701
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Mount SM, Avsec Ž, Carmel L, Casadio R, Çelik MH, Chen K, Cheng J, Cohen NE, Fairbrother WG, Fenesh T, Gagneur J, Gotea V, Holzer T, Lin CF, Martelli PL, Naito T, Nguyen TYD, Savojardo C, Unger R, Wang R, Yang Y, Zhao H. Assessing predictions of the impact of variants on splicing in CAGI5. Hum Mutat 2019; 40:1215-1224. [PMID: 31301154 DOI: 10.1002/humu.23869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/20/2019] [Accepted: 07/10/2019] [Indexed: 12/28/2022]
Abstract
Precision medicine and sequence-based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. In the past, few CAGI challenges have addressed the impact of sequence variants on splicing. In CAGI5, two challenges (Vex-seq and MaPSY) involved prediction of the effect of variants, primarily single-nucleotide changes, on splicing. Although there are significant differences between these two challenges, both involved prediction of results from high-throughput exon inclusion assays. Here, we discuss the methods used to predict the impact of these variants on splicing, their performance, strengths, and weaknesses, and prospects for predicting the impact of sequence variation on splicing and disease phenotypes.
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Affiliation(s)
- Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | | | - Ken Chen
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Jun Cheng
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Noa E Cohen
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,The integrated program for Computer Science and Computational Biology, School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Center For Computational Biology, Brown University, Providence, Rhode Island
| | - Tzila Fenesh
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Valer Gotea
- National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Tamar Holzer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Chiao-Feng Lin
- Translational Informatics, DNAnexus, Mountain View, California
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Tatsuhiko Naito
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, Biocomputing Group, University of Bologna, Bologna, Italy
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Robert Wang
- Department of Bioengineering, University of California, Berkeley, California.,Department of Plant and Molecular Biology, University of California, Berkeley, California
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Huiying Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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702
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Pietilä-Effati P, Saarinen JT, Löyttyniemi E, Autio R, Saarenhovi M, Haanpää MK, Kantola I. Natural course of Fabry disease with the p. Arg227Ter (p.R227*) mutation in Finland: Fast study. Mol Genet Genomic Med 2019; 7:e00930. [PMID: 31411008 PMCID: PMC6785458 DOI: 10.1002/mgg3.930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/06/2019] [Accepted: 07/23/2019] [Indexed: 12/02/2022] Open
Abstract
Background Fabry disease is caused by a deficient or an absent alfa‐galactosidase A activity and is an X‐linked disorder that results in organ damage and a shortened life span, especially in males. The severity of the disease depends on the type of mutation, gender, skewed X‐chromosome inactivation, and other still unknown factors. Methods In this article, we describe the natural course of a common classic Fabry disease mutation, p.Arg227Ter or p.R227*, in Finland. Results Four males and ten females belonged to two extended families. The mean age was 46 years (SD 18.4). Six patients (43%) had cardiac hypertrophy, three patients (21%) had ischemic stroke, and none had severe kidney dysfunction. Three patients had atrial fibrillation; two patients who had atrial fibrillation also had pacemakers. All males over 30 years of age had at least one of the following manifestations: cardiac hypertrophy, stroke, or proteinuria. In females, the severity of Fabry disease varied from classic multiorgan disease to a condition that mimicked the attenuated cardiac variant. No one was totally asymptomatic without any signs of Fabry disease. Cardiac magnetic resonance imaging was performed on nine of 14 patients was the most sensitive for detecting early cardiac manifestations. Five patients (55%) had late gadolinium enhancement‐positive segments. Conclusion Cardiac involvement should be effectively detected in females before considering them asymptomatic mutation carriers.
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Affiliation(s)
| | | | | | - Reijo Autio
- Department of Radiology, Vaasa Central Hospital, Vaasa, Finland
| | - Maria Saarenhovi
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Maria K Haanpää
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Ilkka Kantola
- Division of Medicine, Turku University Hospital, University of Turku, Turku, Finland
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703
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Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun 2019; 10:3583. [PMID: 31395865 PMCID: PMC6687891 DOI: 10.1038/s41467-019-11526-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we perform saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitutions and deletions. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and comprise a rich dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.
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704
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Muiño-Mosquera L, Steijns F, Audenaert T, Meerschaut I, De Paepe A, Steyaert W, Symoens S, Coucke P, Callewaert B, Renard M, De Backer J. Tailoring the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines for the Interpretation of Sequenced Variants in the FBN1 Gene for Marfan Syndrome: Proposal for a Disease- and Gene-Specific Guideline. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002039. [PMID: 29875124 DOI: 10.1161/circgen.117.002039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/09/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND The introduction of next-generation sequencing techniques has substantially increased the identification of new genetic variants and hence the necessity of accurate variant interpretation. In 2015, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology proposed new variant interpretation guidelines. Gene-specific characteristics were, however, not considered, sometimes leading to inconsistent variant interpretation. METHODS To allow a more uniform interpretation of variants in the FBN1 (fibrillin-1) gene, causing Marfan syndrome, we tailored these guidelines to this gene and disease. We adapted 15 of the 28 general criteria and classified 713 FBN1 variants previously identified in our laboratory as causal mutation or variant of uncertain significance according to these adapted guidelines. We then compared the agreement between previous methods and the adapted American College of Medical Genetics and Genomics and the Association for Molecular Pathology criteria. RESULTS Agreement between the methods was 86.4% (K-alpha, 0.6). Application of the tailored guidelines resulted in an increased number of variants of uncertain significance (14.5% to 24.2%). Of the 85 variants that were downscaled to likely benign or variant of uncertain significance, 59.7% were missense variants outside a well-established functional site. Available clinical- or segregation data, necessary to further classify these types of variants, were in many cases insufficient to aid the classification. CONCLUSIONS Our study shows that classification of variants remains challenging and may change over time. Currently, a higher level of evidence is necessary to classify a variant as pathogenic. Gene-specific guidelines may be useful to allow a more precise and uniform interpretation of the variants to accurately support clinical decision-making.
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Affiliation(s)
- Laura Muiño-Mosquera
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.) .,Division of Pediatric Cardiology (L.M.-M.)
| | - Felke Steijns
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Tjorven Audenaert
- Department of Cardiology (T.A., J.D.B.), Ghent University Hospital, Belgium
| | - Ilse Meerschaut
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Anne De Paepe
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Wouter Steyaert
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Sofie Symoens
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Paul Coucke
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Bert Callewaert
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Marjolijn Renard
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Julie De Backer
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.).,Department of Cardiology (T.A., J.D.B.), Ghent University Hospital, Belgium
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705
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Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat 2019; 40:1030-1038. [PMID: 31116477 PMCID: PMC6772141 DOI: 10.1002/humu.23798] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/21/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023]
Abstract
The growing availability of human genetic variation has given rise to novel methods of measuring genetic tolerance that better interpret variants of unknown significance. We recently developed a concept based on protein domain homology in the human genome to improve variant interpretation. For this purpose, we mapped population variation from the Exome Aggregation Consortium (ExAC) and pathogenic mutations from the Human Gene Mutation Database (HGMD) onto Pfam protein domains. The aggregation of these variation data across homologous domains into meta-domains allowed us to generate amino acid resolution of genetic intolerance profiles for human protein domains. Here, we developed MetaDome, a fast and easy-to-use web server that visualizes meta-domain information and gene-wide profiles of genetic tolerance. We updated the underlying data of MetaDome to contain information from 56,319 human transcripts, 71,419 protein domains, 12,164,292 genetic variants from gnomAD, and 34,076 pathogenic mutations from ClinVar. MetaDome allows researchers to easily investigate their variants of interest for the presence or absence of variation at corresponding positions within homologous domains. We illustrate the added value of MetaDome by an example that highlights how it may help in the interpretation of variants of unknown significance. The MetaDome web server is freely accessible at https://stuart.radboudumc.nl/metadome.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Coos Baakman
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Daan Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Bio‐informaticaHAN University of Applied SciencesNijmegenThe Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Institute of Genetic Medicine, International Centre for LifeNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Gerrit Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
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706
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Jolly A, Bayram Y, Turan S, Aycan Z, Tos T, Abali ZY, Hacihamdioglu B, Coban Akdemir ZH, Hijazi H, Bas S, Atay Z, Guran T, Abali S, Bas F, Darendeliler F, Colombo R, Barakat TS, Rinne T, White JJ, Yesil G, Gezdirici A, Gulec EY, Karaca E, Pehlivan D, Jhangiani SN, Muzny DM, Poyrazoglu S, Bereket A, Gibbs RA, Posey JE, Lupski JR. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease. J Clin Endocrinol Metab 2019; 104:3049-3067. [PMID: 31042289 PMCID: PMC6563799 DOI: 10.1210/jc.2019-00248] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
Abstract
CONTEXT Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait. OBJECTIVE To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI. DESIGN, SETTING, AND PARTICIPANTS We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity. RESULTS This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds. CONCLUSIONS ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zehra Aycan
- Department of Pediatric Endocrinology, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Zehra Yavas Abali
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | | | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serpil Bas
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zeynep Atay
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Saygin Abali
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Firdevs Bas
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Darendeliler
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Roberto Colombo
- Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
- Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli University Hospital, Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sukran Poyrazoglu
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Abdullah Bereket
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
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707
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Pace NP, Benoit V, Agius D, Grima MA, Parascandalo R, Hilbert P, Borg I. Two novel GJA1 variants in oculodentodigital dysplasia. Mol Genet Genomic Med 2019; 7:e882. [PMID: 31347275 PMCID: PMC6732303 DOI: 10.1002/mgg3.882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/20/2022] Open
Abstract
Background Oculodentodigital dysplasia (ODDD) is a rare disorder with pleiotropic effects involving multiple body systems, caused by mutations in the gap junction protein alpha 1 (GJA1) gene. GJA1 gene encodes a polytopic connexin membrane protein, Cx43, that is a component of connexon membrane channels. Methods We describe two unrelated female probands referred for a genetic review in view of a dysmorphic clinical phenotype. Results Two novel missense mutations in GJA1 that substitute conserved amino acids in the first and second transmembrane domains (NM_000165.5: c.77T>C p.Leu26Pro and NM_000165.5:c.287T>G p.Val96Gly) were detected through targeted sequencing of GJA1. These variants were detected in the heterozygous state in the two Maltese probands and segregated with the disease phenotype. Conclusion This report further expands the mutational spectrum of ODDD.
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Affiliation(s)
- Nikolai P. Pace
- Centre for Molecular Medicine and BiobankingUniversity of MaltaMsidaMalta
| | - Valerie Benoit
- Département de Biologie MoléculaireInstitut de Pathologie et de Génétique ASBLGosseliesBelgium
| | - David Agius
- Department of OphthalmologyMater Dei HospitalMsidaMalta
| | | | | | - Pascale Hilbert
- Département de Biologie MoléculaireInstitut de Pathologie et de Génétique ASBLGosseliesBelgium
| | - Isabella Borg
- Centre for Molecular Medicine and BiobankingUniversity of MaltaMsidaMalta
- Department of Pathology, Faculty of Medicine and SurgeryUniversity of MaltaMsidaMalta
- Medical Genetics Unit, Department of PathologyMater Dei HospitalMsidaMalta
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708
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The clinical and radiological profile of primary lateral sclerosis: a population-based study. J Neurol 2019; 266:2718-2733. [PMID: 31325016 DOI: 10.1007/s00415-019-09473-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Primary lateral sclerosis is a progressive upper-motor-neuron disorder associated with markedly longer survival than ALS. In contrast to ALS, the genetic susceptibility, histopathological profile and imaging signature of PLS are poorly characterised. Suspected PLS patients often face considerable diagnostic delay and prognostic uncertainty. OBJECTIVE To characterise the distinguishing clinical, genetic and imaging features of PLS in contrast to ALS and healthy controls. METHODS A prospective population-based study was conducted with 49 PLS patients, 100 ALS patients and 100 healthy controls using genetic profiling, standardised clinical assessments and neuroimaging. Whole-brain and region-of-interest analyses were undertaken to evaluate patterns of grey and white matter degeneration. RESULTS In PLS, disease burden in the motor cortex is more medial than in ALS consistent with its lower limb symptom-predominance. PLS is associated with considerable cerebellar white and grey matter degeneration and the extra-motor profile of PLS includes marked insular, inferior frontal and left pars opercularis pathology. Contrary to ALS, PLS spares the postcentral gyrus. The body and splenium of the corpus callosum are preferentially affected in PLS, in contrast to the genu involvement observed in ALS. Clinical measures show anatomically meaningful correlations with imaging metrics in a somatotopic distribution. PLS patients tested negative for C9orf72 repeat expansions, known ALS and HSP-associated genes. CONCLUSIONS Multiparametric imaging in PLS highlights disease-specific motor and extra-motor involvement distinct from ALS. In a condition where limited post-mortem data are available, imaging offers invaluable pathological insights. Anatomical correlations with clinical metrics confirm the biomarker potential of quantitative neuroimaging in PLS.
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709
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Martinez-Matilla M, Blanco-Verea A, Santori M, Ansede-Bermejo J, Ramos-Luis E, Gil R, Bermejo AM, Lotufo-Neto F, Hirata MH, Brisighelli F, Paramo M, Carracedo A, Brion M. Genetic susceptibility in pharmacodynamic and pharmacokinetic pathways underlying drug-induced arrhythmia and sudden unexplained deaths. Forensic Sci Int Genet 2019; 42:203-212. [PMID: 31376648 DOI: 10.1016/j.fsigen.2019.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 12/21/2022]
Abstract
Drug-induced arrhythmia is an adverse drug reaction that can be potentially fatal since it is mostly related to drug-induced QT prolongation, a known risk factor for Torsade de Pointes and sudden cardiac death (SCD). Several risk factors have been described in association to these drug-induced events, such as preexistent cardiac disease and genetic variation. Our objective was to study the genetic susceptibility in pharmacodynamic and pharmacokinetic pathways underlying suspected drug-induced arrhythmias and sudden unexplained deaths in 32 patients. The genetic component in the pharmacodynamic pathway was studied by analysing 96 genes associated with higher risk of SCD through massive parallel sequencing. Pharmacokinetic-mediated genetic susceptibility was investigated by studying the genes encoding cytochrome P450 enzymes using medium-throughput genotyping. Pharmacodynamic analysis showed three probably pathogenic variants and 45 variants of uncertain significance in 28 patients, several of them previously described in relation to mild or late onset cardiomyopathies. These results suggest that genetic variants in cardiomyopathy genes, in addition to those related with channelopathies, could be relevant to drug-induced cardiotoxicity and contribute to the arrhythmogenic phenotype. Pharmacokinetic analysis showed three patients that could have an altered metabolism of the drugs they received involving CYP2C19 and/or CYP2D6, probably contributing to the arrhythmogenic phenotype. The study of genetic variants in both pharmacodynamic and pharmacokinetic pathways may be a useful strategy to understand the multifactorial mechanism of drug-induced events in both clinical practice and forensic field. However, it is necessary to comprehensively study and evaluate the contribution of the genetic susceptibility to drug-induced cardiotoxicity.
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Affiliation(s)
- M Martinez-Matilla
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.
| | - A Blanco-Verea
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - M Santori
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - J Ansede-Bermejo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
| | - E Ramos-Luis
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - R Gil
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - A M Bermejo
- Instituto de Ciencias Forenses "Luis Concheiro" (INCIFOR), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - F Lotufo-Neto
- Psiquiatry Institute - Faculty of Medicine at University of São Paulo, São Paulo, Brazil
| | - M H Hirata
- Institute Dante Pazzanese of Cardiology, São Paulo, Brazil; School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - F Brisighelli
- Institute of Public Health, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M Paramo
- Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
| | - M Brion
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (A Coruña), Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain; Centro Nacional de Genotipado-CeGen-USC-PRB3-ISCIII, Santiago de Compostela, Spain
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710
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Siavrienė E, Petraitytė G, Mikštienė V, Rančelis T, Maldžienė Ž, Morkūnienė A, Byčkova J, Utkus A, Kučinskas V, Preikšaitienė E. A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. BMC MEDICAL GENETICS 2019; 20:127. [PMID: 31315586 PMCID: PMC6637606 DOI: 10.1186/s12881-019-0859-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
Background CHARGE syndrome (MIM# 214800)—which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay—is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing. Case presentation In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband’s DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient’s RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome. Conclusion Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis. Electronic supplementary material The online version of this article (10.1186/s12881-019-0859-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikštienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Aušra Morkūnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Jekaterina Byčkova
- Center of Ear, Nose and Throat Diseases, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
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711
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Neerman N, Faust G, Meeks N, Modai S, Kalfon L, Falik-Zaccai T, Kaplun A. A clinically validated whole genome pipeline for structural variant detection and analysis. BMC Genomics 2019; 20:545. [PMID: 31307387 PMCID: PMC6631445 DOI: 10.1186/s12864-019-5866-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background With the continuing decrease in cost of whole genome sequencing (WGS), we have already approached the point of inflection where WGS testing has become economically feasible, facilitating broader access to the benefits that are helping to define WGS as the new diagnostic standard. WGS provides unique opportunities for detection of structural variants; however, such analyses, despite being recognized by the research community, have not previously made their way into routine clinical practice. Results We have developed a clinically validated pipeline for highly specific and sensitive detection of structural variants basing on 30X PCR-free WGS. Using a combination of breakpoint analysis of split and discordant reads, and read depth analysis, the pipeline identifies structural variants down to single base pair resolution. False positives are minimized using calculations for loss of heterozygosity and bi-modal heterozygous variant allele frequencies to enhance heterozygous deletion and duplication detection respectively. Compound and potential compound combinations of structural variants and small sequence changes are automatically detected. To facilitate clinical interpretation, identified variants are annotated with phenotype information derived from HGMD Professional and population allele frequencies derived from public and Variantyx allele frequency databases. Single base pair resolution enables easy visual inspection of potentially causal variants using the IGV genome browser as well as easy biochemical validation via PCR. Analytical and clinical sensitivity and specificity of the pipeline has been validated using analysis of Genome in a Bottle reference genomes and known positive samples confirmed by orthogonal sequencing technologies. Conclusion Consistent read depth of PCR-free WGS enables reliable detection of structural variants of any size. Annotation both on gene and variant level allows clinicians to match reported patient phenotype with detected variants and confidently report causative finding in all clinical cases used for validation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5866-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Limor Kalfon
- Institute of Human Genetics, Galilee Medical Center, Naharia, Israel
| | - Tzipora Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Naharia, Israel.,The Azrieli Faculty of Medicine, Bar Ilan, Safed, Israel
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712
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Macias I, Laín A, Bernardo-Seisdedos G, Gil D, Gonzalez E, Falcon-Perez JM, Millet O. Hereditary tyrosinemia type I-associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate. J Biol Chem 2019; 294:13051-13060. [PMID: 31300554 PMCID: PMC6721957 DOI: 10.1074/jbc.ra119.009367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
More than 100 mutations in the gene encoding fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1), a metabolic disorder characterized by elevated blood levels of tyrosine. Some of these mutations are known to decrease FAH catalytic activity, but the mechanisms of FAH mutation–induced pathogenicity remain poorly understood. Here, using diffusion ordered NMR spectroscopy, cryo-EM, and CD analyses, along with site-directed mutagenesis, enzymatic assays, and molecular dynamics simulations, we investigated the putative role of thermodynamic and kinetic stability in WT FAH and a representative set of 19 missense mutations identified in individuals with HT1. We found that at physiological temperatures and concentrations, WT FAH is in equilibrium between a catalytically active dimer and a monomeric species, with the latter being inactive and prone to oligomerization and aggregation. We also found that the majority of the deleterious mutations reduce the kinetic stability of the enzyme and always accelerate the FAH aggregation pathway. Depending mainly on the position of the amino acid in the structure, pathogenic mutations either reduced the dimer population or decreased the energy barrier that separates the monomer from the aggregate. The mechanistic insights reported here pave the way for the development of pharmacological chaperones that target FAH to tackle the severe disease HT1.
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Affiliation(s)
- Iratxe Macias
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ana Laín
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ganeko Bernardo-Seisdedos
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - David Gil
- Electron Microscopy Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Esperanza Gonzalez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Juan M Falcon-Perez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, 48013 Spain
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain.
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713
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The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach. Structure 2019; 27:1384-1394.e4. [PMID: 31303482 DOI: 10.1016/j.str.2019.06.006] [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: 04/10/2019] [Revised: 05/21/2019] [Accepted: 06/17/2019] [Indexed: 01/09/2023]
Abstract
The unique membrane composition of cilia is maintained by a diffusion barrier at the transition zone that is breached when the BBSome escorts signaling receptors out of cilia. Understanding how the BBSome removes proteins from cilia has been hampered by a lack of structural information. Here, we present a nearly complete Cα model of BBSome purified from cow retina. The model is based on a single-particle cryo-electron microscopy density map at 4.9-Å resolution that was interpreted with the help of comprehensive Rosetta-based structural modeling constrained by crosslinking mass spectrometry data. We find that BBSome subunits have a very high degree of interconnectivity, explaining the obligate nature of the complex. Furthermore, like other coat adaptors, the BBSome exists in an autoinhibited state in solution and must thus undergo a conformational change upon recruitment to membranes by the small GTPase ARL6/BBS3. Our model provides the first detailed view of the machinery enabling ciliary exit.
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714
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Alméciga-Diaz CJ, Hidalgo OA, Olarte-Avellaneda S, Rodríguez-López A, Guzman E, Garzón R, Pimentel-Vera LN, Puentes-Tellez MA, Rojas-Rodriguez AF, Gorshkov K, Li R, Zheng W. Identification of Ezetimibe and Pranlukast as Pharmacological Chaperones for the Treatment of the Rare Disease Mucopolysaccharidosis Type IVA. J Med Chem 2019; 62:6175-6189. [PMID: 31188588 PMCID: PMC11292729 DOI: 10.1021/acs.jmedchem.9b00428] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mucopolysaccharidosis type IVA (MPS IVA) is a rare disease caused by mutations in the gene encoding the lysosomal enzyme N-acetylgalactosamine-6-sulfate sulfatase (GALNS). We report here two GALNS pharmacological chaperones, ezetimibe and pranlukast, identified by molecular docking-based virtual screening. These compounds bound to the active cavity of GALNS and increased its thermal stability as well as the production of recombinant GALNS in bacteria, yeast, and HEK293 cells. MPS IVA fibroblasts treated with these chaperones exhibited increases in GALNS protein and enzyme activity and reduced the size of enlarged lysosomes. Abnormalities in autophagy markers p62 and LC3B-II were alleviated by ezetimibe and pranlukast. Combined treatment of recombinant GALNS with ezetimibe or pranlukast produced an additive effect. Altogether, the results demonstrate that ezetimibe and pranlukast can increase the yield of recombinant GALNS and be used as a monotherapy or combination therapy to improve the therapeutic efficacy of MPS IVA enzyme replacement therapy.
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Affiliation(s)
- Carlos J. Alméciga-Diaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Oscar A. Hidalgo
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Sergio Olarte-Avellaneda
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
- Pharmacy Department, Faculty of Science, Universidad Nacional de Colombia, Bogotá D.C., 111321, Colombia
| | - Alexander Rodríguez-López
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
- Chemistry Department, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Esteban Guzman
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Rafael Garzón
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Luisa Natalia Pimentel-Vera
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - María Alejandra Puentes-Tellez
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Andrés Felipe Rojas-Rodriguez
- Computational and Structural Biochemistry, Departamento de Nutrición y Bioquímica, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C., 110231, Colombia
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rong Li
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
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715
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Gaertner-Rommel A, Tiesmeier J, Jakob T, Strickmann B, Veit G, Bachmann-Mennenga B, Paluszkiewicz L, Klingel K, Schulz U, Laser KT, Karger B, Pfeiffer H, Milting H. Molecular autopsy and family screening in a young case of sudden cardiac death reveals an unusually severe case of FHL1 related hypertrophic cardiomyopathy. Mol Genet Genomic Med 2019; 7:e841. [PMID: 31293105 PMCID: PMC6687666 DOI: 10.1002/mgg3.841] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a genetic cardiomyopathy with a prevalence of about 1:200. It is characterized by left ventricular hypertrophy, diastolic dysfunction and interstitial fibrosis; HCM might lead to sudden cardiac death (SCD) especially in the young. Due to low autopsy frequencies of sudden unexplained deaths (SUD) the true prevalence of SCD and especially of HCM among SUD remains unclear. Even in cases of proven SCD genetic testing is not a routine procedure precluding appropriate risk stratification and counseling of relatives. METHODS Here we report a case of SCD in a 19-year-old investigated by combined forensic and molecular autopsy. RESULTS During autopsy of the index-patient HCM was detected. As no other possible cause of death could be uncovered by forensic autopsy the event was classified as SCD. Molecular autopsy identified two (probably) pathogenic genetic variants in FHL1 and MYBPC3. The MYBPC3 variant had an incomplete penetrance. The FHL1 variant was a de novo mutation. We detected reduced FHL1 mRNA levels and no FHL1 protein in muscle samples suggesting nonsense-mediated mRNA decay and/or degradation of the truncated protein in the SCD victim revealing a plausible disease mechanism. CONCLUSION The identification of the genetic cause of the SCD contributed to the rational counseling of the relatives and risk assessment within the family. Furthermore our study revealed evidences for the pathomechanism of FHL1 mutations.
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Affiliation(s)
- Anna Gaertner-Rommel
- Klinikum der Ruhr-Universität Bochum, Klinik für Thorax- und Kardiovaskularchirurgie und Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Herz- und Diabeteszentrum NRW, Bad Oeynhausen, Germany
| | - Jens Tiesmeier
- Mühlenkreiskliniken, Krankenhaus Lübbecke-Rahden, Institut für Anästhesiologie, Intensiv- und Notfallmedizin, Medizin Campus OWL, Ruhr-Universität Bochum, Bochum, Germany
| | - Thomas Jakob
- Klinikum Herford, Universitätsklinik für Anästhesiologie, Medizin Campus OWL, Ruhr-Universität Bochum, Herford, Germany
| | | | - Gunter Veit
- Mühlenkreiskliniken, Krankenhaus Lübbecke-Rahden, Institut für Anästhesiologie, Intensiv- und Notfallmedizin, Medizin Campus OWL, Ruhr-Universität Bochum, Bochum, Germany
| | - Bernd Bachmann-Mennenga
- Mühlenkreiskliniken, Johannes Wesling Klinikum, Universitätsinstitut für Anästhesiologie, Intensiv- und Notfallmedizin, Medizin Campus OWL, Ruhr-Universität Bochum, Minden, Germany
| | - Lech Paluszkiewicz
- Klinikum der Ruhr-Universität Bochum, Klinik für Thorax- und Kardiovaskularchirurgie und Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Herz- und Diabeteszentrum NRW, Bad Oeynhausen, Germany
| | - Karin Klingel
- Kardiopathologie, Universitätsklinikum Tübingen, Institut für Pathologie und Neuropathologie, Tubingen, Germany
| | - Uwe Schulz
- Klinikum der Ruhr-Universität Bochum, Klinik für Thorax- und Kardiovaskularchirurgie und Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Herz- und Diabeteszentrum NRW, Bad Oeynhausen, Germany
| | - Kai T Laser
- Zentrum für angeborene Herzfehler, Herz- und Diabeteszentrum NRW, Klinikum der Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Bernd Karger
- Universitätsklinikum Münster, Institut für Rechtsmedizin, Münster, Germany
| | - Heidi Pfeiffer
- Universitätsklinikum Münster, Institut für Rechtsmedizin, Münster, Germany
| | - Hendrik Milting
- Klinikum der Ruhr-Universität Bochum, Klinik für Thorax- und Kardiovaskularchirurgie und Erich und Hanna Klessmann-Institut für Kardiovaskuläre Forschung und Entwicklung, Herz- und Diabeteszentrum NRW, Bad Oeynhausen, Germany
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716
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Chaves-Markman ÂV, Markman M, Calado EB, Pires RF, Santos-Veloso MAO, Pereira CMF, Lordsleem ABDMDS, Lima SGD, Markman Filho B, Oliveira DCD. GLA Gene Mutation in Hypertrophic Cardiomyopathy with a New Variant Description: Is it Fabry's Disease? Arq Bras Cardiol 2019; 113:77-84. [PMID: 31291414 PMCID: PMC6684188 DOI: 10.5935/abc.20190112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the alpha galactosidase A gene (GLA) that lead to the enzymatic deficiency of alpha galactosidase (α-Gal A), resulting in the accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3), causing multiple organ dysfunctions. OBJECTIVE To perform GLA gene screening in a group of patients with echocardiographic diagnosis of hypertrophic cardiomyopathy (HCM). METHODS a cross-sectional study was conducted with HCM patients from a university hospital. Patients with coronary artery disease and valvulopathies were excluded. Mutation analysis of the GLA gene was performed. In male subjects, the analysis was performed after evidence of low α-Gal A activity. RESULTS 60 patients with echocardiographic diagnosis of HCM were included. Age ranged from 12 to 85 years and 60% were women. Mean myocardial fibrosis percentage on MRI was 10.7 ± 13.1% and mean ventricular thickness was18.7 ± 6.7 mm. Four patients had the following GLA gene mutations: c.967C>A (p.Pro323Thr), not yet described in the literature; c.937G>T (p.Asp313Tyr); and c.352C>T (p.Arg118Cys). All patients had normal levels of lyso-Gb3 and non-ischemic myocardial fibrosis on magnetic resonance imaging; one patient had proteinuria and one patient had ventricular tachycardia. CONCLUSION in this study, the frequency of mutation in the GLA gene in patients with HCM was 6.7%. A novel mutation in exon 6 of the GLA gene, c.967C>A (p.Pro323Thr), was identified. Patients with HCM may have GLA mutations and FD should be ruled out. Plasma (lyso-Gb3) levels do not seem to be sufficient to attain a diagnosis and organ biopsy should be considered.
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Affiliation(s)
- Ândrea Virgínia Chaves-Markman
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil.,Hospital Agamenon Magalhães, Recife, PE - Brazil.,Universidade Federal de Pernambuco - Grupo de pesquisa em Epidemiologia e Cardiologia (EPICARDIO), Recife, PE - Brazil.,Pós Graduação em Inovação Terapêutica (PPGIT) - Universidade Federal de Pernambuco, Recife, PE - Brasil.,Centro Universitário Mauricio de Nassau - Curso de Medicina, Recife, PE - Brasil
| | | | - Eveline Barros Calado
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil
| | | | - Marcelo Antônio Oliveira Santos-Veloso
- Universidade Federal de Pernambuco - Grupo de pesquisa em Epidemiologia e Cardiologia (EPICARDIO), Recife, PE - Brazil.,Pós Graduação em Inovação Terapêutica (PPGIT) - Universidade Federal de Pernambuco, Recife, PE - Brasil.,Centro Universitário Mauricio de Nassau - Curso de Medicina, Recife, PE - Brasil
| | | | - Andréa Bezerra de Melo da Silveira Lordsleem
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil.,Universidade Federal de Pernambuco - Grupo de pesquisa em Epidemiologia e Cardiologia (EPICARDIO), Recife, PE - Brazil.,Centro Universitário Mauricio de Nassau - Curso de Medicina, Recife, PE - Brasil
| | - Sandro Gonçalves de Lima
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil.,Universidade Federal de Pernambuco - Grupo de pesquisa em Epidemiologia e Cardiologia (EPICARDIO), Recife, PE - Brazil.,Centro Universitário Mauricio de Nassau - Curso de Medicina, Recife, PE - Brasil
| | - Brivaldo Markman Filho
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil
| | - Dinaldo Cavalcanti de Oliveira
- Universidade Federal de Pernambuco - Hospital das Clínicas - Área Acadêmica de Medicina Clínica - Centro de Medicina Clínica - CCM, Recife, PE - Brazil.,Pós Graduação em Inovação Terapêutica (PPGIT) - Universidade Federal de Pernambuco, Recife, PE - Brasil.,Centro Universitário Mauricio de Nassau - Curso de Medicina, Recife, PE - Brasil
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717
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Liu H, Xu L, Huang H, Zhao P, Yang R, Zhou Q, Liu G. Systematic profiling of clinical missence mutation effects on the intermolecular interaction between human growth hormone and its receptor in isolated growth hormone deficiency. J Mol Graph Model 2019; 92:1-7. [PMID: 31279174 DOI: 10.1016/j.jmgm.2019.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/17/2022]
Abstract
Isolated growth hormone deficiency (IGHD) is the most common pituitary hormone deficiency and can result from congenital or acquired causes. Among the known factors, genetic mutations in human growth hormone (hGH) remain the most frequent cause of IGHD, which influence the binding of hGH to its cognate receptor (hGHbp). Although previous studies have systematically investigated the residue importance at hGH-hGHbp complex interface, the molecular role of IGHD-associated residue mutations in the complex function still remains largely unexplored. Here, a total of 21 known hGH naturally-occurring missence mutations that have been clinically observed to be involved in IGHD disorder are collected and confirmed by original literature; they effects on the conformation, energetics and dynamics of hGH-hGHbp recognition and interaction are dissected at molecular level by using atomistic dynamics simulations, binding energy calculations and fluorescence spectroscopy assays. A systematic profile of hGH-hGHbp binding response to these clinical missence mutations is created, based on which it is revealed that (i) most mutations have appreciably unfavorable effect on the binding, which potentially destabilize the complex interaction, while only very few are predicted as moderate stabilizers for the complex system, and (ii) these disease-related mutations can locate either at complex interface or in hGH protein interior far away from the interface; both can influence the complex binding through either direct interaction or indirect allostericity. Two mutations, E100K (non-interface) and G146R (interface), are identified to address potent destabilization effect on hGH-hGHbp complex system; they can reduce the complex binding affinity by 8-fold (Kd changes from 0.76 to 5.9 nM) and 46-fold (Kd changes from 0.76 to 34.7 nM), respectively.
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Affiliation(s)
- Hui Liu
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Peiran Zhao
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Rongrong Yang
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Qing Zhou
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Guanghua Liu
- Department of Pediatrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China.
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718
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Chiara M, Primon I, Tarantini L, Agnelli L, Brancaleoni V, Granata F, Bollati V, Di Pierro E. Targeted resequencing of FECH locus reveals that a novel deep intronic pathogenic variant and eQTLs may cause erythropoietic protoporphyria (EPP) through a methylation-dependent mechanism. Genet Med 2019; 22:35-43. [DOI: 10.1038/s41436-019-0584-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/05/2019] [Indexed: 12/29/2022] Open
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719
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Gribouval O, Boyer O, Hummel A, Dantal J, Martinez F, Sberro-Soussan R, Etienne I, Chauveau D, Delahousse M, Lionet A, Allard J, Pouteil Noble C, Tête MJ, Heidet L, Antignac C, Servais A. Identification of genetic causes for sporadic steroid-resistant nephrotic syndrome in adults. Kidney Int 2019; 94:1013-1022. [PMID: 30348286 DOI: 10.1016/j.kint.2018.07.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/18/2018] [Accepted: 07/12/2018] [Indexed: 01/15/2023]
Abstract
Monogenic forms of Steroid-Resistant Nephrotic Syndrome (SRNS) have been widely characterized, but genetic screening paradigms preferentially address congenital, infantile onset, and familial cases. Our aim was to characterize the distribution of disease-causing gene mutations in adults with sporadic SRNS or focal segmental glomerulosclerosis (FSGS). We selected adult patients with non-syndromic, biopsy-proven FSGS or SRNS in the absence of known family history. Strict clinical criteria included lack of response to glucocorticoids and cyclosporine, and no recurrence after kidney transplantation. Mutations in SRNS genes were detected using a targeted gene panel. Sixteen of 135 tested participants (11.8%) carried pathogenic mutations in monogenic SRNS genes, and 14 others (10.4%) carried two APOL1 high-risk alleles. Autosomal recessive disease was diagnosed in 5 participants, autosomal dominant disease in 9, and X-linked disease in 2. Four participants carried a de novo heterozygous mutation. Among the 16 participants with identified mutations in monogenic SNRS genes, 7 (43.7%) had type IV collagen mutations. Mutations in monogenic SNRS genes were identified primarily in participants with proteinuria onset before 25 years of age, while the age at disease onset was variable in those with APOL1 high-risk genotype. Mean age at diagnosis was lower and renal survival was worse in participants with identified mutations in SNRS genes than in those without mutations. We found a significant rate of pathogenic mutations in adults with SRNS, with Type IV collagen mutations being the most frequent. These findings may have immediate impact on clinical practice.
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Affiliation(s)
- Olivier Gribouval
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France
| | - Olivia Boyer
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France; Pediatric Nephrology, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France
| | - Aurélie Hummel
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France; Adult Nephrology & Transplantation, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France
| | | | - Frank Martinez
- Adult Nephrology & Transplantation, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France
| | - Rebecca Sberro-Soussan
- Adult Nephrology & Transplantation, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France
| | - Isabelle Etienne
- Nephrology Department, Hôpital de Bois-Guillaume, CHU Rouen, Rouen, France
| | - Dominique Chauveau
- Department of Nephrology and Organ Transplantation, CHU Rangueil, Toulouse, France
| | | | - Arnaud Lionet
- Nephrology Department, Hôpital Huriez, CHU Lille, Lille, France
| | | | - Claire Pouteil Noble
- Nephrology-Transplantation Department, Hôpital Edouard Herriot, Lyon I University, Lyon, France
| | - Marie-Josèphe Tête
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France
| | - Laurence Heidet
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France; Pediatric Nephrology, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France; Genetic Department, Necker Hospital, APHP, Paris, France
| | - Corinne Antignac
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France; Genetic Department, Necker Hospital, APHP, Paris, France.
| | - Aude Servais
- Inserm U1163, Imagine Institute, Paris Descartes University, Paris, France; Adult Nephrology & Transplantation, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, Paris, France.
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720
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Machini K, Ceyhan-Birsoy O, Azzariti DR, Sharma H, Rossetti P, Mahanta L, Hutchinson L, McLaughlin H, Green RC, Lebo M, Rehm HL, Rehm HL. Analyzing and Reanalyzing the Genome: Findings from the MedSeq Project. Am J Hum Genet 2019; 105:177-188. [PMID: 31256874 DOI: 10.1016/j.ajhg.2019.05.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Although genome sequencing is increasingly available in clinical and research settings, many questions remain about the interpretation of sequencing data. In the MedSeq Project, we explored how much effort is required to evaluate and report on more than 4,500 genes reportedly associated with monogenic conditions, as well as pharmacogenomic (PGx) markers, blood antigen serotyping, and polygenic risk scores in 100 individuals (50 with cardiomyopathy and 50 healthy) randomized to the sequencing arm. We defined the quality thresholds for determining the need for Sanger confirmation. Finally, we examined the effort needed and new findings revealed by reanalyzing each genome (6-23 months after initial analysis; mean 13 months). Monogenic disease risk and carrier status were reported in 21% and 94% of participants, respectively. Only two participants had no monogenic disease risk or carrier status identified. For the PGx results (18 genotypes in six genes for five drugs), the identified diplotypes prompted recommendation for non-standard dosing of at least one of the analyzed drugs in 95% of participants. For blood antigen studies, we found that 31% of participants had a rare blood antigen genotype. In the cardiomyopathy cohort, an explanation for disease was identified in 48% of individuals. Over the course of the study, 14 variants were reclassified and, upon reanalysis, 18 new variants met criteria for reporting. These findings highlight the quantity of medically relevant findings from a broad analysis of genomic sequencing data as well as the need for periodic reinterpretation and reanalysis of data for both diagnostic indications and secondary findings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA 02139, USA; Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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721
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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722
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Doan RN, Lim ET, De Rubeis S, Betancur C, Cutler DJ, Chiocchetti AG, Overman LM, Soucy A, Goetze S, Freitag CM, Daly MJ, Walsh CA, Buxbaum JD, Yu TW. Recessive gene disruptions in autism spectrum disorder. Nat Genet 2019; 51:1092-1098. [PMID: 31209396 PMCID: PMC6629034 DOI: 10.1038/s41588-019-0433-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/02/2019] [Indexed: 01/27/2023]
Abstract
Autism spectrum disorder (ASD) affects up to 1 in 59 individuals1. Genome-wide association and large-scale sequencing studies strongly implicate both common variants2-4 and rare de novo variants5-10 in ASD. Recessive mutations have also been implicated11-14 but their contribution remains less well defined. Here we demonstrate an excess of biallelic loss-of-function and damaging missense mutations in a large ASD cohort, corresponding to approximately 5% of total cases, including 10% of females, consistent with a female protective effect. We document biallelic disruption of known or emerging recessive neurodevelopmental genes (CA2, DDHD1, NSUN2, PAH, RARB, ROGDI, SLC1A1, USH2A) as well as other genes not previously implicated in ASD including FEV (FEV transcription factor, ETS family member), which encodes a key regulator of the serotonergic circuitry. Our data refine estimates of the contribution of recessive mutation to ASD and suggest new paths for illuminating previously unknown biological pathways responsible for this condition.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elaine T Lim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Neuroscience Paris Seine, Institut de Biologie Paris Seine, Sorbonne Université, INSERM, CNRS, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lynne M Overman
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, UK
| | - Aubrie Soucy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Susanne Goetze
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Mark J Daly
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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723
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Gao P, Zhang R, Li J. Comprehensive elaboration of database resources utilized in next-generation sequencing-based tumor somatic mutation detection. Biochim Biophys Acta Rev Cancer 2019; 1872:122-137. [PMID: 31265877 DOI: 10.1016/j.bbcan.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022]
Abstract
The rapid evolution of next-generation sequencing (NGS)-based tumor genomic profile detection and the emergence of molecularly targeted therapies have enabled precision oncology. In NGS-based analysis, various types of databases have been developed to perform different functions. However, many problems still exist when using these public databases. Therefore, it is important to better understand the characteristics and limitations of each database and have them complement each other to provide useful clinical evidence for NGS testing. In this review, we elaborate on the important role of databases and their concrete applications in NGS-based somatic mutation detection. We introduce the typically used databases for sequence alignment, variant filtration, and variant interpretation, and compare the differences between the databases with similar functions. Subsequently, we determine the limitations of each database and provide the corresponding solutions. Furthermore, we present an overview diagram to clearly illustrate the database used in the entire NGS-based somatic mutation detection pipeline.
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Affiliation(s)
- Peng Gao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
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724
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Bogard N, Linder J, Rosenberg AB, Seelig G. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. Cell 2019; 178:91-106.e23. [PMID: 31178116 PMCID: PMC6599575 DOI: 10.1016/j.cell.2019.04.046] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over 3 million APA reporters. APARENT's predictions are highly accurate when tasked with inferring APA in synthetic and human 3'UTRs. Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of 3' end processing, and integrates these features into a comprehensive, interpretable, cis-regulatory code. We apply APARENT to forward engineer functional polyadenylation signals with precisely defined cleavage position and isoform usage and validate predictions experimentally. Finally, we use APARENT to quantify the impact of genetic variants on APA. Our approach detects pathogenic variants in a wide range of disease contexts, expanding our understanding of the genetic origins of disease.
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Affiliation(s)
- Nicholas Bogard
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Johannes Linder
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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725
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Lin JH, Tang XY, Boulling A, Zou WB, Masson E, Fichou Y, Raud L, Le Tertre M, Deng SJ, Berlivet I, Ka C, Mort M, Hayden M, Leman R, Houdayer C, Le Gac G, Cooper DN, Li ZS, Férec C, Liao Z, Chen JM. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Hum Mutat 2019; 40:1856-1873. [PMID: 31131953 DOI: 10.1002/humu.23821] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/10/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
It has long been known that canonical 5' splice site (5'SS) GT>GC variants may be compatible with normal splicing. However, to date, the actual scale of canonical 5'SSs capable of generating wild-type transcripts in the case of GT>GC substitutions remains unknown. Herein, combining data derived from a meta-analysis of 45 human disease-causing 5'SS GT>GC variants and a cell culture-based full-length gene splicing assay of 103 5'SS GT>GC substitutions, we estimate that ~15-18% of canonical GT 5'SSs retain their capacity to generate between 1% and 84% normal transcripts when GT is substituted by GC. We further demonstrate that the canonical 5'SSs in which substitution of GT by GC-generated normal transcripts exhibit stronger complementarity to the 5' end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were capable of reliably distinguishing 5'SS GT>GC variants that generated wild-type transcripts from those that did not. Our findings imply that 5'SS GT>GC variants in human disease genes may not invariably be pathogenic.
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Affiliation(s)
- Jin-Huan Lin
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Xin-Ying Tang
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Arnaud Boulling
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France
| | - Yann Fichou
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Loann Raud
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | | | - Shun-Jiang Deng
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | | | - Chandran Ka
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Raphaël Leman
- Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France.,Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Gerald Le Gac
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
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726
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Leong HY, Abdul Azize NA, Chew HB, Keng WT, Thong MK, Mohd Khalid MKN, Hung LC, Mohamed Zainudin N, Ramlee A, Md Haniffa MA, Yakob Y, Ngu LH. Clinical, biochemical and genetic profiles of patients with mucopolysaccharidosis type IVA (Morquio A syndrome) in Malaysia: the first national natural history cohort study. Orphanet J Rare Dis 2019; 14:143. [PMID: 31200731 PMCID: PMC6570902 DOI: 10.1186/s13023-019-1105-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/26/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Mucopolysaccharidosis IVA (MPS IVA) is an autosomal recessive lysosomal storage disease due to N-acetylgalactosamine-6-sulfatase (GALNS) deficiency. It results in accumulation of the glycosaminoglycans, keratan sulfate and chondroitin-6-sulfate, leading to skeletal and other systemic impairments. Data on MPS IVA in Asian populations are scarce. METHODS This is a multicentre descriptive case series of 21 patients comprising all MPS IVA patients in Malaysia. Mutational analysis was performed by PCR and Sanger sequencing of the GALNS gene in 17 patients. RESULTS The patients (15 females and 6 males) had a mean age (± SD) of 15.5 (± 8.1) years. Mean age at symptom onset was 2.6 (± 2.1) years and at confirmed diagnosis was 6.9 (± 4.5) years. The study cohort included patients from all the main ethnic groups in Malaysia - 57% Malay, 29% Chinese and 14% Indian. Common presenting symptoms included pectus carinatum (57%) and genu valgum (43%). Eight patients (38%) had undergone surgery, most commonly knee surgeries (29%) and cervical spine decompression (24%). Patients had limited endurance with lower mean walking distances with increasing age. GALNS gene analysis identified 18 distinct mutations comprising 13 missense, three nonsense, one small deletion and one splice site mutation. Of these, eight were novel mutations (Tyr133Ser, Glu158Valfs*12, Gly168*, Gly168Val, Trp184*, Leu271Pro, Glu320Lys, Leu508Pro). Mutations in exons 1, 5 and 9 accounted for 51% of the mutant alleles identified. CONCLUSIONS All the MPS IVA patients in this study had clinical impairments. A better understanding of the natural history and the clinical and genetic spectrum of MPS IVA in this population may assist early diagnosis, improve management and permit timely genetic counselling and prenatal diagnosis.
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Affiliation(s)
- Huey Yin Leong
- Genetics Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
| | - Nor Azimah Abdul Azize
- Unit of Molecular Diagnostics & Protein, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Hui Bein Chew
- Genetics Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
| | - Wee Teik Keng
- Genetics Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
| | - Meow Keong Thong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Mohd Khairul Nizam Mohd Khalid
- Unit of Molecular Diagnostics & Protein, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Liang Choo Hung
- Paediatric Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Norzila Mohamed Zainudin
- Paediatric Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Azura Ramlee
- Ophthalmology Department, Hospital Selayang, Ministry of Health Malaysia, Selayang, Malaysia
| | - Muzhirah Aisha Md Haniffa
- Genetics Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
| | - Yusnita Yakob
- Unit of Molecular Diagnostics & Protein, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Lock Hock Ngu
- Genetics Department, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
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727
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Doan RN, Shin T, Walsh CA. Evolutionary Changes in Transcriptional Regulation: Insights into Human Behavior and Neurological Conditions. Annu Rev Neurosci 2019; 41:185-206. [PMID: 29986162 DOI: 10.1146/annurev-neuro-080317-062104] [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: 11/09/2022]
Abstract
Understanding the biological basis for human-specific cognitive traits presents both immense challenges and unique opportunities. Although the question of what makes us human has been investigated with several different methods, the rise of comparative genomics, epigenomics, and medical genetics has provided tools to help narrow down and functionally assess the regions of the genome that seem evolutionarily relevant along the human lineage. In this review, we focus on how medical genetic cases have provided compelling functional evidence for genes and loci that appear to have interesting evolutionary signatures in humans. Furthermore, we examine a special class of noncoding regions, human accelerated regions (HARs), that have been suggested to show human-lineage-specific divergence, and how the use of clinical and population data has started to provide functional information to examine these regions. Finally, we outline methods that provide new insights into functional noncoding sequences in evolution.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02138, USA
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728
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Yue Z, Zhao L, Cheng N, Yan H, Xia J. dbCID: a manually curated resource for exploring the driver indels in human cancer. Brief Bioinform 2019; 20:1925-1933. [DOI: 10.1093/bib/bby059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/22/2018] [Indexed: 12/12/2022] Open
Abstract
Abstract
While recent advances in next-generation sequencing technologies have enabled the creation of a multitude of databases in cancer genomic research, there is no comprehensive database focusing on the annotation of driver indels (insertions and deletions) yet. Therefore, we have developed the database of Cancer driver InDels (dbCID), which is a collection of known coding indels that likely to be engaged in cancer development, progression or therapy. dbCID contains experimentally supported and putative driver indels derived from manual curation of literature and is freely available online at http://bioinfo.ahu.edu.cn:8080/dbCID. Using the data deposited in dbCID, we summarized features of driver indels in four levels (gene, DNA, transcript and protein) through comparing with putative neutral indels. We found that most of the genes containing driver indels in dbCID are known cancer genes playing a role in tumorigenesis. Contrary to the expectation, the sequences affected by driver frameshift indels are not larger than those by neutral ones. In addition, the frameshift and inframe driver indels prefer to disrupt high-conservative regions both in DNA sequences and protein domains. Finally, we developed a computational method for discriminating cancer driver from neutral frameshift indels based on the deposited data in dbCID. The proposed method outperformed other widely used non-cancer-specific predictors on an external test set, which demonstrated the usefulness of the data deposited in dbCID. We hope dbCID will be a benchmark for improving and evaluating prediction algorithms, and the characteristics summarized here may assist with investigating the mechanism of indel–cancer association.
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Affiliation(s)
- Zhenyu Yue
- Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China
| | - Le Zhao
- Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China
| | - Na Cheng
- Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China
| | - Hua Yan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Junfeng Xia
- Institute of Physical Science and Information Technology, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China
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729
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Posukh OL, Zytsar MV, Bady-Khoo MS, Danilchenko VY, Maslova EA, Barashkov NA, Bondar AA, Morozov IV, Maximov VN, Voevoda MI. Unique Mutational Spectrum of the GJB2 Gene and its Pathogenic Contribution to Deafness in Tuvinians (Southern Siberia, Russia): A High Prevalence of Rare Variant c.516G>C (p.Trp172Cys). Genes (Basel) 2019; 10:E429. [PMID: 31195736 PMCID: PMC6627114 DOI: 10.3390/genes10060429] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
Mutations in the GJB2 gene are the main cause for nonsyndromic autosomal recessive deafness 1A (DFNB1A) in many populations. GJB2 mutational spectrum and pathogenic contribution are widely varying in different populations. Significant efforts have been made worldwide to define DFNB1A molecular epidemiology, but this issue still remains open for some populations. The main aim of study is to estimate the DFNB1A prevalence and GJB2 mutational spectrum in Tuvinians-an indigenous population of the Tyva Republic (Southern Siberia, Russia). Sanger sequencing was applied to analysis of coding (exon 2) and non-coding regions of GJB2 in a cohort of Tuvinian patients with hearing impairments (n = 220) and ethnically matched controls (n = 157). Diagnosis of DFNB1A was established for 22.3% patients (28.8% of familial vs 18.6% of sporadic cases). Our results support that patients with monoallelic GJB2 mutations (8.2%) are coincidental carriers. Recessive mutations p.Trp172Cys, c.-23+1G>A, c.235delC, c.299_300delAT, p.Val37Ile and several benign variants were found in examined patients. A striking finding was a high prevalence of rare variant p.Trp172Cys (c.516G>C) in Tuvinians accounting for 62.9% of all mutant GJB2 alleles and a carrier frequency of 3.8% in controls. All obtained data provide important targeted information for genetic counseling of affected Tuvinian families and enrich current information on variability of GJB2 worldwide.
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Affiliation(s)
- Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marita S Bady-Khoo
- Research Institute of Medical-Social Problems and Management of the Republic of Tyva, 667000 Kyzyl, Russia.
- Perinatal Center of the Republic of Tyva, 667000 Kyzyl, Russia.
| | - Valeria Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Nikolay A Barashkov
- Yakut Scientific Centre of Complex Medical Problems, 677019 Yakutsk, Russia.
- M.K. Ammosov North-Eastern Federal University, 677027 Yakutsk, Russia.
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Igor V Morozov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Vladimir N Maximov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Michael I Voevoda
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
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730
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ssODN-Mediated In-Frame Deletion with CRISPR/Cas9 Restores FVIII Function in Hemophilia A-Patient-Derived iPSCs and ECs. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:198-209. [PMID: 31261034 PMCID: PMC6610636 DOI: 10.1016/j.omtn.2019.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022]
Abstract
Given that the cDNA of F8 is too large to be packaged into adeno-associated virus (AAV) capsids, gene transfer of some versions of B-domain-deleted F8 (BDD-F8) for hemophilia A (HA) treatment has been attempted with promising results. Here, we describe an efficient gene correction via single-stranded-oligodeoxynucleotide (ssODN)-mediated in-frame deletion within the B domain of F8 with CRISPR/Cas9 in HA-patient-derived induced pluripotent stem cells (HA-iPSCs). The expression and activity of FVIII was restored in corrected HA-iPSC-derived induced endothelial progenitor cells (C-iEPCs) in vitro and in vivo. The bleeding phenotype was rescued in HA mice after C-iEPC infusion. Our results demonstrate an efficient approach for in situ gene correction via introduction of a tiny deletion using ssODN and CRISPR/Cas9 to reframe the F8 transcript and restore FVIII function in HA-iPSC-derived EPCs with potential clinical impact in HA gene therapy. For the first time, we demonstrated in vitro and in vivo the FVIII function that is encoded by the endogenous F8 gene with a partially deleted B domain. This work also suggests an applicable strategy for genetic correction of other gene frameshift mutations.
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731
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Cheng N, Li M, Zhao L, Zhang B, Yang Y, Zheng CH, Xia J. Comparison and integration of computational methods for deleterious synonymous mutation prediction. Brief Bioinform 2019; 21:970-981. [DOI: 10.1093/bib/bbz047] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/03/2023] Open
Abstract
Abstract
Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predict deleterious synonymous mutations, which have greatly facilitated the development of this important field. Consequently, there is an urgent need to assess the state-of-the-art computational methods for deleterious synonymous mutation prediction to further advance the existing methodologies and to improve performance. In this regard, we systematically compared a total of 10 computational methods (including specific method for deleterious synonymous mutation and general method for single nucleotide mutation) in terms of the algorithms used, calculated features, performance evaluation and software usability. In addition, we constructed two carefully curated independent test datasets and accordingly assessed the robustness and scalability of these different computational methods for the identification of deleterious synonymous mutations. In an effort to improve predictive performance, we established an ensemble model, named Prediction of Deleterious Synonymous Mutation (PrDSM), which averages the ratings generated by the three most accurate predictors. Our benchmark tests demonstrated that the ensemble model PrDSM outperformed the reviewed tools for the prediction of deleterious synonymous mutations. Using the ensemble model, we developed an accessible online predictor, PrDSM, available at http://bioinfo.ahu.edu.cn:8080/PrDSM/. We hope that this comprehensive survey and the proposed strategy for building more accurate models can serve as a useful guide for inspiring future developments of computational methods for deleterious synonymous mutation prediction.
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Affiliation(s)
- Na Cheng
- Institutes of Physical Science and Information Technology, Anhui University
| | - Menglu Li
- School of Computer Science and Technology, Anhui University
| | - Le Zhao
- School of Computer Science and Technology, Anhui University
| | - Bo Zhang
- School of Computer Science and Technology, Anhui University
| | - Yuhua Yang
- School of Computer Science and Technology, Anhui University
| | - Chun-Hou Zheng
- School of Computer Science and Technology, Anhui University
| | - Junfeng Xia
- Institutes of Physical Science and Information Technology, Anhui University
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732
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Khan AO, Basamh O, Alkatan HM. Ophthalmic diagnosis and optical coherence tomography of abetalipoproteinemia, a treatable form of pediatric retinal dystrophy. J AAPOS 2019; 23:176-177. [PMID: 30731125 DOI: 10.1016/j.jaapos.2019.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/27/2018] [Accepted: 01/09/2019] [Indexed: 11/26/2022]
Abstract
A 16-year-old boy with early-childhood-onset retinal dystrophy and developmental delay was diagnosed with abetalipoproteinemia based on ophthalmic examination, history, and results of a peripheral blood smear. The diagnosis was confirmed by lipid profile and genetic testing, and an older sister was confirmed to be affected as well. Although abetalipoproteinemia is treatable in early childhood, most cases are diagnosed late if at all. We highlight clinical features that should raise suspicion for this treatable but likely under-diagnosed form of early-onset retinal dystrophy and document retinal optical coherence tomography findings for a genetically proven case.
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Affiliation(s)
- Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Omar Basamh
- Department of Ophthalmology, King Abdullah Medical City, Mecca, Saudi Arabia; Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Hind M Alkatan
- Department of Ophthalmology, King Saud University, Riyadh, Saudi Arabia
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733
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Jha RM, Desai SM, Zusman BE, Koleck TA, Puccio AM, Okonkwo DO, Park SY, Shutter LA, Kochanek PM, Conley YP. Downstream TRPM4 Polymorphisms Are Associated with Intracranial Hypertension and Statistically Interact with ABCC8 Polymorphisms in a Prospective Cohort of Severe Traumatic Brain Injury. J Neurotrauma 2019; 36:1804-1817. [PMID: 30484364 PMCID: PMC6551973 DOI: 10.1089/neu.2018.6124] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Sulfonylurea-receptor-1(SUR1) and its associated transient-receptor-potential cation channel subfamily-M (TRPM4) channel are key contributors to cerebral edema and intracranial hypertension in traumatic brain injury (TBI) and other neurological disorders. Channel inhibition by glyburide is clinically promising. ABCC8 (encoding SUR1) single-nucleotide polymorphisms (SNPs) are reported as predictors of raised intracranial pressure (ICP). This project evaluated whether TRPM4 SNPs predicted ICP and TBI outcome. DNA was extracted from 435 consecutively enrolled severe TBI patients. Without a priori selection, all 11 TRPM4 SNPs available on the multiplex platform (Illumina:Human-Core-Exome v1.0) were genotyped spanning the 25 exon gene. A total of 385 patients were analyzed after quality control. Outcomes included ICP and 6 month Glasgow Outcome Scale (GOS) score. Proxy SNPs, spatial modeling, and functional predictions were determined using established software programs. rs8104571 (intron-20) and rs150391806 (exon-24) were predictors of ICP. rs8104571 heterozygotes predicted higher average ICP (β = 10.3 mm Hg, p = 0.00000029), peak ICP (β = 19.6 mm Hg, p = 0.0007), and proportion ICP >25 mm Hg (β = 0.16 p = 0.004). rs150391806 heterozygotes had higher mean (β = 7.2 mm Hg, p = 0.042) and peak (β = 28.9 mm Hg, p = 0.0015) ICPs. rs8104571, rs150391806, and 34 associated proxy SNPs in linkage-disequilibrium clustered downstream. This region encodes TRPM4's channel pore and a region postulated to juxtapose SUR1 sequences encoded by an ABCC8 DNA segment containing previously identified relevant SNPs. There was an interaction effect on ICP between rs8104571 and a cluster of predictive ABCC8 SNPs (rs2237982, rs2283261, rs11024286). Although not significant in univariable or a basic multivariable model, in an expanded model additionally accounting for injury pattern, computed tomographic (CT) appearance, and intracranial hypertension, heterozygous rs8104571 was associated with favorable 6 month GOS (odds ratio [OR] = 16.7, p = 0.007951). This trend persisted in a survivor-only subcohort (OR = 20.67, p = 0.0168). In this cohort, two TRPM4 SNPs predicted increased ICP with large effect sizes. Both clustered downstream, spanning a region encoding the channel pore and interacting with SUR1. If validated, this may guide risk stratification and eventually inform treatment-responder classification for SUR1-TRPM4 inhibition in TBI. Larger studies are warranted.
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Affiliation(s)
- Ruchira M. Jha
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Safar Center for Resuscitation Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shashvat M. Desai
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Benjamin E. Zusman
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ava M. Puccio
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David O. Okonkwo
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seo-Young Park
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lori A. Shutter
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick M. Kochanek
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Safar Center for Resuscitation Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Anesthesia, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania
- University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yvette P. Conley
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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734
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Abali ZY, Yesil G, Kirkgoz T, Kaygusuz SB, Eltan M, Turan S, Bereket A, Guran T. Evaluation of growth and puberty in a child with a novel TBX19 gene mutation and review of the literature. Hormones (Athens) 2019; 18:229-236. [PMID: 30747411 DOI: 10.1007/s42000-019-00096-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Biallelic mutations in the TBX19 gene cause severe early-onset adrenal failure due to isolated ACTH deficiency (IAD). This rare disease is characterized by low plasma ACTH and cortisol levels, with normal secretion of other pituitary hormones. Herein, we report a patient with IAD due to a novel TBX19 gene mutation, who is also of tall stature. CASE REPORT A 48/12-year-old girl was presented with loss of consciousness due to hypoglycemia. The patient was born at term with a birth weight of 3800 g. Her parents were first-degree cousins. She had a history of several hospitalizations for recurrent seizures, abdominal pain, and vomiting. At presentation, her weight and height were + 1.8 and + 2.2 SDS, respectively. Serum glucose was 25 mg/dl (1.4 mmol/L), with normal sodium, potassium, and insulin concentrations. The child was hypocortisolemic (0.1 μg/dl), and ACTH levels were extremely low (< 5.0 pg/ml). A diagnosis of IAD was made and hydrocortisone treatment was started. Hypoglycemic episodes, seizures, and recurrent gastrointestinal complaints disappeared after hydrocortisone replacement. Magnetic resonance imaging of the pituitary was normal. Whole exome sequencing revealed a novel homozygous c.302G > A (W101*) mutation in the TBX19 gene. CONCLUSION We report a new mutation in the TBX19 gene in a patient with isolated ACTH deficiency. While overgrowth is a known feature of some types of adrenal insufficiencies, including MC2R gene defects and POMC deficiency, it may be a novel feature for TPIT deficiency, as in our patient.
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Affiliation(s)
- Zehra Yavas Abali
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem Vakıf University School of Medicine, Istanbul, Turkey
| | - Tarik Kirkgoz
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Sare Betul Kaygusuz
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Mehmet Eltan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Abdullah Bereket
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey.
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735
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Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput Biol 2019; 15:e1007112. [PMID: 31199787 PMCID: PMC6594643 DOI: 10.1371/journal.pcbi.1007112] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/26/2019] [Accepted: 05/17/2019] [Indexed: 11/19/2022] Open
Abstract
Differentiation between phenotypically neutral and disease-causing genetic variation remains an open and relevant problem. Among different types of variation, non-frameshifting insertions and deletions (indels) represent an understudied group with widespread phenotypic consequences. To address this challenge, we present a machine learning method, MutPred-Indel, that predicts pathogenicity and identifies types of functional residues impacted by non-frameshifting insertion/deletion variation. The model shows good predictive performance as well as the ability to identify impacted structural and functional residues including secondary structure, intrinsic disorder, metal and macromolecular binding, post-translational modifications, allosteric sites, and catalytic residues. We identify structural and functional mechanisms impacted preferentially by germline variation from the Human Gene Mutation Database, recurrent somatic variation from COSMIC in the context of different cancers, as well as de novo variants from families with autism spectrum disorder. Further, the distributions of pathogenicity prediction scores generated by MutPred-Indel are shown to differentiate highly recurrent from non-recurrent somatic variation. Collectively, we present a framework to facilitate the interrogation of both pathogenicity and the functional effects of non-frameshifting insertion/deletion variants. The MutPred-Indel webserver is available at http://mutpred.mutdb.org/.
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Affiliation(s)
- Kymberleigh A. Pagel
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, United States of America
| | - Danny Antaki
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - AoJie Lian
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America
| | - Predrag Radivojac
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, United States of America
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States of America
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736
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Vinje T, Laerdahl JK, Bjune K, Leren TP, Strøm TB. Characterization of the mechanisms by which missense mutations in the lysosomal acid lipase gene disrupt enzymatic activity. Hum Mol Genet 2019; 28:3043-3052. [DOI: 10.1093/hmg/ddz114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/14/2019] [Accepted: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract
Hydrolysis of cholesteryl esters and triglycerides in the lysosome is performed by lysosomal acid lipase (LAL). In this study we have investigated how 23 previously identified missense mutations in the LAL gene (LIPA) (OMIM# 613497) affect the structure of the protein and thereby disrupt LAL activity. Moreover, we have performed transfection studies to study intracellular transport of the 23 mutants. Our main finding was that most pathogenic mutations result in defective enzyme activity by affecting the normal folding of LAL. Whereas, most of the mutations leading to reduced stability of the cap domain did not alter intracellular transport, nearly all mutations that affect the stability of the core domain gave rise to a protein that was not efficiently transported from the endoplasmic reticulum (ER) to the Golgi apparatus. As a consequence, ER stress was generated that is assumed to result in ER-associated degradation of the mutant proteins. The two LAL mutants Q85K and S289C were selected to study whether secretion-defective mutants could be rescued from ER-associated degradation by the use of chemical chaperones. Of the five chemical chaperones tested, only the proteasomal inhibitor MG132 markedly increased the amount of mutant LAL secreted. However, essentially no increased enzymatic activity was observed in the media. These data indicate that the use of chemical chaperones to promote the exit of folding-defective LAL mutants from the ER, may not have a great therapeutic potential as long as these mutants appear to remain enzymatically inactive.
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Affiliation(s)
- Terje Vinje
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jon K Laerdahl
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- ELIXIR Norway, Department of Informatics, University of Oslo, Oslo, Norway
| | - Katrine Bjune
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trond P Leren
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Thea Bismo Strøm
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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737
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Bosio M, Drechsel O, Rahman R, Muyas F, Rabionet R, Bezdan D, Domenech Salgado L, Hor H, Schott JJ, Munell F, Colobran R, Macaya A, Estivill X, Ossowski S. eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics. Hum Mutat 2019; 40:865-878. [PMID: 31026367 PMCID: PMC6767450 DOI: 10.1002/humu.23772] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
Mendelian diseases have shown to be an and efficient model for connecting genotypes to phenotypes and for elucidating the function of genes. Whole‐exome sequencing (WES) accelerated the study of rare Mendelian diseases in families, allowing for directly pinpointing rare causal mutations in genic regions without the need for linkage analysis. However, the low diagnostic rates of 20–30% reported for multiple WES disease studies point to the need for improved variant pathogenicity classification and causal variant prioritization methods. Here, we present the exome Disease Variant Analysis (eDiVA; http://ediva.crg.eu), an automated computational framework for identification of causal genetic variants (coding/splicing single‐nucleotide variants and small insertions and deletions) for rare diseases using WES of families or parent–child trios. eDiVA combines next‐generation sequencing data analysis, comprehensive functional annotation, and causal variant prioritization optimized for familial genetic disease studies. eDiVA features a machine learning‐based variant pathogenicity predictor combining various genomic and evolutionary signatures. Clinical information, such as disease phenotype or mode of inheritance, is incorporated to improve the precision of the prioritization algorithm. Benchmarking against state‐of‐the‐art competitors demonstrates that eDiVA consistently performed as a good or better than existing approach in terms of detection rate and precision. Moreover, we applied eDiVA to several familial disease cases to demonstrate its clinical applicability.
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Affiliation(s)
- Mattia Bosio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Oliver Drechsel
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Francesc Muyas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raquel Rabionet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut de Recerca Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Daniela Bezdan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura Domenech Salgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hyun Hor
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Jacques Schott
- L'Institut du Thorax, INSERM, CNRS, Univ Nantes, Nantes, France.,Service de Cardiologie, L'institut du thorax, CHU Nantes, Nantes, France
| | | | - Roger Colobran
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Alfons Macaya
- Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Xavier Estivill
- Sidra Medicine, Doha, Qatar.,Women's Health Dexeus, Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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738
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Liu Y, Yang W, Hua R, Huang Y, Zhang X. Pathogenic mutations in two Chinese patients exhibiting severe early-onset obesity. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1554-1556. [PMID: 31102178 DOI: 10.1007/s11427-018-9443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/05/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Yanshan Liu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Wei Yang
- Capital Institute of Pediatrics, Beijing, 100020, China
| | - Rui Hua
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yingzhi Huang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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739
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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740
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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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741
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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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742
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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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743
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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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744
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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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745
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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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746
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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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747
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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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748
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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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749
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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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750
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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: 40] [Impact Index Per Article: 8.0] [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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