751
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Bonafont J, Mencía Á, García M, Torres R, Rodríguez S, Carretero M, Chacón-Solano E, Modamio-Høybjør S, Marinas L, León C, Escamez MJ, Hausser I, Del Río M, Murillas R, Larcher F. Clinically Relevant Correction of Recessive Dystrophic Epidermolysis Bullosa by Dual sgRNA CRISPR/Cas9-Mediated Gene Editing. Mol Ther 2019; 27:986-998. [PMID: 30930113 PMCID: PMC6520462 DOI: 10.1016/j.ymthe.2019.03.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022] Open
Abstract
Gene editing constitutes a novel approach for precisely correcting disease-causing gene mutations. Frameshift mutations in COL7A1 causing recessive dystrophic epidermolysis bullosa are amenable to open reading frame restoration by non-homologous end joining repair-based approaches. Efficient targeted deletion of faulty COL7A1 exons in polyclonal patient keratinocytes would enable the translation of this therapeutic strategy to the clinic. In this study, using a dual single-guide RNA (sgRNA)-guided Cas9 nuclease delivered as a ribonucleoprotein complex through electroporation, we have achieved very efficient targeted deletion of COL7A1 exon 80 in recessive dystrophic epidermolysis bullosa (RDEB) patient keratinocytes carrying a highly prevalent frameshift mutation. This ex vivo non-viral approach rendered a large proportion of corrected cells producing a functional collagen VII variant. The effective targeting of the epidermal stem cell population enabled long-term regeneration of a properly adhesive skin upon grafting onto immunodeficient mice. A safety assessment by next-generation sequencing (NGS) analysis of potential off-target sites did not reveal any unintended nuclease activity. Our strategy could potentially be extended to a large number of COL7A1 mutation-bearing exons within the long collagenous domain of this gene, opening the way to precision medicine for RDEB.
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Affiliation(s)
- Jose Bonafont
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Ángeles Mencía
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Marta García
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Raúl Torres
- Molecular Cytogenetics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sandra Rodríguez
- Molecular Cytogenetics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marta Carretero
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Esteban Chacón-Solano
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Silvia Modamio-Høybjør
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Lucía Marinas
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain
| | - Carlos León
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - María J Escamez
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Ingrid Hausser
- Institute of Pathology IPH, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcela Del Río
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Rodolfo Murillas
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.
| | - Fernando Larcher
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.
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752
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Goncharova M, Pshenichnikova O, Luchinina Y, Pustovoit Y, Karpova I, Surin V. Molecular genetic study of acute intermittent porphyria in Russia: HMBS gene mutation spectrum and problem of penetrance. Clin Genet 2019; 96:91-97. [PMID: 31044425 DOI: 10.1111/cge.13558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/22/2019] [Accepted: 04/28/2019] [Indexed: 01/21/2023]
Abstract
Acute intermittent porphyria (AIP) is the most common and severe form of porphyrias. This is a dominant inherited disorder with low penetrance, caused by mutations in gene coding hydroxymethylbilane synthase (HMBS). We present the results of our long-term genetic study of AIP patients and their relatives (N = 153 and 302, respectively). We detected 88 HMBS gene mutations, 24 of which never described before. To identify additional factors conditioning AIP manifestation, we carried out whole exome sequencing on the group of AIP patients (N = 6). Mutation spectra of different patients virtually did not overlap. In 5 out of 6 patients, we found defects in genes regulating nervous system (UNC13A, ALG8, FBXO38, AGRN, DOK7, SCN4A). As usually acute AIP attacks have various neurological symptoms, we proposed a hypothesis of possible contribution of mutations in such genes in AIP manifestation.
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Affiliation(s)
- Maria Goncharova
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Olesya Pshenichnikova
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Yulia Luchinina
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Yaroslav Pustovoit
- Department of Chemotherapy of Hematological Diseases and Intensive Care, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Irina Karpova
- Biochemical Group of Centralised Clinical Diagnostic Laboratory, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
| | - Vadim Surin
- Laboratory of Gene Engineering, National Medical Research Center for Hematology of Ministry of Health, Moscow, Russia
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753
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Novel loss-of-function variants of TRAPPC2 manifesting X-linked spondyloepiphyseal dysplasia tarda: report of two cases. BMC MEDICAL GENETICS 2019; 20:70. [PMID: 31053099 PMCID: PMC6500034 DOI: 10.1186/s12881-019-0802-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/08/2019] [Indexed: 11/10/2022]
Abstract
Background X-linked spondyloepiphyseal dysplasia tarda (SEDT-XL) is a skeletal disorder characterized by defective structures of vertebral bodies and/or of epiphyses of the long bones, resulting in moderately short stature and early joint degeneration. TRAPPC2 gene, which is important for collagen secretion, has been reported as causative for SEDT-XL. Case presentation Here, we report two variants of TRAPPC2 gene of SEDT-XL patients, a missense variant of start codon, c.1A > T, and a deletion variant, c.40delG. To understand molecular consequence of the variants, we establish an in vitro gene expression assay system and demonstrate that both mutated genes are transcribed, but are not properly translated, indicative of the pathogenic nature of those TRAPPC2 variants. Conclusions In the current study, we provide additional experimental data showing that loss-of-function TRAPPC2 variants are probably causative for SEDT-XL phenotype. These findings further contribute to the understanding the clinical picture related to TRAPPC2 gene.
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754
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Zhou WZ, Zhang J, Li Z, Lin X, Li J, Wang S, Yang C, Wu Q, Ye AY, Wang M, Wang D, Pu TZ, Wu YY, Wei L. Targeted resequencing of 358 candidate genes for autism spectrum disorder in a Chinese cohort reveals diagnostic potential and genotype-phenotype correlations. Hum Mutat 2019; 40:801-815. [PMID: 30763456 PMCID: PMC6593842 DOI: 10.1002/humu.23724] [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: 08/23/2018] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 12/30/2022]
Abstract
Autism spectrum disorder (ASD) is a childhood neuropsychiatric disorder with a complex genetic architecture. The diagnostic potential of a targeted panel of ASD genes has only been evaluated in small cohorts to date and is especially understudied in the Chinese population. Here, we designed a capture panel with 358 genes (111 syndromic and 247 nonsyndromic) for ASD and sequenced a Chinese cohort of 539 cases evaluated with the Autism Diagnostic Interview‐Revised (ADI‐R) and the Autism Diagnostic Observation Schedule (ADOS) as well as 512 controls. ASD cases were found to carry significantly more ultra‐rare functional variants than controls. A subset of 78 syndromic and 54 nonsyndromic genes was the most significantly associated and should be given high priority in the future screening of ASD patients. Pathogenic and likely pathogenic variants were detected in 9.5% of cases. Variants in SHANK3 and SHANK2 were the most frequent, especially in females, and occurred in 1.2% of cases. Duplications of 15q11–13 were detected in 0.8% of cases. Variants in CNTNAP2 and MEF2C were correlated with epilepsy/tics in cases. Our findings reveal the diagnostic potential of ASD genetic panel testing and new insights regarding the variant spectrum. Genotype–phenotype correlations may facilitate the diagnosis and management of ASD.
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Affiliation(s)
- Wei-Zhen Zhou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Diagnostic Laboratory Service, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Zhang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ziyi Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaojing Lin
- National Institute of Biological Sciences, Beijing, China
| | - Jiarui Li
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Changhong Yang
- National Institute of Biological Sciences, Beijing, China.,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qixi Wu
- School of Life Sciences, Peking University, Beijing, China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Meng Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Dandan Wang
- National Institute of Biological Sciences, Beijing, China
| | | | - Yu-Yu Wu
- Yuning Psychiatry Clinic, Taipei, Taiwan
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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755
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Hammond N, Munkacsi AB, Sturley SL. The complexity of a monogenic neurodegenerative disease: More than two decades of therapeutic driven research into Niemann-Pick type C disease. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1109-1123. [PMID: 31002946 DOI: 10.1016/j.bbalip.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/31/2019] [Accepted: 04/06/2019] [Indexed: 12/17/2022]
Abstract
Niemann-Pick type C (NP-C) disease is a rare and fatal neurodegenerative disease typified by aberrations in intracellular lipid transport. Cholesterol and other lipids accumulate in the late endosome/lysosome of all diseased cells thereby causing neuronal and visceral atrophy. A cure for NP-C remains elusive despite the extensive molecular advances emanating from the identification of the primary genetic defect in 1997. Penetration of the blood-brain barrier and efficacy in the viscera are prerequisites for effective therapy, however the rarity of NP-C disease is the major impediment to progress. Disease diagnosis is challenging and establishment of appropriate test populations for clinical trials difficult. Fortunately, disease models that span the diversity of microbial and metazoan life have been utilized to advance the quest for a therapy. The complexity of lipid storage in this disorder and in the model systems, has led to multiple theories on the primary disease mechanism and consequently numerous and varied proposed interventions. Here, we conduct an evaluation of these studies.
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Affiliation(s)
- Natalie Hammond
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Andrew B Munkacsi
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
| | - Stephen L Sturley
- Department of Biology, Barnard College-Columbia University, New York, NY 10027, United States of America.
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756
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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757
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Mathorne SW, Sørensen K, Fagerberg C, Bode M, Hertz JM. A novel PDGFRB sequence variant in a family with a mild form of primary familial brain calcification: a case report and a review of the literature. BMC Neurol 2019; 19:60. [PMID: 30979360 PMCID: PMC6460731 DOI: 10.1186/s12883-019-1292-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/31/2019] [Indexed: 12/14/2022] Open
Abstract
Background Primary familial brain calcification is a rare autosomal dominant or recessive neurodegenerative disease, characterized by bilateral brain calcifications in different areas of the brain. It is a clinically heterogeneous disease and patients are reported to exhibit a wide spectrum of neurological and psychiatric symptoms. Mutations in five genes have been identified so far including SLC20A2, PDGFRB, PDGFB, XPR1, and MYORG. PDGFRB encodes the platelet-derived growth factor receptor-beta, and is expressed in neurons, vascular smooth muscle cells and pericytes. Patients with a PDGFRB mutation seem to exhibit a milder phenotype and milder brain calcification on brain imaging than patients with SLC20A2 and PDGFB mutations. However, this is based on a few observations so far. Case presentation We present a Danish family with bilateral brain calcifications and mild clinical symptoms of primary familial brain calcification, segregating with a novel PDGFRB sequence variant: c.1834G > A; p.(Gly612Arg), detected by whole exome sequencing. The variant results in physiochemical changes at the amino acid level, and affects a highly conserved nucleotide as well as amino acid. It is located in the tyrosine kinase domain of PDGFRβ. Segregation analysis and in silico analyses predicted the missense variant to be disease causing. Conclusion Our study confirms that PDGFRB mutation carriers in general have a mild clinical phenotype, and basal ganglia calcifications can be detected by a CT scan, also in asymptomatic mutation carriers.
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Affiliation(s)
- Stine Westergaard Mathorne
- Department of Clinical Genetics, Odense University Hospital, J. B. Winsløvs Vej 4, DK-5000, Odense, Denmark
| | - Kristina Sørensen
- Department of Clinical Genetics, Odense University Hospital, J. B. Winsløvs Vej 4, DK-5000, Odense, Denmark
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, J. B. Winsløvs Vej 4, DK-5000, Odense, Denmark
| | - Matthias Bode
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, J. B. Winsløvs Vej 4, DK-5000, Odense, Denmark. .,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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758
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Zeeshan S, Xiong R, Liang BT, Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants. Brief Bioinform 2019; 21:885-905. [PMID: 30972412 DOI: 10.1093/bib/bbz038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.
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Affiliation(s)
- Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Bruce T Liang
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA.,Pat and Jim Calhoun Cardiology Center, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
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759
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Kloth K, Synofzik M, Kernstock C, Schimpf-Linzenbold S, Schuettauf F, Neu A, Wissinger B, Weisschuh N. Novel likely pathogenic variants in TMEM126A identified in non-syndromic autosomal recessive optic atrophy: two case reports. BMC MEDICAL GENETICS 2019; 20:62. [PMID: 30961538 PMCID: PMC6454730 DOI: 10.1186/s12881-019-0795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/29/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Reports on autosomal recessive optic atrophy (arOA) are sparse and so far, only one gene has been specifically associated with non-syndromic arOA, namely TMEM126A. To date, all reports of pathogenic TMEM126A variants are from affected individuals of Maghrebian origin, who all carry an identical nonsense variant. Here we report two novel variants in the TMEM126A gene from non-Maghreb individuals, both found in affected individuals with an arOA phenotype. CASE PRESENTATION We report three affected individuals from two families. The proband of family A, a 24-year-old Turkish woman, was diagnosed with visual loss in early childhood but a diagnosis of optic atrophy was only made at 14 years. A diagnostic gene panel revealed a splice donor variant (c.86 + 2 T > C) in homozygous state in the TMEM126A gene. Analysis of this variant based on RNA from whole blood revealed a single aberrant transcript lacking exon 2, presumably representing a functional null allele. Two siblings from family B, a 16-year old Iraqi girl and her 14-year old brother, were diagnosed with optic atrophy in early childhood. A missense variant p.(S36 L) in the TMEM126A gene was identified in homozygous state in a gene panel-based diagnostic setting in both siblings. This missense variant is ultra rare in the general population, affects a highly evolutionarily conserved amino acid and segregates with the disease within the family. The three probands reported in this study had a relatively mild clinical course without any evidence of a syndromic (e.g. neurological) comorbidity, which is in line with previous studies. CONCLUSIONS We provide additional evidence for the implication of biallelic pathogenic TMEM126A variants in arOA. Our findings extend both the mutational spectrum and geographic presence of TMEM126A in arOA. Screening of the entire gene should be considered in affected individuals presenting with features resembling arOA and also from non-Maghrebian descent.
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Affiliation(s)
- Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Christoph Kernstock
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Frank Schuettauf
- Department of Ophthalmology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bernd Wissinger
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Nicole Weisschuh
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
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760
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Maroilley T, Tarailo-Graovac M. Uncovering Missing Heritability in Rare Diseases. Genes (Basel) 2019; 10:E275. [PMID: 30987386 PMCID: PMC6523881 DOI: 10.3390/genes10040275] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
The problem of 'missing heritability' affects both common and rare diseases hindering: discovery, diagnosis, and patient care. The 'missing heritability' concept has been mainly associated with common and complex diseases where promising modern technological advances, like genome-wide association studies (GWAS), were unable to uncover the complete genetic mechanism of the disease/trait. Although rare diseases (RDs) have low prevalence individually, collectively they are common. Furthermore, multi-level genetic and phenotypic complexity when combined with the individual rarity of these conditions poses an important challenge in the quest to identify causative genetic changes in RD patients. In recent years, high throughput sequencing has accelerated discovery and diagnosis in RDs. However, despite the several-fold increase (from ~10% using traditional to ~40% using genome-wide genetic testing) in finding genetic causes of these diseases in RD patients, as is the case in common diseases-the majority of RDs are also facing the 'missing heritability' problem. This review outlines the key role of high throughput sequencing in uncovering genetics behind RDs, with a particular focus on genome sequencing. We review current advances and challenges of sequencing technologies, bioinformatics approaches, and resources.
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Affiliation(s)
- Tatiana Maroilley
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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761
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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762
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Debus JD, Milting H, Brodehl A, Kassner A, Anselmetti D, Gummert J, Gaertner-Rommel A. In vitro analysis of arrhythmogenic cardiomyopathy associated desmoglein-2 (DSG2) mutations reveals diverse glycosylation patterns. J Mol Cell Cardiol 2019; 129:303-313. [DOI: 10.1016/j.yjmcc.2019.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/06/2019] [Accepted: 03/14/2019] [Indexed: 12/12/2022]
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763
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Wu C, Devkota B, Evans P, Zhao X, Baker SW, Niazi R, Cao K, Gonzalez MA, Jayaraman P, Conlin LK, Krock BL, Deardorff MA, Spinner NB, Krantz ID, Santani AB, Tayoun ANA, Sarmady M. Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach. Eur J Hum Genet 2019; 27:612-620. [PMID: 30626929 PMCID: PMC6460638 DOI: 10.1038/s41431-018-0328-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/10/2018] [Accepted: 12/11/2018] [Indexed: 01/26/2023] Open
Abstract
Clinical exome sequencing (CES) has become the preferred diagnostic platform for complex pediatric disorders with suspected monogenic etiologies. Despite rapid advancements, the major challenge still resides in identifying the casual variants among the thousands of variants detected during CES testing, and thus establishing a molecular diagnosis. To improve the clinical exome diagnostic efficiency, we developed Phenoxome, a robust phenotype-driven model that adopts a network-based approach to facilitate automated variant prioritization. Phenoxome dissects the phenotypic manifestation of a patient in concert with their genomic profile to filter and then prioritize variants that are likely to affect the function of the gene (potentially pathogenic variants). To validate our method, we have compiled a clinical cohort of 105 positive patient samples that represent a wide range of genetic heterogeneity. Phenoxome identifies the causative variants within the top 5, 10, or 25 candidates in more than 50%, 71%, or 88% of these exomes, respectively. Furthermore, we show that our method is optimized for clinical testing by outperforming the current state-of-art method. We have demonstrated the performance of Phenoxome using a clinical cohort and showed that it enables rapid and accurate interpretation of clinical exomes. Phenoxome is available at https://phenoxome.chop.edu/ .
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Affiliation(s)
- Chao Wu
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Perry Evans
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rojeen Niazi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael A Gonzalez
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pushkala Jayaraman
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryan L Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Deardorff
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Roberts individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Roberts individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Avni B Santani
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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764
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Zastrow DB, Kohler JN, Bonner D, Reuter CM, Fernandez L, Grove ME, Fisk DG, Yang Y, Eng CM, Ward PA, Bick D, Worthey EA, Fisher PG, Ashley EA, Bernstein JA, Wheeler MT. A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. J Genet Couns 2019; 28:213-228. [PMID: 30964584 PMCID: PMC7385984 DOI: 10.1002/jgc4.1119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/11/2022]
Abstract
There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.
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Affiliation(s)
- Diane B Zastrow
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Chloe M Reuter
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Megan E Grove
- Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Stanford, California
| | | | | | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Neurology, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Clinical Genomics Program, Stanford Health Care, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
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765
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Farr M, Ferreira S, Al-Dilaimi A, Bögeholz S, Goesmann A, Kalinowski J, Knabbe C, Faber L, Oliveira JP, Rudolph V. Fabry disease: Detection of Alu-mediated exon duplication by NGS. Mol Cell Probes 2019; 45:79-83. [PMID: 30936019 DOI: 10.1016/j.mcp.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/25/2022]
Abstract
Monogenetic diseases can be analyzed routinely by targeted DNA sequencing. If causative variants are not found, complementary methods like RNA sequencing or analysis of copy number variations by multiplex ligation-dependent probe amplification have to be considered. In the latter, especially exonic duplications or deletions can be detected, but the precise sites of mutations remain unclear. As we demonstrate in this casuistic report of Fabry disease, next-generation sequencing (NGS) of a long-range PCR product can identify the recombination site directly and illuminate the underlying molecular mechanism.
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Affiliation(s)
- Martin Farr
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany.
| | - Susana Ferreira
- Unidade de Genética, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal; i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Arwa Al-Dilaimi
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Sonja Bögeholz
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Cornelius Knabbe
- Institute for Laboratory and Transfusion Medicine, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Lothar Faber
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - João Paulo Oliveira
- Unidade de Genética, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal; i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal; Serviço de Genética Médica, Centro Hospitalar Universitário de São João, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Volker Rudolph
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
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766
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Systematic evaluation of gene variants linked to hearing loss based on allele frequency threshold and filtering allele frequency. Sci Rep 2019; 9:4583. [PMID: 30872718 PMCID: PMC6418148 DOI: 10.1038/s41598-019-41068-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/25/2019] [Indexed: 02/02/2023] Open
Abstract
As the number of genes identified for linkage to hearing loss has been increasing and more public databases have become available, we aimed to systematically evaluate all variants reported for nonsyndromic hearing loss (NSHL) based on their allele frequencies (AFs) in the general population. Among the 3,549 variants in 97 NSHL genes reported as pathogenic/likely pathogenic in ClinVar and HGMD, 1,618 were found in public databases (gnomAD, ExAC, EVS, and 1000G). To evaluate the pathogenicity of these variants, we employed AF thresholds and NSHL-optimized ACMG guidelines. AF thresholds were determined using a high-resolution variant frequency framework and Hardy-Weinberg equilibrium calculation: 0.6% and 0.1% for recessive and dominant genes, respectively. Filtering AFs of variants linked to NSHL were obtained based on AFs reported in gnomAD and ExAC. We found that 48 variants in 23 genes had filtering AFs above the suggested thresholds and assumed that these variants might be benign based on their filtering AFs. 47 variants, except for one notorious high-frequency GJB2 mutation (c.109G > A; p.Val37Ile), were confirmed to be benign/likely benign by the NSHL-optimized ACMG guidelines. The proposed systematic approach will aid in precise evaluation of NSHL variant pathogenicity in the context of filtering AFs, AF thresholds, and NSHL-specific ACMG guidelines, thus improving NSHL diagnostics.
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767
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Wheway G, Mitchison HM. Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. Front Genet 2019; 10:127. [PMID: 30915099 PMCID: PMC6421331 DOI: 10.3389/fgene.2019.00127] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/05/2019] [Indexed: 01/11/2023] Open
Abstract
Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.
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Affiliation(s)
- Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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768
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Shi Z, Xin H, Tian D, Lian J, Wang J, Liu G, Ran R, Shi S, Zhang Z, Shi Y, Deng Y, Hou C, Chen Y. Modeling human point mutation diseases in
Xenopus tropicalis
with a modified CRISPR/Cas9 system. FASEB J 2019; 33:6962-6968. [DOI: 10.1096/fj.201802661r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zhaoying Shi
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Huhu Xin
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Dandan Tian
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Jingru Lian
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Jianhui Wang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Guanghui Liu
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Rensen Ran
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Songyuan Shi
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Zixuan Zhang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Yu Shi
- Department of Clinical LaboratoryChildren's Hospital of Chongqing Medical UniversityChongqingChina
- Ministry of Education Key Laboratory of Child Development and DisordersChildren's Hospital of Chongqing Medical UniversityChongqingChina
- Chongqing Key Laboratory of PediatricsChildren's Hospital of Chongqing Medical UniversityChongqingChina
- Chongqing Key Laboratory of Translational Medical Research in Cognitive DevelopmentLearning and Memory DisordersChildren's Hospital of Chongqing Medical UniversityChongqingChina
| | - Yi Deng
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
| | - Chunhui Hou
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Yonglong Chen
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouthern University of Science and TechnologyShenzhenChina
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769
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Xu H, Wang B, Ono M, Kagita A, Fujii K, Sasakawa N, Ueda T, Gee P, Nishikawa M, Nomura M, Kitaoka F, Takahashi T, Okita K, Yoshida Y, Kaneko S, Hotta A. Targeted Disruption of HLA Genes via CRISPR-Cas9 Generates iPSCs with Enhanced Immune Compatibility. Cell Stem Cell 2019; 24:566-578.e7. [PMID: 30853558 DOI: 10.1016/j.stem.2019.02.005] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) have strong potential in regenerative medicine applications; however, immune rejection caused by HLA mismatching is a concern. B2M gene knockout and HLA-homozygous iPSC stocks can address this issue, but the former approach may induce NK cell activity and fail to present antigens, and it is challenging to recruit rare donors for the latter method. Here, we show two genome-editing strategies for making immunocompatible donor iPSCs. First, we generated HLA pseudo-homozygous iPSCs with allele-specific editing of HLA heterozygous iPSCs. Second, we generated HLA-C-retained iPSCs by disrupting both HLA-A and -B alleles to suppress the NK cell response while maintaining antigen presentation. HLA-C-retained iPSCs could evade T cells and NK cells in vitro and in vivo. We estimated that 12 lines of HLA-C-retained iPSCs combined with HLA-class II knockout are immunologically compatible with >90% of the world's population, greatly facilitating iPSC-based regenerative medicine applications.
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Affiliation(s)
- Huaigeng Xu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bo Wang
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Miyuki Ono
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Akihiro Kagita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kaho Fujii
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Noriko Sasakawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Tatsuki Ueda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Peter Gee
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Fumiyo Kitaoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shin Kaneko
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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770
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Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet 2019; 104:466-483. [PMID: 30827497 PMCID: PMC6407525 DOI: 10.1016/j.ajhg.2019.01.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Gene-panel and whole-exome analyses are now standard methodologies for mutation detection in Mendelian disease. However, the diagnostic yield achieved is at best 50%, leaving the genetic basis for disease unsolved in many individuals. New approaches are thus needed to narrow the diagnostic gap. Whole-genome sequencing is one potential strategy, but it currently has variant-interpretation challenges, particularly for non-coding changes. In this study we focus on transcriptome analysis, specifically total RNA sequencing (RNA-seq), by using monogenetic neuromuscular disorders as proof of principle. We examined a cohort of 25 exome and/or panel "negative" cases and provided genetic resolution in 36% (9/25). Causative mutations were identified in coding and non-coding exons, as well as in intronic regions, and the mutational pathomechanisms included transcriptional repression, exon skipping, and intron inclusion. We address a key barrier of transcriptome-based diagnostics: the need for source material with disease-representative expression patterns. We establish that blood-based RNA-seq is not adequate for neuromuscular diagnostics, whereas myotubes generated by transdifferentiation from an individual's fibroblasts accurately reflect the muscle transcriptome and faithfully reveal disease-causing mutations. Our work confirms that RNA-seq can greatly improve diagnostic yield in genetically unresolved cases of Mendelian disease, defines strengths and challenges of the technology, and demonstrates the suitability of cell models for RNA-based diagnostics. Our data set the stage for development of RNA-seq as a powerful clinical diagnostic tool that can be applied to the large population of individuals with undiagnosed, rare diseases and provide a framework for establishing minimally invasive strategies for doing so.
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Affiliation(s)
- Hernan D Gonorazky
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Viswateja Nelakuditi
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Pouria Mashouri
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peiqui Wang
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dennis Kao
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Krish Ohri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Katherine D Mathews
- Departments of Pediatrics and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Andres N Osorio
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Hospital Universitari Sant Joan de Deu, Barcelona 08950, Spain; Center for the Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona 08950, Spain
| | - David Villanova
- GenomicTales Parc de la Mola, 10, AD700 Escaldes-Engordany, Andorra
| | - Dwi U Kemaladewi
- Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michael Brudno
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - James J Dowling
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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771
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Doubková M, Staňo Kozubík K, Radová L, Pešová M, Trizuljak J, Pál K, Svobodová K, Réblová K, Svozilová H, Vrzalová Z, Pospíšilová Š, Doubek M. A novel germline mutation of the SFTPA1 gene in familial interstitial pneumonia. Hum Genome Var 2019; 6:12. [PMID: 30854216 PMCID: PMC6399245 DOI: 10.1038/s41439-019-0044-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/03/2019] [Accepted: 02/03/2019] [Indexed: 12/11/2022] Open
Abstract
Different genes related to alveolar stability have been associated with familial interstitial pneumonia (FIP). Here, we report a novel, rare SFTPA1 variant in a family with idiopathic interstitial pneumonia (IIP). We performed whole-exome sequencing on germline DNA samples from four members of one family; three of them showed signs of pulmonary fibrosis (idiopathic interstitial pneumonia) with autosomal-dominant inheritance. A heterozygous single nucleotide variant c.532 G > A in the SFTPA1 gene has been identified. This variant encodes the substitution p.(Val178Met), localized within the carbohydrate recognition domain of surfactant protein A and segregates with the genes causing idiopathic interstitial pneumonia. This rare variant has not been previously reported. We also analyzed the detected sequence variant in the protein structure in silico. The replacement of valine by the larger methionine inside the protein may cause a disruption in the protein structure. The c.532 G > A variant was further validated using Sanger sequencing of the amplicons, confirming the diagnosis in all symptomatic family members. Moreover, this variant was also found by Sanger sequencing in one other symptomatic family member and one young asymptomatic family member. The autosomal-dominant inheritance, the family history of IIP, and the evidence of a mutation occurring in part of the SFTPA1 gene all suggest a novel variant that causes FIP. Researchers have identified a novel mutation that causes inheritable and ultimately deadly scarring of the tiny air sacs in the lungs, the alveoli. In familial interstitial pneumonia (FIP), alveoli are scarred and stiffened by inflammation, not by bacterial infection as the word ‘pneumonia’ usually indicates. Michael Doubek at University Hospital and Central European Institute of Technology, Brno, Czech Republic and co-workers investigated a suspected case of FIP following the early death of one family member. Sequencing the genomes of other family members revealed that they shared a mutation in a protein that keeps alveoli moist, aiding oxygen absorption. Computer analysis showed that the mutation probably changed the protein’s shape, preventing it from functioning. Identifying mutations that cause FIP will help provide proactive treatment for family members who are at risk but not yet showing symptoms.
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Affiliation(s)
- Martina Doubková
- 1Department of Pneumology and Phtiseology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Kateřina Staňo Kozubík
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Lenka Radová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pešová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Trizuljak
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Karol Pál
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Klára Svobodová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Réblová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Svozilová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Zuzana Vrzalová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Šárka Pospíšilová
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
| | - Michael Doubek
- 2Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,3Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Brno, Czech Republic
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772
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Khan AO. Recessive pediatric-onset cone-rod dysfunction or dominant maculopathy in a consanguineous family harboring the peripherin mutation p.Arg220Gln. Ophthalmic Genet 2019; 40:60-63. [PMID: 30822235 DOI: 10.1080/13816810.2019.1579346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
PURPOSE Heterozygous peripherin mutation is associated with a wide range of typically adult-onset retinal phenotypes which can include asymptomatic maculopathy. There are few reports of biallelic peripherin mutations, only one of which detailed the ophthalmic phenotype. This report documents the retinal phenotype associated with homozygosity for a known peripherin mutation (c.659G>A; p.Arg220Gln), highlights its similar appearance to what was described in the one previous report, and shows how examination of family members can be useful in genetic diagnosis. METHODS Retrospective case series. RESULTS A 13-year-old Emirati boy was referred for low vision. The parents felt he was blind at birth but noted improvement with time. Retinal examination was significant for central macula horizontal ovoid discoloration as was documented for young adults with homozygous peripherin mutations in the one previous report. Electroretinography revealed cone-rod dysfunction. Both asymptomatic parents were examined and found to have central macular abnormalities. Sanger sequencing of peripherin based on clinical features uncovered the pathogenic variant c.659G>A; p.Arg22Gln (NM_000322.4) in homozygosity in the child and in heterozygosity in each parent. Exome sequencing in the child excluded pathologic variants in other retinal dystrophy genes. CONCLUSIONS The experience with this family highlights clinical features suggestive for biallelic peripherin mutations, documents cone-rod dysfunction as associated with homozygosity for the p.Arg220Gln peripherin mutation, and is an example of how examination of family members can help to guide genetic testing.
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Affiliation(s)
- Arif O Khan
- a Eye Institute , Cleveland Clinic Abu Dhabi , Abu Dhabi , United Arab Emirates.,b Department of Ophthalmology , Cleveland Clinic Lerner College of Medicine of Case Western University , Cleveland , OH , USA
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773
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Perdomo-Ramirez A, Aguirre M, Davitaia T, Ariceta G, Ramos-Trujillo E, Claverie-Martin F. Characterization of two novel mutations in the claudin-16 and claudin-19 genes that cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis. Gene 2019; 689:227-234. [DOI: 10.1016/j.gene.2018.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
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774
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Sitsel A, De Raeymaecker J, Drachmann ND, Derua R, Smaardijk S, Andersen JL, Vandecaetsbeek I, Chen J, De Maeyer M, Waelkens E, Olesen C, Vangheluwe P, Nissen P. Structures of the heart specific SERCA2a Ca 2+-ATPase. EMBO J 2019; 38:embj.2018100020. [PMID: 30777856 DOI: 10.15252/embj.2018100020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 12/29/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
The sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2a (SERCA2a) performs active reuptake of cytoplasmic Ca2+ and is a major regulator of cardiac muscle contractility. Dysfunction or dysregulation of SERCA2a is associated with heart failure, while restoring its function is considered as a therapeutic strategy to restore cardiac performance. However, its structure has not yet been determined. Based on native, active protein purified from pig ventricular muscle, we present the first crystal structures of SERCA2a, determined in the CPA-stabilized E2-AlF4- form (3.3 Å) and the Ca2+-occluded [Ca2]E1-AMPPCP form (4.0 Å). The structures are similar to the skeletal muscle isoform SERCA1a pointing to a conserved mechanism. We seek to explain the kinetic differences between SERCA1a and SERCA2a. We find that several isoform-specific residues are acceptor sites for post-translational modifications. In addition, molecular dynamics simulations predict that isoform-specific residues support distinct intramolecular interactions in SERCA2a and SERCA1a. Our experimental observations further indicate that isoform-specific intramolecular interactions are functionally relevant, and may explain the kinetic differences between SERCA2a and SERCA1a.
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Affiliation(s)
- Aljona Sitsel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Center for Membrane Proteins in Cells and Disease - PUMPkin, Danish National Research Foundation, Aarhus C, Denmark.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus C, Denmark
| | | | - Nikolaj Düring Drachmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Center for Membrane Proteins in Cells and Disease - PUMPkin, Danish National Research Foundation, Aarhus C, Denmark
| | - Rita Derua
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,SyBioMa, KU Leuven, Leuven, Belgium
| | - Susanne Smaardijk
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jacob Lauwring Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Center for Membrane Proteins in Cells and Disease - PUMPkin, Danish National Research Foundation, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | - Jialin Chen
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,SyBioMa, KU Leuven, Leuven, Belgium
| | - Claus Olesen
- Center for Membrane Proteins in Cells and Disease - PUMPkin, Danish National Research Foundation, Aarhus C, Denmark .,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Peter Vangheluwe
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark .,Center for Membrane Proteins in Cells and Disease - PUMPkin, Danish National Research Foundation, Aarhus C, Denmark.,Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus C, Denmark
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775
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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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776
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Owaidah T, Saleh M, Baz B, Abdulaziz B, Alzahrani H, Tarawah A, Almusa A, AlNounou R, AbaAlkhail H, Al-Numair N, Altahan R, Abouelhoda M, Alamoudi T, Monies D, Jabaan A, Al Tassan N. Molecular yield of targeted sequencing for Glanzmann thrombasthenia patients. NPJ Genom Med 2019; 4:4. [PMID: 30792900 PMCID: PMC6375963 DOI: 10.1038/s41525-019-0079-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/23/2019] [Indexed: 12/19/2022] Open
Abstract
Glanzmann thrombasthenia (GT) is a rare autosomal recessive bleeding disorder. Around 490 mutations in ITGA2B and ITGB3 genes were reported. We aimed to use targeted next-generation sequencing (NGS) to identify variants in patients with GT. We screened 72 individuals (including unaffected family members) using a panel of 393 genes (SHGP heme panel). Validation was done by Sanger sequencing and pathogenicity was predicted using multiple tools. In 83.5% of our cohort, 17 mutations were identified in ITGA2B and ITGB3 (including 6 that were not previously reported). In addition to variants in the two known genes, we found variants in ITGA2, VWF and F8. The SHGP heme panel can be used as a high-throughput molecular diagnostic assay to screen for mutations and variants in GT cases and carriers. Our findings expand the molecular landscape of GT and emphasize the robustness and usefulness of this panel.
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Affiliation(s)
- Tarek Owaidah
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mahasen Saleh
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Batoul Baz
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Basma Abdulaziz
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hazza Alzahrani
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ahmed Tarawah
- Medina Maternity and Children Hospital, Medina, Saudi Arabia
| | - Abdulrahman Almusa
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Randa AlNounou
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hala AbaAlkhail
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nouf Al-Numair
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Rahaf Altahan
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Abouelhoda
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Thamer Alamoudi
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Amjad Jabaan
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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777
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Affiliation(s)
- Arif O Khan
- a Eye Institute, Cleveland Clinic Abu Dhabi , Abu Dhabi , United Arab Emirates
- b Department of Ophthalmology , Cleveland Clinic Lerner College of Medicine of Case Western University , Cleveland , OH , USA
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778
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Deacon DC, Happe CL, Chen C, Tedeschi N, Manso AM, Li T, Dalton ND, Peng Q, Farah EN, Gu Y, Tenerelli KP, Tran VD, Chen J, Peterson KL, Schork NJ, Adler ED, Engler AJ, Ross RS, Chi NC. Combinatorial interactions of genetic variants in human cardiomyopathy. Nat Biomed Eng 2019; 3:147-157. [PMID: 30923642 PMCID: PMC6433174 DOI: 10.1038/s41551-019-0348-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Dilated cardiomyopathy (DCM) is a leading cause of morbidity and mortality worldwide; yet how genetic variation and environmental factors impact DCM heritability remains unclear. Here, we report that compound genetic interactions between DNA sequence variants contribute to the complex heritability of DCM. By using genetic data from a large family with a history of DCM, we discovered that heterozygous sequence variants in the TROPOMYOSIN 1 (TPM1) and VINCULIN (VCL) genes cose-gregate in individuals affected by DCM. In vitro studies of patient-derived and isogenic human-pluripotent-stem-cell-derived cardio-myocytes that were genome-edited via CRISPR to create an allelic series of TPM1 and VCL variants revealed that cardiomyocytes with both TPM1 and VCL variants display reduced contractility and sarcomeres that are less organized. Analyses of mice genetically engineered to harbour these human TPM1 and VCL variants show that stress on the heart may also influence the variable penetrance and expressivity of DCM-associated genetic variants in vivo. We conclude that compound genetic variants can interact combinatorially to induce DCM, particularly when influenced by other disease-provoking stressors.
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Affiliation(s)
- Dekker C Deacon
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra L Happe
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Chao Chen
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Neil Tedeschi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ana Maria Manso
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Veterans Administration Healthcare San Diego, San Diego, CA, USA
| | - Ting Li
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nancy D Dalton
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qian Peng
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Elie N Farah
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yusu Gu
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kevin P Tenerelli
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Vivien D Tran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ju Chen
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kirk L Peterson
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas J Schork
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Eric D Adler
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
| | - Robert S Ross
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Veterans Administration Healthcare San Diego, San Diego, CA, USA.
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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779
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Molecular expression, characterization and mechanism of ALAS2 gain-of-function mutants. Mol Med 2019; 25:4. [PMID: 30678654 PMCID: PMC6344999 DOI: 10.1186/s10020-019-0070-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
Background X-linked protoporphyria (XLP) (MIM 300752) is an erythropoietic porphyria due to gain-of-function mutations in the last exon (Ducamp et al., Hum Mol Genet 22:1280-88, 2013) of the erythroid-specific aminolevulinate synthase gene (ALAS2). Five ALAS2 exon 11 variants identified by the NHBLI Exome sequencing project (p.R559H, p.E565D, p.R572C, p.S573F and p.Y586F) were expressed, purified and characterized in order to assess their possible contribution to XLP. To further characterize the XLP gain-of-function region, five novel ALAS2 truncation mutations (p.P561X, p.V562X, p.H563X, p.E569X and p.F575X) were also expressed and studied. Methods Site-directed mutagenesis was used to generate ALAS2 mutant clones and all were prokaryotically expressed, purified to near homogeneity and characterized by protein and enzyme kinetic assays. Standard deviations were calculated for 3 or more assay replicates. Results The five ALAS2 single nucleotide variants had from 1.3- to 1.9-fold increases in succinyl-CoA Vmax and 2- to 3-fold increases in thermostability suggesting that most could be gain-of-function modifiers of porphyria instead of causes. One SNP (p.R559H) had markedly low purification yield indicating enzyme instability as the likely cause for XLSA in an elderly patient with x-linked sideroblastic anemia. The five novel ALAS2 truncation mutations had increased Vmax values for both succinyl-CoA and glycine substrates (1.4 to 5.6-fold over wild-type), while the Kms for both substrates were only modestly changed. Of interest, the thermostabilities of the truncated ALAS2 mutants were significantly lower than wild-type, with an inverse relationship to Vmax fold-increase. Conclusions Patients with porphyrias should always be assessed for the presence of the ALAS2 gain-of-function modifier variants identified here. A key region of the ALAS2 carboxyterminal region is identified by the truncation mutations studied here and the correlation of increased thermolability with activity suggests that increased molecular flexibility/active site openness is the mechanism of enhanced function of mutations in this region providing further insights into the role of the carboxyl-terminal region of ALAS2 in the regulation of erythroid heme synthesis. Electronic supplementary material The online version of this article (10.1186/s10020-019-0070-9) contains supplementary material, which is available to authorized users.
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780
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Zheng C, Lin X, Xu X, Wang C, Zhou J, Gao B, Fan J, Lu W, Hu Y, Jie Q, Luo Z, Yang L. Suppressing UPR-dependent overactivation of FGFR3 signaling ameliorates SLC26A2-deficient chondrodysplasias. EBioMedicine 2019; 40:695-709. [PMID: 30685387 PMCID: PMC6413327 DOI: 10.1016/j.ebiom.2019.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/21/2022] Open
Abstract
Background Mutations in the SLC26A2 gene cause a spectrum of currently incurable human chondrodysplasias. However, genotype-phenotype relationships of SLC26A2-deficient chondrodysplasias are still perplexing and thus stunt therapeutic development. Methods To investigate the causative role of SLC26A2 deficiency in chondrodysplasias and confirm its skeleton-specific pathology, we generated and analyzed slc26a2−/− and Col2a1-Cre; slc26a2fl/fl mice. The therapeutic effect of NVP-BGJ398, an FGFR inhibitor, was tested with both explant cultures and timed pregnant females. Findings Two lethal forms of human SLC26A2-related chondrodysplasias, achondrogenesis type IB (ACG1B) and atelosteogenesis type II (AO2), are phenocopied by slc26a2−/− mice. Unexpectedly, slc26a2−/− chondrocytes are defective for collagen secretion, exhibiting intracellular retention and compromised extracellular deposition of ColII and ColIX. As a consequence, the ATF6 arm of the unfolded protein response (UPR) is preferentially triggered to overactivate FGFR3 signaling by inducing excessive FGFR3 in slc26a2−/− chondrocytes. Consistently, suppressing FGFR3 signaling by blocking either FGFR3 or phosphorylation of the downstream effector favors the recovery of slc26a2−/− cartilage cultures from impaired growth and unbalanced cell proliferation and apoptosis. Moreover, administration of an FGFR inhibitor to pregnant females shows therapeutic effects on pathological features in slc26a2−/− newborns. Finally, we confirm the skeleton-specific lethality and pathology of global SLC26A2 deletion through analyzing the Col2a1-Cre; slc26a2fl/fl mouse line. Interpretation Our study unveils a previously unrecognized pathogenic mechanism underlying ACG1B and AO2, and supports suppression of FGFR3 signaling as a promising therapeutic approach for SLC26A2-related chondrodysplasias. Fund This work was supported by National Natural Science Foundation of China (81871743, 81730065 and 81772377).
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Affiliation(s)
- Chao Zheng
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xisheng Lin
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaolong Xu
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Cheng Wang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Jinru Zhou
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Bo Gao
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jing Fan
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weiguang Lu
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yaqian Hu
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiang Jie
- Department of Orthopedic Surgery, HongHui Hospital, Xi'an Jiaotong University, College of Medicine, Xi'an, China
| | - Zhuojing Luo
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Medical Research Institute, Northwestern Polytechnical University, Xi'an, China
| | - Liu Yang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Medical Research Institute, Northwestern Polytechnical University, Xi'an, China.
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781
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Feng B, Liu X, Chen Y. A Rhodopsin Transport Assay by High-Content Imaging Analysis. J Vis Exp 2019. [PMID: 30735172 DOI: 10.3791/58703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Rhodopsin misfolding mutations lead to rod photoreceptor death that is manifested as autosomal dominant retinitis pigmentosa (RP), a progressive blinding disease that lacks effective treatment. We hypothesize that the cytotoxicity of the misfolded rhodopsin mutant can be alleviated by pharmacologically stabilizing the mutant rhodopsin protein. The P23H mutation, among the other Class II rhodopsin mutations, encodes a structurally unstable rhodopsin mutant protein that is accumulated in the endoplasmic reticulum (ER), whereas the wild type rhodopsin is transported to the plasma membrane in mammalian cells. We previously performed a luminescence-based high-throughput screen (HTS) and identified a group of pharmacological chaperones that rescued the transport of the P23H rhodopsin from ER to the plasma membrane. Here, using an immunostaining method followed by a high-content imaging analysis, we quantified the mutant rhodopsin protein amount in the whole cell and on the plasma membrane. This method is informative and effective to identify true hits from false positives following HTS. Additionally, the high-content image analysis enabled us to quantify multiple parameters from a single experiment to evaluate the pharmacological properties of each compound. Using this assay, we analyzed the effect of 11 different compounds towards six RP associated rhodopsin mutants, obtaining a 2-D pharmacological profile for a quantitative and qualitative understanding about the structural stability of these rhodopsin mutants and efficacy of different compounds towards these mutants.
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Affiliation(s)
- Bing Feng
- Department of Ophthalmology, University of Pittsburgh
| | - Xujie Liu
- Department of Ophthalmology, University of Pittsburgh
| | - Yuanyuan Chen
- Department of Ophthalmology, University of Pittsburgh; McGowan Institute for Regenerative Medicine, University of Pittsburgh;
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782
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Perdomo-Ramirez A, de Armas-Ortiz M, Ramos-Trujillo E, Suarez-Artiles L, Claverie-Martin F. Exonic CLDN16 mutations associated with familial hypomagnesemia with hypercalciuria and nephrocalcinosis can induce deleterious mRNA alterations. BMC MEDICAL GENETICS 2019; 20:6. [PMID: 30621608 PMCID: PMC6325764 DOI: 10.1186/s12881-018-0713-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/30/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis type 1 is an autosomal recessive disease characterized by excessive renal magnesium and calcium excretion, bilateral nephrocalcinosis, and progressive chronic renal failure. This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations. The functional consequences of some of these claudin-16 mutant proteins have been analysed after heterologous expression showing indeed a significant loss of function compared to the wild-type claudin-16. We hypothesize that a number of CLDN16 exonic mutations can be responsible for the disease phenotype by disrupting the pre-mRNA splicing process. METHODS We selected 12 previously described presumed CLDN16 missense mutations and analysed their potential effect on pre-mRNA splicing using a minigene assay. RESULTS Our results indicate that five of these mutations induce significant splicing alterations. Mutations c.453G > T and c.446G > T seem to inactivate exonic splicing enhancers and promote the use of an internal cryptic acceptor splice site resulting in inclusion of a truncated exon 3 in the mature mRNA. Mutation c.571G > A affects an exonic splicing enhancer resulting in partial skipping of exon 3. Mutations c.593G > C and c.593G > A disturb the acceptor splice site of intron 3 and cause complete exon 4 skipping. CONCLUSIONS To our knowledge, this is the first report of CLDN16 exonic mutations producing alterations in splicing. We suggest that in the absence of patients RNA samples, splicing functional assays with minigenes could be valuable for evaluating the effect of exonic CLDN16 mutations on pre-mRNA splicing.
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Affiliation(s)
- Ana Perdomo-Ramirez
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Marian de Armas-Ortiz
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Elena Ramos-Trujillo
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Lorena Suarez-Artiles
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Felix Claverie-Martin
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
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783
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Khan M, Fadaie Z, Cornelis SS, Cremers FPM, Roosing S. Identification and Analysis of Genes Associated with Inherited Retinal Diseases. Methods Mol Biol 2019; 1834:3-27. [PMID: 30324433 DOI: 10.1007/978-1-4939-8669-9_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inherited retinal diseases (IRDs) display a very high degree of clinical and genetic heterogeneity, which poses challenges in finding the underlying defects in known IRD-associated genes and in identifying novel IRD-associated genes. Knowledge on the molecular and clinical aspects of IRDs has increased tremendously in the last decade. Here, we outline the state-of-the-art techniques to find the causative genetic variants, with special attention for next-generation sequencing which can combine molecular diagnostics and retinal disease gene identification. An important aspect is the functional assessment of rare variants with RNA and protein effects which can only be predicted in silico. We therefore describe the in vitro assessment of putative splice defects in human embryonic kidney cells. In addition, we outline the use of stem cell technology to generate photoreceptor precursor cells from patients' somatic cells which can subsequently be used for RNA and protein studies. Finally, we outline the in silico methods to interpret the causality of variants associated with inherited retinal disease and the registry of these variants.
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Affiliation(s)
- Mubeen Khan
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zeinab Fadaie
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stéphanie S Cornelis
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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784
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Kluska A, Kulecka M, Litwin T, Dziezyc K, Balabas A, Piatkowska M, Paziewska A, Dabrowska M, Mikula M, Kaminska D, Wiernicka A, Socha P, Czlonkowska A, Ostrowski J. Whole-exome sequencing identifies novel pathogenic variants across the ATP7B gene and some modifiers of Wilson's disease phenotype. Liver Int 2019; 39:177-186. [PMID: 30230192 DOI: 10.1111/liv.13967] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/05/2018] [Accepted: 09/09/2018] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Wilson's disease (WD) is an autosomal recessive disorder associated with disease-causing alterations across the ATP7B gene, with highly variable symptoms and age of onset. We aimed to assess whether the clinical variability of WD relates to modifier genes. METHODS A total of 248 WD patients were included, of whom 148 were diagnosed after age of 17. Human exome libraries were constructed using AmpliSeq technology and sequenced using the IonProton platform. RESULTS ATP7B p.His1069Gln mutation was present in 215 patients, with 112 homozygotes and 103 heterozygotes. Three other mutations: p.Gln1351Ter, p.Trp779Ter and c.3402delC were identified in >10 patients. Among patients, 117 had a homozygous mutation, 101 were compound heterozygotes, 27 had one heterozygous mutation, and 3 other patients had no identifiable pathogenic variant of ATP7B. Sixteen mutations were novel, found as part of a compound mutation or as a sole, homozygous mutation. For disease phenotype prediction, age at diagnosis was a deciding factor, while frameshift allelic variants of ATP7B and being male increased the odds of developing a neurological phenotype. Rare allelic variants in ESD and INO80 increased and decreased chances for the neurological phenotype, respectively, while rare variants in APOE and MBD6 decreased the chances of WD early manifestation. Compound mutations contributed to earlier age of onset. CONCLUSIONS In a Polish population, genetic screening for WD may help genotype for four variants (p.His1069Gln, p.Gln1351Ter, p.Trp779Ter and c.3402delC), with direct sequencing of all ATP7B amplicons as a second diagnostic step. We also identified some allelic variants that may modify a WD phenotype.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Tomasz Litwin
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Karolina Dziezyc
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | | | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | | | - Michal Mikula
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | - Diana Kaminska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Wiernicka
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Czlonkowska
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland.,Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
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785
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Molecular Subtypes and Genomic Signatures of Hepatocellular Carcinoma for Prognostication and Therapeutic Decision-Making. MOLECULAR AND TRANSLATIONAL MEDICINE 2019. [DOI: 10.1007/978-3-030-21540-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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786
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Takata A. Estimating contribution of rare non-coding variants to neuropsychiatric disorders. Psychiatry Clin Neurosci 2019; 73:2-10. [PMID: 30293238 DOI: 10.1111/pcn.12774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
Owing to recent advances in DNA sequencing technology, a number of large-scale comprehensive analyses of genetic variations in protein-coding regions (i.e., whole-exome sequencing studies), have been conducted for neuropsychiatric and neurodevelopmental disorders, such as autism spectrum disorders, intellectual disability, and schizophrenia. These studies, especially those focusing on de novo (newly arising) mutations and extremely rare variants, have successfully identified previously unrecognized disease genes/mutations with a large effect size and deepen our understanding of the biology of neuropsychiatric diseases. Along with the continuously dropping sequencing cost, now the target of sequencing studies is expanding from the exome to the whole human genome. Several pioneering works have provided important insights into the contribution of rare non-coding variants to neuropsychiatric diseases. At the same time, these studies highlight need for further larger sample sizes and improvement in annotation of non-coding regulatory variants. In this review, key findings from recent studies as well as likely future directions are overviewed.
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Affiliation(s)
- Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan
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787
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Fischetto R, Palmieri VV, Tripaldi ME, Gaeta A, Michelucci A, Delvecchio M, Francavilla R, Giordano P. Alagille Syndrome: A Novel Mutation in JAG1 Gene. Front Pediatr 2019; 7:199. [PMID: 31157196 PMCID: PMC6529843 DOI: 10.3389/fped.2019.00199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Alagille syndrome is an autosomal dominant multisystem disorder with variable phenotypic penetrance, caused by heterozygous mutations in JAG1 or NOTCH2, encoding for the components of the Notch signaling pathway. In this paper, we described a novel mutation not yet reported in literature. This 3-years old male child was referred to our Clinical Genetics Unit because of delayed psychomotor development, systolic murmur, dysmorphic facial features, and hypertransaminasemia. The novel JAG1 heterozygous c.2026delT variant in exon 16 was found. JAG1 mutations are classified as protein truncating and non-protein truncating, without any genotype-phenotype correlation. The detected mutation determines a stop codon (p.Cys676AlafsTer67) in the gene sequence, encoding a truncated protein. Our report broadens the spectrum of JAG1 gene mutations.
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Affiliation(s)
- Rita Fischetto
- Clinical Genetics Unit, Department of Paediatric Medicine, Giovanni XXIII Children's Hospital, Bari, Italy
| | - Viviana V Palmieri
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Maria E Tripaldi
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Alberto Gaeta
- PediatricRadiology Unit, Giovanni XXIII Children's Hospital, Bari, Italy
| | - Angela Michelucci
- Laboratory of Molecular Genetics, University Hospital of Pisa, Pisa, Italy
| | | | - Ruggiero Francavilla
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
| | - Paola Giordano
- Pediatric Section, Department of Biomedicine and Human Oncology, University A. Moro, Bari, Italy
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788
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Chen B, Solis-Villa C, Erwin AL, Balwani M, Nazrenko I, Phillips JD, Desnick RJ, Yasuda M. Identification and characterization of 40 novel hydroxymethylbilane synthase mutations that cause acute intermittent porphyria. J Inherit Metab Dis 2019; 42:186-194. [PMID: 30740734 PMCID: PMC6162174 DOI: 10.1002/jimd.12040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute intermittent porphyria (AIP), an autosomal dominant disorder due to the half-normal activity of hydroxymethylbilane synthase (HMBS), is characterized by acute neurovisceral attacks that are precipitated by factors that induce heme biosynthesis. Molecular diagnosis is the most sensitive and specific diagnostic test for AIP, and importantly, it permits the identification of asymptomatic family members for genetic counseling and avoidance of precipitating factors. Here, we report the identification of 40 novel HMBS mutations, including 11 missense, four nonsense, 16 small insertions or deletions, eight consensus splice site mutations, and a complex insertion-deletion mutation in unrelated individuals with AIP. Prokaryotic expression of the missense mutations demonstrated that all mutants had ≤5% of expressed wildtype activity, except for c.1039G>C (p.A347P), which had 51% residual HMBS activity but was markedly thermolabile. Of note, the mutation c.612G>T (p.Q204H) altered the last nucleotide of exon 10, which resulted in an alternative HMBS transcript with an in-frame nine base-pair deletion at the 3'-terminus of exon 10 (encoding protein Q204HΔ3). When expressed, Q204HΔ3 and an in-frame three base-pair deletion (c.639_641delTGC) had no detectable HMBS activity. Western blot analyses and mapping of the missense mutations on the human HMBS crystal structure revealed that mutations near the active site or at the dimerization interface resulted in stably expressed proteins, while most that altered surface residues resulted in unstable proteins, presumably due to improper protein folding. These studies identified novel pathogenic HMBS mutations and expanded the molecular heterogeneity of AIP.
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Affiliation(s)
- Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Constanza Solis-Villa
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Angelika L. Erwin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Manisha Balwani
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Irina Nazrenko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John D. Phillips
- Department of Internal Medicine, University of Utah, Salt Lake City, UT
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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789
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Hoss GRW, Poloni S, Blom HJ, Schwartz IVD. Three Main Causes of Homocystinuria: CBS, cblC and MTHFR Deficiency. What do they Have in Common? JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2019. [DOI: 10.1590/2326-4594-jiems-2019-0007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
| | - Soraia Poloni
- Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brazil
| | - Henk J Blom
- University Medical Centre Amsterdam, Netherlands
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790
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Lovato DV, Herai RR, Pignatari GC, Beltrão-Braga PCB. The Relevance of Variants With Unknown Significance for Autism Spectrum Disorder Considering the Genotype-Phenotype Interrelationship. Front Psychiatry 2019; 10:409. [PMID: 31231258 PMCID: PMC6567929 DOI: 10.3389/fpsyt.2019.00409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
Several efforts in basic and clinical research have been contributing to unveiling the genetics behind autism spectrum disorders (ASD). However, despite these advancements, many individuals diagnosed with ASD and related neuropsychiatric conditions have been genetically investigated without elucidative results. The enormous genetic complexity of ASD-related conditions makes it a significant challenge to achieve, with a growing number of genes (close to a thousand) involved, belonging to different molecular pathways and presenting distinct genetic variations. Next-generation sequencing (NGS) is the approach most used in genetic research related to ASD, identifying de novo mutation, which is closely related to more severe clinical phenotypes, especially when they affect constrained and loss-of-function intolerant genes. On the other hand, de novo mutation findings contribute to a small percentage of the ASD population, since most of the cases and genetic variants associated with neuropsychiatric conditions are inherited and phenotypes are results of additive polygenic models, which makes statistical efforts more difficult. As a result, NGS investigation can sound vainly or unsuccessful, and new mutations on genes already related with ASD are classified as variants of unknown significance (VUS), hampering their endorsement to a clinical phenotype. This review is focused on currently available strategies to clarify the impact of VUS and to describe the efforts to identify more pieces of evidence throughout clinical interpretation and genetic curation process.
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Affiliation(s)
- Diogo V Lovato
- Laboratory of Disease Modeling, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Roberto R Herai
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil.,Lico Kaesemodel Institute (ILK), Curitiba, Brazil
| | - Graciela C Pignatari
- Laboratory of Disease Modeling, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Patricia C B Beltrão-Braga
- Laboratory of Disease Modeling, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Laboratory of Disease Modeling, Scientific Platform Pasteur-USP, São Paulo, Brazil
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791
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Rasouly HM, Groopman EE, Heyman-Kantor R, Fasel DA, Mitrotti A, Westland R, Bier L, Weng C, Ren Z, Copeland B, Krithivasan P, Chung WK, Sanna-Cherchi S, Goldstein DB, Gharavi AG. The Burden of Candidate Pathogenic Variants for Kidney and Genitourinary Disorders Emerging From Exome Sequencing. Ann Intern Med 2019; 170:11-21. [PMID: 30476936 DOI: 10.7326/m18-1241] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Exome sequencing is increasingly being used for clinical diagnostics, with an impetus to expand reporting of incidental findings across a wide range of disorders. Analysis of population cohorts can help reduce risk for genetic variant misclassification and resultant unnecessary referrals to subspecialists. OBJECTIVE To examine the burden of candidate pathogenic variants for kidney and genitourinary disorders emerging from exome sequencing. DESIGN Secondary analysis of genetic data. SETTING A tertiary care academic medical center. PATIENTS A convenience sample of exome sequence data from 7974 self-declared healthy adults. MEASUREMENTS Assessment of the prevalence of candidate pathogenic variants in 625 genes associated with Mendelian kidney and genitourinary disorders. RESULTS Of all participants, 23.3% carried a candidate pathogenic variant, most of which were attributable to previously reported variants that had implausibly high allele frequencies. In particular, 25 genes (discovered before the creation of the Exome Aggregation Consortium, a genetic database comprising data from a large control population) accounted for 67.7% of persons with candidate pathogenic variants. After stringent filtering based on allele frequency, 1.4% of persons still had a candidate pathogenic variant, an excessive rate given the prevalence of monogenic kidney and genitourinary disorders. Manual annotation of a subset of variants showed that the majority would be classified as nonbenign under current guidelines for clinical sequence interpretation and could prompt subspecialty referrals if returned. LIMITATION Limited access to health record data prevented comprehensive assessment of the phenotypic concordance with genetic diagnoses. CONCLUSION Widespread reporting of incidental genetic findings related to kidney and genitourinary disorders will require stringent curation of clinical variant databases and detailed case-level review to avoid genetic misdiagnosis and unnecessary referrals. These findings motivate similar analyses for genes relevant to other medical subspecialties. PRIMARY FUNDING SOURCE National Institute of Diabetes and Digestive and Kidney Diseases and National Human Genome Research Institute.
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Affiliation(s)
- Hila Milo Rasouly
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Emily E Groopman
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Reuben Heyman-Kantor
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - David A Fasel
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Adele Mitrotti
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Rik Westland
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Louise Bier
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Chunhua Weng
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Zhong Ren
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Brett Copeland
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Priya Krithivasan
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - Wendy K Chung
- Columbia University Medical Center, New York, New York (W.K.C., D.B.G.)
| | - Simone Sanna-Cherchi
- Columbia University, New York, New York (H.M.R., E.E.G., R.H., D.A.F., A.M., R.W., L.B., C.W., Z.R., B.C., P.K., S.S.)
| | - David B Goldstein
- Columbia University Medical Center, New York, New York (W.K.C., D.B.G.)
| | - Ali G Gharavi
- Columbia University and Columbia University Medical Center, New York, New York (A.G.G.)
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792
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Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proc Natl Acad Sci U S A 2018; 116:950-959. [PMID: 30591557 DOI: 10.1073/pnas.1808403116] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.
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793
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Behlmann AM, Goyal NA, Yang X, Chen PH, Ankala A. A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency. JIMD Rep 2018; 45:105-110. [PMID: 30570712 PMCID: PMC6336546 DOI: 10.1007/8904_2018_147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/24/2018] [Accepted: 09/25/2018] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase-1 (PGK1) deficiency is a rare X-linked disorder caused by pathogenic variants in the PGK1 gene. Complete loss-of-function variants have not been reported in this gene, indicating that residual enzyme function is critical for viability in males. Therefore, copy number variants (CNVs) that include single exon or multiple exon deletions or duplications are generally not expected in individuals with PGK1 deficiency. Here we describe a 64-year-old male presenting with a family history (three additional affected males) and a personal history of childhood-onset metabolic myopathy that involves episodes of muscle pain, stiffness after activity, exercise intolerance, and myoglobinuria after exertion. Biochemical analysis on a muscle biopsy indicated significantly reduced activity (15% compared to normal) for phosphoglycerate kinase (PGK1), a glycolytic enzyme encoded by PGK1. A diagnosis of PGK1 deficiency was established by molecular analysis which detected an approximately 886 kb deletion involving the polyadenylation site in the 3'UTR of the PGK1 gene. RNA analysis showed significantly reduced PGK1 transcript levels (30% compared to normal). This is the first deletion reported in the PGK1 gene and is the first pathogenic variant involving the 3'UTR polyadenylation site of this gene. Our report emphasizes the role of 3'UTR variants in human disorders and underscores the need for exploring noncoding regions of disease-associated genes when seeking a molecular diagnosis.
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Affiliation(s)
- Andrea Medrano Behlmann
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Namita A. Goyal
- grid.266093.80000 0001 0668 7243Department of Neurology, University of California, Irvine, CA USA
| | - Xiaoyu Yang
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Ping H. Chen
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Arunkanth Ankala
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,EGL Genetic Diagnostics LLC, Tucker, GA USA
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794
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Mohammed Ismail W, Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P. The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS One 2018; 13:e0208901. [PMID: 30566479 PMCID: PMC6300249 DOI: 10.1371/journal.pone.0208901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.
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Affiliation(s)
- Wazim Mohammed Ismail
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Kymberleigh A. Pagel
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Vikas Pejaver
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Simo V. Zhang
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
| | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Matthew W. Hahn
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Predrag Radivojac
- College of Computer and Information Science, Northeastern University, Boston, Massachusetts, United States of America
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795
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Nagaraja MR, Gubbala SP, Delphine Silvia CRW, Amanchy R. Molecular diagnostics of disorders of sexual development: an Indian survey and systems biology perspective. Syst Biol Reprod Med 2018; 65:105-120. [PMID: 30550360 DOI: 10.1080/19396368.2018.1549619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We aimed to survey the monogenic causes of disorders of sex development (DSD) and thereby its prevalence in India. This study revealed mutations resulting in androgen insensitivity syndrome, 5α-reductase type 2 deficiency, and gonadal dysgenesis were commonly reported. Intriguingly, AR deficits were the most prevalent (32 mutations) and of 11/26 missense mutations were in exons 4-8 (encoding ligand binding domain). The unique features of SRD5A2 defects were p.R246Q (most prevalent) and p.G196S could be mutational hotspots, dual gene defects (p.A596T in AR and p.G196S in SRD5A2) in a patient with hypospadias and novel 8 nucleotide deletion (exon 1) found in a patient with perineal hypospadias. Deficits in SRY, WT1, DHH, NR5A1, and DMRT1 caused 46,XY gonadal dysgenesis. Notably, mutations in AR, SRD5A2, MAMLD1, WT1, and MAP3K1 have led to hypospadias and only one CYP19A1 mutation caused aromatase deficiency was reported to date. Data mining from various databases has not only reinforced the role of well-established genes (e.g., SRY, WT1, DHH, NR5A1, DMRT1, AR, SRD5A2, MAMLD1) involved in DSD but also provided us 12 more potential candidate genes (ACVR1, AMHR2, CTNNB1, CYP11A1, CYP19A1, FGFR2, FGF9, PRKACA, PRKACG, SMAD9, TERT, ZFPM2), which benefit from a close association with the well-established genes involved in DSD and might be useful to screen owing to their direct gene-phenotype relationship or through direct functional interaction. As more genes have been revealed in relation to DSD, we believe ultimately it holds a better scenario for therapeutic regimen. Despite the advances in translational medicine, hospitals are yet to adopt genetic testing and counseling facilities in India that shall have potential impact on clinical diagnosis. Abbreviations: 5α-RD2: 5α-Reductase type 2; AIS: androgen insensitivity syndrome; AMH: antimullerian hormone; AMHR: antimullerian hormone receptor; AR: androgen receptor gene; CAH: congenital adrenal hyperplasia; CAIS: complete AIS; CAH: congenital adrenal hyperplasia; CHH: congenital hypogonadotropic hypogonadism; CXORF6: chromosome X open reading frame 6 gene; CYP19A1: cytochrome P450 family 19 subfamily A member 1 gene; DHT: dihydrotestosterone; DMRT1: double sex and mab-3 related transcription factor 1 gene; DSD: disorders of sexual development; GD: gonadal dysgenesis; HGMD: human gene mutation database; IH: isolated hypospadias; MAMLD1: mastermind like domain containing 1 gene; MIS: mullerian inhibiting substance; NTD: N-terminal domain; OT DSD: ovotesticular DSD; PAIS: partial AIS; SOX9: SRY-related HMG-box 9 gene; SRY: sex-determining region Y gene; STAR: steroidogenic acute regulatory protein gene; SRD5A2: steroid 5 alpha-reductase 2 gene; T DSD: testicular DSD; T: testosterone; WNT4: Wnt family member 4 gene; WT1: Wilms tumor 1 gene; Δ4: androstenedione.
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Affiliation(s)
- M R Nagaraja
- a Department of Biochemistry , Akash Institute of Medical Sciences & Research Centre , Bangalore , India
| | - Satya Prakash Gubbala
- b Division of Pharmacology and Toxicology , CSIR- Indian Institute of Chemical Technology , Hyderabad , India
| | - C R Wilma Delphine Silvia
- a Department of Biochemistry , Akash Institute of Medical Sciences & Research Centre , Bangalore , India
| | - Ramars Amanchy
- b Division of Pharmacology and Toxicology , CSIR- Indian Institute of Chemical Technology , Hyderabad , India
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796
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Ng M, Zhang H, Weil A, Singh V, Jamiolkowski R, Baradaran-Heravi A, Roberge M, Jacobson A, Friesen W, Welch E, Goldman YE, Cooperman BS. New in Vitro Assay Measuring Direct Interaction of Nonsense Suppressors with the Eukaryotic Protein Synthesis Machinery. ACS Med Chem Lett 2018; 9:1285-1291. [PMID: 30613341 PMCID: PMC6295867 DOI: 10.1021/acsmedchemlett.8b00472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/21/2018] [Indexed: 02/06/2023] Open
Abstract
Nonsense suppressors (NonSups) induce "readthrough", i.e., the selection of near cognate tRNAs at premature termination codons and insertion of the corresponding amino acid into nascent polypeptide. Prior readthrough measurements utilized contexts in which NonSups can promote readthrough directly, by binding to one or more of the components of the protein synthesis machinery, or indirectly, by several other mechanisms. Here we utilize a new, highly purified in vitro assay to measure exclusively direct nonsense suppressor-induced readthrough. Of 16 NonSups tested, 12 display direct readthrough, with results suggesting that such NonSups act by at least two different mechanisms. In preliminary work we demonstrate the potential of single molecule fluorescence energy transfer measurements to elucidate mechanisms of NonSup-induced direct readthrough, which will aid efforts to identify NonSups having improved clinical efficacy.
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Affiliation(s)
- Martin
Y. Ng
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Haibo Zhang
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amy Weil
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vijay Singh
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ryan Jamiolkowski
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alireza Baradaran-Heravi
- Department
of Biochemistry and Molecular Biology, University
of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michel Roberge
- Department
of Biochemistry and Molecular Biology, University
of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Allan Jacobson
- Department
of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Westley Friesen
- PTC
Therapeutics, 100 Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Ellen Welch
- PTC
Therapeutics, 100 Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Yale E. Goldman
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Barry S. Cooperman
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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797
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Capriotti E, Ozturk K, Carter H. Integrating molecular networks with genetic variant interpretation for precision medicine. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1443. [PMID: 30548534 PMCID: PMC6450710 DOI: 10.1002/wsbm.1443] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 02/01/2023]
Abstract
More reliable and cheaper sequencing technologies have revealed the vast mutational landscapes characteristic of many phenotypes. The analysis of such genetic variants has led to successful identification of altered proteins underlying many Mendelian disorders. Nevertheless the simple one‐variant one‐phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders. Although experimental and computational approaches have improved detection of functionally deleterious variants and important interactions between gene products, the development of comprehensive models relating genotype and phenotypes remains a challenge in the field of genomic medicine. In this context, a new view of the pathologic state as significant perturbation of the network of interactions between biomolecules is crucial for the identification of biochemical pathways associated with complex phenotypes. Seminal studies in systems biology combined the analysis of genetic variation with protein–protein interaction networks to demonstrate that even as biological systems evolve to be robust to genetic variation, their topologies create disease vulnerabilities. More recent analyses model the impact of genetic variants as changes to the “wiring” of the interactome to better capture heterogeneity in genotype–phenotype relationships. These studies lay the foundation for using networks to predict variant effects at scale using machine‐learning or algorithmic approaches. A wealth of databases and resources for the annotation of genotype–phenotype relationships have been developed to support developments in this area. This overview describes how study of the molecular interactome has generated insights linking the organization of biological systems to disease mechanism, and how this information can enable precision medicine. This article is categorized under:
Translational, Genomic, and Systems Medicine > Translational Medicine Biological Mechanisms > Cell Signaling Models of Systems Properties and Processes > Mechanistic Models Analytical and Computational Methods > Computational Methods
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Affiliation(s)
- Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Kivilcim Ozturk
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California
| | - Hannah Carter
- Department of Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, California
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798
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Wehrle A, Witkos TM, Schneider JC, Hoppmann A, Behringer S, Köttgen A, Elting M, Spranger J, Lowe M, Lausch E. A common pathomechanism in GMAP-210- and LBR-related diseases. JCI Insight 2018; 3:121150. [PMID: 30518689 PMCID: PMC6328090 DOI: 10.1172/jci.insight.121150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022] Open
Abstract
Biallelic loss-of-function mutations in TRIP11, encoding the golgin GMAP-210, cause the lethal human chondrodysplasia achondrogenesis 1A (ACG1A). We now find that a homozygous splice-site mutation of the lamin B receptor (LBR) gene results in the same phenotype. Intrigued by the genetic heterogeneity, we compared GMAP-210- and LBR-deficient primary cells to unravel how particular mutations in LBR cause a phenocopy of ACG1A. We could exclude a regulatory interaction between LBR and GMAP-210 in patients' cells. However, we discovered a common disruption of Golgi apparatus architecture that was accompanied by decreased secretory trafficking in both cases. Deficiency of Golgi-dependent glycan processing indicated a similar downstream effect of the disease-causing mutations upon Golgi function. Unexpectedly, our results thus point to a common pathogenic mechanism in GMAP-210- and LBR-related diseases attributable to defective secretory trafficking at the Golgi apparatus.
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Affiliation(s)
- Anika Wehrle
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomasz M. Witkos
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Judith C. Schneider
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anselm Hoppmann
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Genetic Epidemiology, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sidney Behringer
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mariet Elting
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, Netherlands
| | - Jürgen Spranger
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Centre-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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799
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Structural assembly of the megadalton-sized receptor for intestinal vitamin B 12 uptake and kidney protein reabsorption. Nat Commun 2018; 9:5204. [PMID: 30523278 PMCID: PMC6283879 DOI: 10.1038/s41467-018-07468-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/01/2018] [Indexed: 11/08/2022] Open
Abstract
The endocytic receptor cubam formed by the 460-kDa protein cubilin and the 45-kDa transmembrane protein amnionless (AMN), is essential for intestinal vitamin B12 (B12) uptake and for protein (e.g. albumin) reabsorption from the kidney filtrate. Loss of function of any of the two components ultimately leads to serious B12 deficiency and urinary protein loss in humans (Imerslund-Gräsbeck’s syndrome, IGS). Here, we present the crystal structure of AMN in complex with the amino-terminal region of cubilin, revealing a sophisticated assembly of three cubilin subunits combining into a single intertwined β-helix domain that docks to a corresponding three-faced β-helix domain in AMN. This β-helix-β-helix association thereby anchors three ligand-binding cubilin subunits to the transmembrane AMN. Electron microscopy of full-length cubam reveals a 700–800 Å long tree-like structure with the potential of dimerization into an even larger complex. Furthermore, effects of known human mutations causing IGS are explained by the structural information. Cubilin and the transmembrane protein amnionless (AMN) form the endocytic receptor cubam that is essential for intestinal vitamin B12 uptake. Here the authors present the 2.3 Å crystal structure of AMN in complex with the amino-terminal region of cubilin and discuss cubam architecture and disease causing mutations.
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800
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Cystinuria: genetic aspects, mouse models, and a new approach to therapy. Urolithiasis 2018; 47:57-66. [PMID: 30515543 DOI: 10.1007/s00240-018-1101-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/27/2018] [Indexed: 01/07/2023]
Abstract
Cystinuria, a genetic disorder of cystine transport, is characterized by excessive excretion of cystine in the urine and recurrent cystine stones in the kidneys and, to a lesser extent, in the bladder. Males generally are more severely affected than females. The disorder may lead to chronic kidney disease in many patients. The cystine transporter (b0,+) is a heterodimer consisting of the rBAT (encoded by SLC3A1) and b0,+AT (encoded by SLC7A9) subunits joined by a disulfide bridge. The molecular basis of cystinuria is known in great detail, and this information is now being used to define genotype-phenotype correlations. Current treatments for cystinuria include increased fluid intake to increase cystine solubility and the administration of thiol drugs for more severe cases. These drugs, however, have poor patient compliance due to adverse effects. Thus, there is a need to reduce or eliminate the risks associated with therapy for cystinuria. Four mouse models for cystinuria have been described and these models provide a resource for evaluating the safety and efficacy of new therapies for cystinuria. We are evaluating a new approach for the treatment of cystine stones based on the inhibition of cystine crystal growth by cystine analogs. Our ongoing studies indicate that cystine diamides are effective in preventing cystine stone formation in the Slc3a1 knockout mouse model for cystinuria. In addition to crystal growth, crystal aggregation is required for stone formation. Male and female mice with cystinuria have comparable levels of crystalluria, but very few female mice form stones. The identification of factors that inhibit cystine crystal aggregation in female mice may provide insight into the gender difference in disease severity in patients with cystinuria.
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