networks. Spatiotemporally regulated domains of BMP, FGF, and other signaling molecules in late gastrula-early neurula stage embryos generate the border region between the neural plate and non-neural ectoderm from which multiple cell types, including lens progenitor cells, emerge and undergo initial tissue formation. Extracellular signaling and DNA-binding transcription factors govern lens and optic cup morphogenesis. Pax6, c-Maf, Hsf4, Prox1, Sox1, and a few additional factors regulate the expression of the lens structural proteins, the crystallins. Extensive crosstalk between a diverse array of signaling pathways controls the complexity and order of lens morphogenetic processes and lens transparency.
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Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Xin Zhang
- Departments of Ophthalmology, Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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50
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Rainger J, Williamson KA, Soares DC, Truch J, Kurian D, Gillessen‐Kaesbach G, Seawright A, Prendergast J, Halachev M, Wheeler A, McTeir L, Gill AC, van Heyningen V, Davey MG, FitzPatrick DR. A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma. Hum Mutat 2017; 38:942-946. [PMID: 28493397 PMCID: PMC5518294 DOI: 10.1002/humu.23246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 11/17/2022]
Abstract
Ocular coloboma (OC) is a defect in optic fissure closure and is a common cause of severe congenital visual impairment. Bilateral OC is primarily genetically determined and shows marked locus heterogeneity. Whole-exome sequencing (WES) was used to analyze 12 trios (child affected with OC and both unaffected parents). This identified de novo mutations in 10 different genes in eight probands. Three of these genes encoded proteins associated with actin cytoskeleton dynamics: ACTG1, TWF1, and LCP1. Proband-only WES identified a second unrelated individual with isolated OC carrying the same ACTG1 allele, encoding p.(Pro70Leu). Both individuals have normal neurodevelopment with no extra-ocular signs of Baraitser-Winter syndrome. We found this mutant protein to be incapable of incorporation into F-actin. The LCP1 and TWF1 variants each resulted in only minor disturbance of actin interactions, and no further plausibly causative variants were identified in these genes on resequencing 380 unrelated individuals with OC.
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Affiliation(s)
- Joe Rainger
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | - Kathleen A Williamson
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - Dinesh C Soares
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - Julia Truch
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - Dominic Kurian
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | | | - Anne Seawright
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - James Prendergast
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | - Mihail Halachev
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - Ann Wheeler
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
| | - Lynn McTeir
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | - Andrew C Gill
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | | | - Megan G Davey
- The Roslin Institute and R(D)SVSUniversity of EdinburghEaster Bush CampusMidlothianUK
| | - UK10K
- Wellcome Trust Sanger InstituteGenome CampusHinxtonCambridgeshireUK
| | - David R FitzPatrick
- MRC Human Genetics Unit, IGMMUniversity of EdinburghWestern General HospitalEdinburghUK
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