901
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Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med 2017; 9:113. [PMID: 29254494 PMCID: PMC5735928 DOI: 10.1186/s13073-017-0509-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.
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Affiliation(s)
| | - Peter W Rose
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA
| | - Andreas Prlić
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.,RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | | | - José M Duarte
- RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | - Andrew S Hoffman
- Human Centered Design & Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Geoffrey J Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Timothy Bergquist
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Christian Bock
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Elizabeth Brunk
- University of California San Diego, La Jolla, CA, 92093, USA
| | - Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Stephen K Burley
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.,RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Binghuang Cai
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Hannah Carter
- University of California San Diego, La Jolla, CA, 92093, USA
| | - JianJiong Gao
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adam Godzik
- SBP Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Michael Heuer
- AMPLab, University of California, Berkeley, CA, 94720, USA
| | | | - Thomas Hrabe
- SBP Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Oncology, Johns Hopkins Medicine, Baltimore, MD, 21287, USA
| | - Julia Koehler Leman
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, 10010, USA.,Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and University of Geneva, CH-1211, Geneva, Switzerland
| | - David L Masica
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, WA, 98109, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Frances Pearl
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA.,The University of Washington eScience Institute, Seattle, WA, 98195, USA
| | | | - Ariel Rokem
- The University of Washington eScience Institute, Seattle, WA, 98195, USA
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics and Biozentrum University of Basel, CH-4056, Basel, Switzerland
| | - Sicheng Song
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Hagen Tilgner
- Brain and Mind Research Institute, Weill Cornell Medicine, New York City, NY, 10021, USA
| | - Yana Valasatava
- RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
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902
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Menezes J, Ventura C, Costa JM, Parreira E, Romão L, Gonçalves J. PROS1 novel splice-site variant decreases protein S expression in patients from two families with thrombotic disease. Clin Case Rep 2017; 5:2062-2065. [PMID: 29225857 PMCID: PMC5715601 DOI: 10.1002/ccr3.1226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/04/2017] [Accepted: 09/19/2017] [Indexed: 11/11/2022] Open
Abstract
Our results prove that c.1871-14T>G is causative of type I PS deficiency, highlighting the importance of performing mRNA-based studies in order to evaluate variants pathogenicity. We evidence the increased risk of venous thromboembolism associated with this cryptic splice-site variant if present in patients with PS deficiency.
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Affiliation(s)
- Juliane Menezes
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Gene Expression and Regulation Group Biosystems & Integrative Sciences Institute (BioISI) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Célia Ventura
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal
| | - João Matos Costa
- Third Department of Internal Medicine Hospital Distrital de Santarém Santarém Portugal
| | | | - Luísa Romão
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Gene Expression and Regulation Group Biosystems & Integrative Sciences Institute (BioISI) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - João Gonçalves
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Centre for Toxicogenomics and Human Health (ToxOmics) Genetics, Oncology and Human Toxicology Nova Medical School Universidade Nova de Lisboa Lisbon Portugal
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903
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Bosch B, Itan Y, Meyts I. Whole-exome sequencing for detecting inborn errors of immunity: overview and perspectives. F1000Res 2017; 6:2056. [PMID: 29225788 PMCID: PMC5710381 DOI: 10.12688/f1000research.12365.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
The study of inborn errors of immunity is based on a comprehensive clinical description of the patient’s phenotype and the elucidation of the underlying molecular mechanisms and their genetic etiology. Deciphering the pathogenesis is key to genetic counseling and the development of targeted therapy. This review shows the power of whole-exome sequencing in detecting inborn errors of immunity along five central steps taken in whole-exome sequencing analysis. In parallel, we highlight the challenges for the clinical and scientific use of the method and how these hurdles are currently being addressed. We end by ruminating on major areas in the field open to future research.
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Affiliation(s)
- Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,St. Giles Laboratory of the Human Genetics of Infectious Disease, Rockefeller University, New York, USA
| | - Yuval Itan
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Childhood Immunology, KULeuven, Leuven, Belgium
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904
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Vona B, Maroofian R, Mendiratta G, Croken M, Peng S, Ye X, Rezazadeh J, Bahena P, Lekszas C, Haaf T, Edelmann L, Shi L. Dual Diagnosis of Ellis-van Creveld Syndrome and Hearing Loss in a Consanguineous Family. Mol Syndromol 2017; 9:5-14. [PMID: 29456477 PMCID: PMC5803684 DOI: 10.1159/000480458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2017] [Indexed: 11/19/2022] Open
Abstract
Multilocus analysis of rare or genetically heterogeneous diseases is a distinct advantage of next-generation sequencing (NGS) over conventional single-gene investigations. Recent studies have begun to uncover an under-recognized prevalence of dual molecular diagnoses in patients with a "blended" phenotype that is the result of 2 clinical diagnoses involving 2 separate genetic loci. This blended phenotype could be mistakenly interpreted as a novel clinical extension of a single-gene disorder. In this study, we ascertained a proband from a large consanguineous Iranian family who manifests postlingual, progressive, moderate hearing loss in addition to suspected Ellis-van Creveld syndrome phenotype. NGS with a customized skeletal dysplasia panel containing over 370 genes and subsequent bioinformatics analysis disclosed 2 homozygous mutations in EVC2 (c.2653C>T; p.Arg885*) and COL11A2 (c.966dup; p.Thr323Hisfs*19), respectively. This study highlights a dual molecular diagnosis in a patient with a blending of 2 distinct phenotypes and illustrates the advantage and importance of this staple technology to facilitate rapid and comprehensive genetic dissection of a heterogeneous phenotype. The differentiation between phenotypic expansion of a genetic disorder and a blended phenotype that is due to more than one distinct genetic aberration is essential in order to reduce the diagnostic odyssey endured by patients.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Reza Maroofian
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Croken
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Siwu Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaoqian Ye
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dentistry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jamileh Rezazadeh
- Genetic Counselling and Rehabilitation Unit, Welfare Organization, South Khorasan, Iran
| | - Paulina Bahena
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Caroline Lekszas
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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905
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Christie KA, Courtney DG, DeDionisio LA, Shern CC, De Majumdar S, Mairs LC, Nesbit MA, Moore CBT. Towards personalised allele-specific CRISPR gene editing to treat autosomal dominant disorders. Sci Rep 2017; 7:16174. [PMID: 29170458 PMCID: PMC5701044 DOI: 10.1038/s41598-017-16279-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 holds immense potential to treat a range of genetic disorders. Allele-specific gene disruption induced by non-homologous end-joining (NHEJ) DNA repair offers a potential treatment option for autosomal dominant disease. Here, we successfully delivered a plasmid encoding S. pyogenes Cas9 and sgRNA to the corneal epithelium by intrastromal injection and acheived long-term knockdown of a corneal epithelial reporter gene, demonstrating gene disruption via NHEJ in vivo. In addition, we used TGFBI corneal dystrophies as a model of autosomal dominant disease to assess the use of CRISPR/Cas9 in two allele-specific systems, comparing cleavage using a SNP-derived PAM to a guide specific approach. In vitro, cleavage via a SNP-derived PAM was found to confer stringent allele-specific cleavage, while a guide-specific approach lacked the ability to distinguish between the wild-type and mutant alleles. The failings of the guide-specific approach highlights the necessity for meticulous guide design and assessment, as various degrees of allele-specificity are achieved depending on the guide sequence employed. A major concern for the use of CRISPR/Cas9 is its tendency to cleave DNA non-specifically at “off-target” sites. Confirmation that S. pyogenes Cas9 lacks the specificity to discriminate between alleles differing by a single base-pair regardless of the position in the guide is demonstrated.
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Affiliation(s)
- Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - David G Courtney
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | | | | | - Shyamasree De Majumdar
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - Laura C Mairs
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK. .,Avellino Laboratories, Menlo Park, California, CA, 94025, USA.
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906
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Rohanizadegan M, Abdo SM, O'Donnell-Luria A, Mihalek I, Chen P, Sanders M, Leeman K, Cho M, Hung C, Bodamer O. Utility of rapid whole-exome sequencing in the diagnosis of Niemann-Pick disease type C presenting with fetal hydrops and acute liver failure. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002147. [PMID: 28802248 PMCID: PMC5701306 DOI: 10.1101/mcs.a002147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/02/2017] [Indexed: 01/07/2023] Open
Abstract
Rapid whole-exome sequencing (rWES) is used in critically ill newborn infants to inform about diagnosis, clinical management, and prognosis. Here we report a male newborn infant with hydrops, pancytopenia, and acute liver failure who was listed for liver transplantation. Given the acuity of the presentation, the procedure-related morbidity and mortality, and lack of diagnosis, we used rWES in the proband and both parents with a turnaround time of 10 business days. rWES returned one maternally inherited, likely pathogenic and one paternally inherited, likely pathogenic variant in NPC1, suggestive of a diagnosis of Niemann–Pick disease type C (NPC). Interestingly, a diagnosis of NPC was entertained prior to rWES, but deemed unlikely in light of absent cholesterol storage on liver biopsy and near-normal oxysterol levels in dried blood. The diagnosis of NPC was confirmed on filipin stain in fibroblasts demonstrating defective cholesterol trafficking. NPC is a slowly progressive neurodegenerative disorder that may also affect the liver with overall poor prognosis. It was decided to take the infant off the transplant list and transfer to palliative care, where he died after 4 wk. This case highlights the utility of rWES in an acute clinical setting for several domains of precision medicine including (1) diagnosis, (2) prognosis and outcome, (3) management and therapy, and (4) utilization of resources.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sara M Abdo
- Division of Biochemistry, Faculty of Science, Helwan University, Cairo, Egypt
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ivana Mihalek
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peggy Chen
- Department of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Marilyn Sanders
- Department of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Kristen Leeman
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Megan Cho
- GeneDx, Gaithersburg, Maryland 20877, USA
| | - Christina Hung
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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907
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Zhao ZY, Jiang YL, Li BR, Yang F, Li J, Jin XW, Ning SB, Sun SH. Sanger sequencing in exonic regions of STK11 gene uncovers a novel de-novo germline mutation (c.962_963delCC) associated with Peutz-Jeghers syndrome and elevated cancer risk: case report of a Chinese patient. BMC MEDICAL GENETICS 2017; 18:130. [PMID: 29141581 PMCID: PMC5688745 DOI: 10.1186/s12881-017-0471-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/27/2017] [Indexed: 01/24/2023]
Abstract
Background Peutz-Jeghers syndrome (PJS) is caused by mutations in the tumor suppressor gene, STK11, and is characterized by gastrointestinal hamartomas, melanin spots on the lips and the extremities, and an increased risk of developing cancer. Case presentation We reported an isolated PJS patient who died of colon cancer, whose blood sample was collected together with all the available family members’. The entire coding region of the STK11 gene was amplified by PCR and analyzed by Sanger sequencing, through which, a novel mutation, c.962_963delCC in exon 8 was identified in this patient. This mutation causes a frameshift mutation and a premature termination at codon 358. Protein structure prediction by Swiss-Model indicated a dramatic change and partial loss of the C-terminal domain. We did not observe this mutation in both parents of the proband. Therefore, it is considered a novel de-novo mutation. Furthermore, the mutation was not found in 50 unrelated healthy people. Conclusions The novel mutation we reported here had not been recorded in databases or literature, and the patient who possessed it suffered from PJS and colon cancer. So our results enlarge the spectrum of STK11 variants in PJS patients. This mutation is most likely responsible for development of the PJS phenotype, especially the cancer occurrence. Electronic supplementary material The online version of this article (10.1186/s12881-017-0471-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zi-Ye Zhao
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China
| | - Yu-Liang Jiang
- Hebei North University, 11 South Zuanshi Rd., Zhangjiakou, Hebei Province, 075061, China.,Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Bai-Rong Li
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Fu Yang
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China
| | - Jing Li
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Xiao-Wei Jin
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Shou-Bin Ning
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China.
| | - Shu-Han Sun
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China.
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908
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A 23-Nucleotide Deletion in STK11 Gene Causes Peutz-Jeghers Syndrome and Malignancy in a Chinese Patient Without a Positive Family History. Dig Dis Sci 2017; 62:3014-3020. [PMID: 28986664 DOI: 10.1007/s10620-017-4741-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/28/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND AIMS Peutz-Jeghers syndrome (PJS) is an autosomal-dominant genetic disease caused by mutations in the tumor suppressor gene, STK11, which is characterized by gastrointestinal hamartomas, melanin spots on the lips and the extremities, and an increased risk of developing both gastrointestinal and extraintestinal malignancies. METHODS AND RESULTS We treated a PJS patient without a positive family history, who possessed typical clinical manifestations including polyp canceration. In order to explore the genotype of this patient, blood samples were collected from all the available family members. The whole coding region and the flanking regions of the STK11 gene were amplified by polymerase chain reaction and analyzed by Sanger sequencing. Molecular analysis of the STK11 gene here revealed a 23-nucleotide deletion (c.426-448delCGTGCCGGAGAAGCGTTTCCCAG) in exon 3, resulting in a change of 13 codons and a truncating protein (p.S142SfsX13). This mutation was not found in normal individuals in this family including her parents or in 100 control individuals. Protein structure prediction indicated a dramatic loss of the kinase domain and complete loss of the C-terminal regulatory domain. CONCLUSIONS The results presented here enlarge the spectrum of STK11 mutation both disease-causing and malignancy-causing.
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909
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Ludwig NF, Velho RV, Sperb-Ludwig F, Acosta AX, Ribeiro EM, Kim CA, Gandelman Horovitz DD, Boy R, Rodovalho-Doriqui MJ, Lourenço CM, Santos ES, Braulke T, Pohl S, Schwartz IVD. GNPTAB missense mutations cause loss of GlcNAc-1-phosphotransferase activity in mucolipidosis type II through distinct mechanisms. Int J Biochem Cell Biol 2017; 92:90-94. [DOI: 10.1016/j.biocel.2017.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
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910
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Aggarwal S, Nayek A, Pradhan D, Verma R, Yadav M, Ponnusamy K, Jain AK. dbGAPs: A comprehensive database of genes and genetic markers associated with psoriasis and its subtypes. Genomics 2017; 110:S0888-7543(17)30115-5. [PMID: 29031638 DOI: 10.1016/j.ygeno.2017.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 01/12/2023]
Abstract
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data. The database contains annotation for 202 manually curated genes associated with psoriasis and its subtypes with cross-references. Functional enrichment of these genes, in context of Gene Ontology and pathways, provide insight into their important role in psoriasis etiology and pathogenesis. The dbGAPs interface is enriched with an interactive search engine for data retrieval along with unique customized tools for Single Nucleotide Polymorphism (SNP)/indel detection and SNP/indel annotations. dbGAPs is accessible at http://www.bmicnip.in/dbgaps/.
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Affiliation(s)
- Shweta Aggarwal
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Arnab Nayek
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Dibyabhaba Pradhan
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Rashi Verma
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Monika Yadav
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | | | - Arun Kumar Jain
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India.
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911
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Ferlaino M, Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC Bioinformatics 2017; 18:442. [PMID: 28985712 PMCID: PMC5955213 DOI: 10.1186/s12859-017-1862-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/02/2017] [Indexed: 11/30/2022] Open
Abstract
Background Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. Results We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. Conclusions FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Ferlaino
- Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK. .,Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, OX3 9DU, UK.
| | - Mark F Rogers
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1UB, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1UB, UK
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912
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Bastida JM, Lozano ML, Benito R, Janusz K, Palma-Barqueros V, Del Rey M, Hernández-Sánchez JM, Riesco S, Bermejo N, González-García H, Rodriguez-Alén A, Aguilar C, Sevivas T, López-Fernández MF, Marneth AE, van der Reijden BA, Morgan NV, Watson SP, Vicente V, Hernández-Rivas JM, Rivera J, González-Porras JR. Introducing high-throughput sequencing into mainstream genetic diagnosis practice in inherited platelet disorders. Haematologica 2017; 103:148-162. [PMID: 28983057 PMCID: PMC5777202 DOI: 10.3324/haematol.2017.171132] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/29/2017] [Indexed: 12/30/2022] Open
Abstract
Inherited platelet disorders are a heterogeneous group of rare diseases, caused by inherited defects in platelet production and/or function. Their genetic diagnosis would benefit clinical care, prognosis and preventative treatments. Until recently, this diagnosis has usually been performed via Sanger sequencing of a limited number of candidate genes. High-throughput sequencing is revolutionizing the genetic diagnosis of diseases, including bleeding disorders. We have designed a novel high-throughput sequencing platform to investigate the unknown molecular pathology in a cohort of 82 patients with inherited platelet disorders. Thirty-four (41.5%) patients presented with a phenotype strongly indicative of a particular type of platelet disorder. The other patients had clinical bleeding indicative of platelet dysfunction, but with no identifiable features. The high-throughput sequencing test enabled a molecular diagnosis in 70% of these patients. This sensitivity increased to 90% among patients suspected of having a defined platelet disorder. We found 57 different candidate variants in 28 genes, of which 70% had not previously been described. Following consensus guidelines, we qualified 68.4% and 26.3% of the candidate variants as being pathogenic and likely pathogenic, respectively. In addition to establishing definitive diagnoses of well-known inherited platelet disorders, high-throughput sequencing also identified rarer disorders such as sitosterolemia, filamin and actinin deficiencies, and G protein-coupled receptor defects. This included disease-causing variants in DIAPH1 (n=2) and RASGRP2 (n=3). Our study reinforces the feasibility of introducing high-throughput sequencing technology into the mainstream laboratory for the genetic diagnostic practice in inherited platelet disorders.
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Affiliation(s)
- José M Bastida
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain .,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Rocío Benito
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Kamila Janusz
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Verónica Palma-Barqueros
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain
| | | | | | - Susana Riesco
- Servicio de Pediatría, Hospital Universitario de Salamanca-IBSAL, Spain
| | - Nuria Bermejo
- Servicio de Hematología, Complejo Hospitalario San Pedro Alcántara, Cáceres, Spain
| | | | - Agustín Rodriguez-Alén
- Servicio de Hematología y Hemoterapia, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Spain
| | - Carlos Aguilar
- Servicio de Hematología, Complejo Asistencial de Soria, Spain
| | - Teresa Sevivas
- Serviço de Imunohemoterapia, Sangue e Medicina Transfusional do Centro Hospitalar e Universitário de Coimbra, EPE, Portugal
| | | | - Anna E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Neil V Morgan
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Steve P Watson
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Vicente Vicente
- On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Jesús M Hernández-Rivas
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain.,IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
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913
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Comander J, Weigel-DiFranco C, Maher M, Place E, Wan A, Harper S, Sandberg MA, Navarro-Gomez D, Pierce EA. The Genetic Basis of Pericentral Retinitis Pigmentosa-A Form of Mild Retinitis Pigmentosa. Genes (Basel) 2017; 8:genes8100256. [PMID: 28981474 PMCID: PMC5664106 DOI: 10.3390/genes8100256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
Pericentral retinitis pigmentosa (RP) is an atypical form of RP that affects the near-peripheral retina first and tends to spare the far periphery. This study was performed to further define the genetic basis of this phenotype. We identified a cohort of 43 probands with pericentral RP based on a comprehensive analysis of their retinal phenotype. Genetic analyses of DNA samples from these patients were performed using panel-based next-generation sequencing, copy number variations, and whole exome sequencing (WES). Mutations provisionally responsible for disease were found in 19 of the 43 families (44%) analyzed. These include mutations in RHO (five patients), USH2A (four patients), and PDE6B (two patients). Of 28 putatively pathogenic alleles, 15 (54%) have been previously identified in patients with more common forms of typical RP, while the remaining 13 mutations (46%) were novel. Burden testing of WES data successfully identified HGSNAT as a cause of pericentral RP in at least two patients, suggesting it is also a relatively common cause of pericentral RP. While additional sequencing might uncover new genes specifically associated with pericentral RP, the current results suggest that genetically pericentral RP is not a separate clinical entity, but rather is part of the spectrum of mild RP phenotypes.
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Affiliation(s)
- Jason Comander
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Carol Weigel-DiFranco
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Matthew Maher
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Emily Place
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Aliete Wan
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Shyana Harper
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Michael A Sandberg
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Eric A Pierce
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
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914
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Deng H, Xiao H. The role of the ATP2C1 gene in Hailey-Hailey disease. Cell Mol Life Sci 2017; 74:3687-3696. [PMID: 28551824 PMCID: PMC11107712 DOI: 10.1007/s00018-017-2544-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/27/2017] [Accepted: 05/18/2017] [Indexed: 12/24/2022]
Abstract
Hailey-Hailey disease (HHD) is a rare autosomal dominant acantholytic dermatosis, characterized by a chronic course of repeated and exacerbated skin lesions in friction regions. The pathogenic gene of HHD was reported to be the ATPase calcium-transporting type 2C member 1 gene (ATP2C1) located on chromosome 3q21-q24. Its function is to maintain normal intracellular concentrations of Ca2+/Mn2+ by transporting Ca2+/Mn2+ into the Golgi apparatus. ATP2C1 gene mutations are reportedly responsible for abnormal cytosolic Ca2+/Mn2+ levels and the clinical manifestations of HHD. Environmental factors and genetic modifiers may also affect the clinical variability of HHD. This article aims to critically discuss the clinical and pathological features of HHD, differential diagnoses, and genetic and functional studies of the ATP2C1 gene in HHD. Further understanding the role of the ATP2C1 gene in the pathogenesis of HHD by genetic, molecular, and animal studies may contribute to a better clinical diagnosis and provide new strategies for the treatment and prevention of HHD.
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Affiliation(s)
- Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Tongzipo Road 138, Changsha, 410013, Hunan, People's Republic of China.
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China.
| | - Heng Xiao
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Tongzipo Road 138, Changsha, 410013, Hunan, People's Republic of China
- Department of Pathology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China
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915
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Ghouse J, Skov MW, Bigseth RS, Ahlberg G, Kanters JK, Olesen MS. Distinguishing pathogenic mutations from background genetic noise in cardiology: The use of large genome databases for genetic interpretation. Clin Genet 2017; 93:459-466. [PMID: 28589536 DOI: 10.1111/cge.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
Advances in clinical genetic testing have led to increased insight into the human genome, including how challenging it is to interpret rare genetic variation. In some cases, the ability to detect genetic mutations exceeds the ability to understand their clinical impact, limiting the advantage of these technologies. Obstacles in genomic medicine are many and include: understanding the level of certainty/uncertainty behind pathogenicity determination, the numerous different variant interpretation-guidelines used by clinical laboratories, delivering the certain or uncertain result to the patient, helping patients evaluate medical decisions in light of uncertainty regarding the consequence of the findings. Through publication of large publicly available exome/genome databases, researchers and physicians are now able to highlight dubious variants previously associated with different cardiac traits. Also, continuous efforts through data sharing, international collaborative efforts to develop disease-gene-specific guidelines, and computational analyses using large data, will indubitably assist in better variant interpretation and classification. This article discusses the current, and quickly changing, state of variant interpretation resources within cardiovascular genetic research, e.g., publicly available databases and ways of how cardiovascular genetic counselors and geneticists can aid in improving variant interpretation in cardiology.
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Affiliation(s)
- J Ghouse
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - M W Skov
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - R S Bigseth
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - G Ahlberg
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M S Olesen
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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916
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Fassio AV, Martins PM, Guimarães SDS, Junior SSA, Ribeiro VS, de Melo-Minardi RC, Silveira SDA. Vermont: a multi-perspective visual interactive platform for mutational analysis. BMC Bioinformatics 2017; 18:403. [PMID: 28929973 PMCID: PMC5606220 DOI: 10.1186/s12859-017-1789-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable. RESULTS We aimed to contribute a novel visual analytics oriented method to analyze and gain insight on the impact of protein point mutations. To assess the ability of VERMONT to do this, we visually examined a set of mutations that were experimentally characterized to determine if VERMONT could identify damaging mutations and why they can be considered so. CONCLUSIONS VERMONT allowed us to understand mutations by interpreting position-specific structural and physicochemical properties. Additionally, we note some specific positions we believe have an impact on protein function/structure in the case of mutation.
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Affiliation(s)
- Alexandre V Fassio
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil. .,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil.
| | - Pedro M Martins
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil.,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Samuel da S Guimarães
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Sócrates S A Junior
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Vagner S Ribeiro
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Raquel C de Melo-Minardi
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Sabrina de A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
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917
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Álvarez-Satta M, Castro-Sánchez S, Valverde D. Bardet-Biedl Syndrome as a Chaperonopathy: Dissecting the Major Role of Chaperonin-Like BBS Proteins (BBS6-BBS10-BBS12). Front Mol Biosci 2017; 4:55. [PMID: 28824921 PMCID: PMC5534436 DOI: 10.3389/fmolb.2017.00055] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/13/2017] [Indexed: 01/01/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare genetic disorder that belongs to the group of ciliopathies, defined as diseases caused by defects in cilia structure and/or function. The six diagnostic features considered for this syndrome include retinal dystrophy, obesity, polydactyly, cognitive impairment and renal and urogenital anomalies. Furthermore, three of the 21 genes currently known to be involved in BBS encode chaperonin-like proteins (MKKS/BBS6, BBS10, and BBS12), so BBS can be also considered a member of the growing group of chaperonopathies. Remarkably, up to 50% of clinically-diagnosed BBS families can harbor disease-causing variants in these three genes, which highlights the importance of chaperone defects as pathogenic factors even for genetically heterogeneous syndromes such as BBS. In addition, it is interesting to note that BBS families with deleterious variants in MKKS/BBS6, BBS10 or BBS12 genes generally display more severe phenotypes than families with changes in other BBS genes. The chaperonin-like BBS proteins have structural homology to the CCT family of group II chaperonins, although they are believed to conserve neither the ATP-dependent folding activity of canonical CCT chaperonins nor the ability to form CCT-like oligomeric complexes. Thus, they play an important role in the initial steps of assembly of the BBSome, which is a multiprotein complex essential for mediating the ciliary trafficking activity. In this review, we present a comprehensive review of those genetic, functional and evolutionary aspects concerning chaperonin-like BBS proteins, trying to provide a new perspective that expands the classical conception of BBS only from a ciliary point of view.
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Affiliation(s)
- María Álvarez-Satta
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
| | - Sheila Castro-Sánchez
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
| | - Diana Valverde
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
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918
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Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 2017; 33:i389-i398. [PMID: 28882004 PMCID: PMC5870554 DOI: 10.1093/bioinformatics/btx272] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Loss-of-function genetic variants are frequently associated with severe clinical phenotypes, yet many are present in the genomes of healthy individuals. The available methods to assess the impact of these variants rely primarily upon evolutionary conservation with little to no consideration of the structural and functional implications for the protein. They further do not provide information to the user regarding specific molecular alterations potentially causative of disease. RESULTS To address this, we investigate protein features underlying loss-of-function genetic variation and develop a machine learning method, MutPred-LOF, for the discrimination of pathogenic and tolerated variants that can also generate hypotheses on specific molecular events disrupted by the variant. We investigate a large set of human variants derived from the Human Gene Mutation Database, ClinVar and the Exome Aggregation Consortium. Our prediction method shows an area under the Receiver Operating Characteristic curve of 0.85 for all loss-of-function variants and 0.75 for proteins in which both pathogenic and neutral variants have been observed. We applied MutPred-LOF to a set of 1142 de novo vari3ants from neurodevelopmental disorders and find enrichment of pathogenic variants in affected individuals. Overall, our results highlight the potential of computational tools to elucidate causal mechanisms underlying loss of protein function in loss-of-function variants. AVAILABILITY AND IMPLEMENTATION http://mutpred.mutdb.org. CONTACT predrag@indiana.edu.
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Affiliation(s)
- Kymberleigh A Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | - Guan Ning Lin
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Hyun-Jun Nam
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Beyster Center for Psychiatric Genomics, Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
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919
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Rehm HL. A new era in the interpretation of human genomic variation. Genet Med 2017; 19:1092-1095. [PMID: 28703787 DOI: 10.1038/gim.2017.90] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 01/19/2023] Open
Affiliation(s)
- Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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920
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Livingstone M, Folkman L, Yang Y, Zhang P, Mort M, Cooper DN, Liu Y, Stantic B, Zhou Y. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants. Hum Mutat 2017. [DOI: 10.1002/humu.23283] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark Livingstone
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Lukas Folkman
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Yuedong Yang
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
- Institute for Glycomics; Griffith University; Southport Queensland 4222 Australia
| | - Ping Zhang
- Menzies Health Institute; Griffith University; Southport Queensland 4222 Australia
| | - Matthew Mort
- Institute of Medical Genetics; Cardiff University; Cardiff CF144XN United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics; Cardiff University; Cardiff CF144XN United Kingdom
| | - Yunlong Liu
- Department of Medical and Molecular Genetics; Indiana University; Indianapolis Indiana 46202
| | - Bela Stantic
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
- Institute for Glycomics; Griffith University; Southport Queensland 4222 Australia
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921
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Khan SA, Peracha H, Ballhausen D, Wiesbauer A, Rohrbach M, Gautschi M, Mason RW, Giugliani R, Suzuki Y, Orii KE, Orii T, Tomatsu S. Epidemiology of mucopolysaccharidoses. Mol Genet Metab 2017; 121:227-240. [PMID: 28595941 PMCID: PMC5653283 DOI: 10.1016/j.ymgme.2017.05.016] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022]
Abstract
The aim of this study was to obtain data about the epidemiology of the different types of mucopolysaccharidoses in Japan and Switzerland and to compare with similar data from other countries. Data for Japan was collected between 1982 and 2009, and 467 cases with MPS were identified. The combined birth prevalence was 1.53 per 100,000 live births. The highest birth prevalence was 0.84 for MPS II, accounting for 55% of all MPS. MPS I, III, and IV accounted for 15, 16, and 10%, respectively. MPS VI and VII were more rare and accounted for 1.7 and 1.3%, respectively. A retrospective epidemiological data collection was performed in Switzerland between 1975 and 2008 (34years), and 41 living MPS patients were identified. The combined birth prevalence was 1.56 per 100,000 live births. The highest birth prevalence was 0.46 for MPS II, accounting for 29% of all MPS. MPS I, III, and IV accounted for 12, 24, and 24%, respectively. As seen in the Japanese population, MPS VI and VII were more rare and accounted for 7.3 and 2.4%, respectively. The high birth prevalence of MPS II in Japan was comparable to that seen in other East Asian countries where this MPS accounted for approximately 50% of all forms of MPS. Birth prevalence was also similar in some European countries (Germany, Northern Ireland, Portugal and the Netherlands) although the prevalence of other forms of MPS is also reported to be higher in these countries. Birth prevalence of MPS II in Switzerland and other European countries is comparatively lower. The birth prevalence of MPS III and IV in Switzerland is higher than in Japan but comparable to that in most other European countries. Moreover, the birth prevalence of MPS VI and VII was very low in both, Switzerland and Japan. Overall, the frequency of MPS varies for each population due to differences in ethnic backgrounds and/or founder effects that affect the birth prevalence of each type of MPS, as seen for other rare genetic diseases. Methods for identification of MPS patients are not uniform across all countries, and consequently, if patients are not identified, recorded prevalence rates will be aberrantly low.
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Affiliation(s)
- Shaukat A Khan
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Hira Peracha
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Diana Ballhausen
- Centre for Molecular Diseases, Service for Genetic Medicine, University Hospital Lausanne, Switzerland
| | - Alfred Wiesbauer
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, Zurich, Switzerland
| | - Matthias Gautschi
- Division of Endocrinology, Diabetology and Metabolism, University Children's Hospital, University Institute of Clinical Chemistry, Inselspital, University of Bern, Bern, Switzerland
| | - Robert W Mason
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Dep. Genetics, UFRGS, and INAGEMP, Porto Alegre, Brazil
| | | | - Kenji E Orii
- Department of Pediatrics, Gifu University, Gifu, Japan
| | - Tadao Orii
- Department of Pediatrics, Gifu University, Gifu, Japan
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Pediatrics, Gifu University, Gifu, Japan; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States.
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922
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Martínez-Ulloa PL, Vallejo M, Corral I, García-Barragán N, Alcazar A, Martínez-Alonso E, Martínez-Poles J, Pian H, Jiménez-Escrig A. A novel ATTR L32V mutation causes familial amyloid polyneuropathy in a Bolivian family. J Peripher Nerv Syst 2017. [PMID: 28646538 DOI: 10.1111/jns.12227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report a new transthyretin (ATTR) gene c.272C>G mutation and variant protein, p.Leu32Val, in a kindred of Bolivian origin with a rapid progressive peripheral neuropathy and cardiomyopathy. Three individuals from a kindred with peripheral nerve and cardiac amyloidosis were examined. Analysis of the TTR gene was performed by Sanger direct sequencing. Neuropathologic examination was obtained on the index patient with mass spectrometry study of the ATTR deposition. Direct DNA sequence analysis of exons 2, 3, and 4 of the TTR gene demonstrated a c.272 C>G mutation in exon 2 (p.L32V). Sural nerve biopsy revealed massive amyloid deposition in the perineurium, endoneurium and vasa nervorum. Mass spectrometric analyses of ATTR immunoprecipitated from nerve biopsy showed the presence of both wild-type and variant proteins. The observed mass results for the wild-type and variant proteins were consistent with the predicted values calculated from the genetic analysis data. The ATTR L32V is associated with a severe course. This has implications for treatment of affected individuals and counseling of family members.
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Affiliation(s)
| | - Manuela Vallejo
- Neurobiología, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain
| | - Iñigo Corral
- Department of Neurology, Hospital Ramón y Cajal, Madrid, Spain
| | | | - Alberto Alcazar
- Departmento de Investigación, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain
| | | | | | - Hector Pian
- Department of Pathology, Hospital Ramón y Cajal, Madrid, Spain
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923
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Abstract
Background Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia. However, acquired somatic mutations in NF1 are also found in a wide variety of malignant neoplasms that are not associated with NF1. Main body Capitalizing upon the availability of next-generation sequencing data from cancer genomes and exomes, we review current knowledge of somatic NF1 mutations in a wide variety of tumours occurring at a number of different sites: breast, colorectum, urothelium, lung, ovary, skin, brain and neuroendocrine tissues, as well as leukaemias, in an attempt to understand their broader role and significance, and with a view ultimately to exploiting this in a diagnostic and therapeutic context. Conclusion As neurofibromin activity is a key to regulating the RAS/MAPK pathway, NF1 mutations are important in the acquisition of drug resistance, to BRAF, EGFR inhibitors, tamoxifen and retinoic acid in melanoma, lung and breast cancers and neuroblastoma. Other curiosities are observed, such as a high rate of somatic NF1 mutation in cutaneous melanoma, lung cancer, ovarian carcinoma and glioblastoma which are not usually associated with neurofibromatosis type 1. Somatic NF1 mutations may be critical drivers in multiple cancers. The mutational landscape of somatic NF1 mutations should provide novel insights into our understanding of the pathophysiology of cancer. The identification of high frequency of somatic NF1 mutations in sporadic tumours indicates that neurofibromin is likely to play a critical role in development, far beyond that evident in the tumour predisposition syndrome NF1.
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924
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The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. Hum Genet 2017; 136:921-939. [PMID: 28600779 PMCID: PMC5502059 DOI: 10.1007/s00439-017-1821-8] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022]
Abstract
In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016–December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most “negative” clinical exome tests are unsolved due to interpretation rather than technical limitations.
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925
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Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J. Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med 2017; 9:49. [PMID: 28558813 PMCID: PMC5448149 DOI: 10.1186/s13073-017-0441-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.
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Affiliation(s)
- Charles A Steward
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK. .,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | | | - Berge A Minassian
- Department of Pediatrics (Neurology), University of Texas Southwestern, Dallas, TX, USA.,Program in Genetics and Genome Biology and Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, WC1N 3BG, UK.,Chalfont Centre for Epilepsy, Chesham Lane, Chalfont St Peter, Buckinghamshire, SL9 0RJ, UK
| | - Adam Frankish
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Illumina Inc, Great Chesterford, Essex, CB10 1XL, UK
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926
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Lualdi S, Del Zotto G, Zegarra-Moran O, Pedemonte N, Corsolini F, Bruschi M, Tomati V, Amico G, Candiano G, Dardis A, Cooper DN, Filocamo M. In vitro recapitulation of the site-specific editing (to wild-type) of mutant IDS mRNA transcripts, and the characterization of IDS protein translated from the edited mRNAs. Hum Mutat 2017; 38:849-862. [PMID: 28477385 DOI: 10.1002/humu.23243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/05/2017] [Accepted: 04/22/2017] [Indexed: 11/06/2022]
Abstract
The transfer of genomic information into the primary RNA sequence can be altered by RNA editing. We have previously shown that genomic variants can be RNA-edited to wild-type. The presence of distinct "edited" iduronate 2-sulfatase (IDS) mRNA transcripts ex vivo evidenced the correction of a nonsense and frameshift variant, respectively, in three unrelated Hunter syndrome patients. This phenomenon was confirmed in various patient samples by a variety of techniques, and was quantified by single-nucleotide primer extension. Western blotting also confirmed the presence of IDS protein similar in size to the wild-type. Since preliminary experimental evidence suggested that the "corrected" IDS proteins produced by the patients were similar in molecular weight and net charge to their wild-type counterparts, an in vitro system employing different cell types was established to recapitulate the site-specific editing of IDS RNA (uridine to cytidine conversion and uridine deletion), and to confirm the findings previously observed ex vivo in the three patients. In addition, confocal microscopy and flow cytometry analyses demonstrated the expression and lysosomal localization in HEK293 cells of GFP-labeled proteins translated from edited IDS mRNAs. Confocal high-content analysis of the two patients' cells expressing wild-type or mutated IDS confirmed lysosomal localization and showed no accumulation in the Golgi or early endosomes.
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Affiliation(s)
- Susanna Lualdi
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | | | | | | | - Fabio Corsolini
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | - Maurizio Bruschi
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Valeria Tomati
- UOC Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Giulia Amico
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Candiano
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Mirella Filocamo
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
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