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Jiang X, Otterdal K, Chung BK, Maucourant C, Rønneberg JD, Zimmer CL, Øgaard J, Boichuk Y, Holm S, Geanon D, Schneditz G, Bergquist A, Björkström NK, Melum E. Cholangiocytes Modulate CD100 Expression in the Liver and Facilitate Pathogenic T-Helper 17 Cell Differentiation. Gastroenterology 2024; 166:667-679. [PMID: 37995866 DOI: 10.1053/j.gastro.2023.11.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND & AIMS Chronic inflammation surrounding bile ducts contributes to the disease pathogenesis of most cholangiopathies. Poor efficacy of immunosuppression in these conditions suggests biliary-specific pathologic principles. Here we performed biliary niche specific functional interpretation of a causal mutation (CD100 K849T) of primary sclerosing cholangitis (PSC) to understand related pathogenic mechanisms. METHODS Biopsy specimens of explanted livers and endoscopy-guided sampling were used to assess the CD100 expression by spatial transcriptomics, immune imaging, and high-dimensional flow cytometry. To model pathogenic cholangiocyte-immune cell interaction, splenocytes from mutation-specific mice were cocultured with cholangiocytes. Pathogenic pathways were pinpointed by RNA sequencing analysis of cocultured cells and cross-validated in patient materials. RESULTS CD100 is mainly expressed by immune cells in the liver and shows a unique pattern around PSC bile ducts with RNA-level colocalization but poor detection at the protein level. This appears to be due to CD100 cleavage as soluble CD100 is increased. Immunophenotyping suggests biliary-infiltrating T cells as the major source of soluble CD100, which is further supported by reduced surface CD100 on T cells and increased metalloproteinases in cholangiocytes after coculturing. Pathogenic T cells that adhered to cholangiocytes up-regulated genes in the T-helper 17 cell differentiation pathway, and the CD100 mutation boosted this process. Consistently, T-helper 17 cells dominate biliary-resident CD4 T cells in patients. CONCLUSIONS CD100 exerts its functional impact through cholangiocyte-immune cell cross talk and underscores an active, proinflammatory role of cholangiocytes that can be relevant to novel treatment approaches.
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Affiliation(s)
- Xiaojun Jiang
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Kari Otterdal
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Brian K Chung
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christopher Maucourant
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jørgen D Rønneberg
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christine L Zimmer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Øgaard
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Yuliia Boichuk
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Daniel Geanon
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Georg Schneditz
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Espen Melum
- Norwegian PSC Research Center, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway; Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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2
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Bellucci G, Buscarinu MC, Reniè R, Rinaldi V, Bigi R, Mechelli R, Romano S, Salvetti M, Ristori G. Disentangling multiple sclerosis phenotypes through Mendelian disorders: A network approach. Mult Scler 2024; 30:325-335. [PMID: 38333907 DOI: 10.1177/13524585241227119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
BACKGROUND The increasing knowledge about multiple sclerosis (MS) pathophysiology has reinforced the need for an improved description of disease phenotypes, connected to disease biology. Growing evidence indicates that complex diseases constitute phenotypical and genetic continuums with "simple," monogenic disorders, suggesting shared pathomechanisms. OBJECTIVES The objective of this study was to depict a novel MS phenotypical framework leveraging shared physiopathology with Mendelian diseases and to identify phenotype-specific candidate drugs. METHODS We performed an enrichment testing of MS-associated variants with Mendelian disorders genes. We defined a "MS-Mendelian network," further analyzed to define enriched phenotypic subnetworks and biological processes. Finally, a network-based drug screening was implemented. RESULTS Starting from 617 MS-associated loci, we showed a significant enrichment of monogenic diseases (p < 0.001). We defined an MS-Mendelian molecular network based on 331 genes and 486 related disorders, enriched in four phenotypic classes: neurologic, immunologic, metabolic, and visual. We prioritized a total of 503 drugs, of which 27 molecules active in 3/4 phenotypical subnetworks and 140 in subnetwork pairs. CONCLUSION The genetic architecture of MS contains the seeds of pathobiological multiplicities shared with immune, neurologic, metabolic and visual monogenic disorders. This result may inform future classifications of MS endophenotypes and support the development of new therapies in both MS and rare diseases.
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Affiliation(s)
- Gianmarco Bellucci
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Maria Chiara Buscarinu
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
| | - Roberta Reniè
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Virginia Rinaldi
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Rachele Bigi
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Rosella Mechelli
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Pisana, Rome, Italy San Raffaele Roma Open University, Rome, Italy
| | - Silvia Romano
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy
| | - Marco Salvetti
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Italy
| | - Giovanni Ristori
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
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Curman P, Jebril W, Evans-Molina C, Bachar-Wikstrom E, Larsson H, Cederlöf M, Wikström JD. Hailey-Hailey Disease is Associated with Diabetes: A Population-based Cohort Study, Clinical Cohort Study, and Pedigree Analysis. Acta Derm Venereol 2023; 103:adv10436. [PMID: 38014829 PMCID: PMC10695124 DOI: 10.2340/actadv.v103.10436] [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: 03/08/2023] [Accepted: 09/27/2023] [Indexed: 11/29/2023] Open
Abstract
Hailey-Hailey disease is a rare hereditary skin disease caused by mutations in the ATP2C1 gene encoding the secretory pathway Ca2+/Mn2+-ATPase 1 (SPCA1) protein. Extracutaneous manifestations of Hailey-Hailey disease are plausible but still largely unknown. The aim of this study was to explore the association between Hailey-Hailey disease and diabetes. A population-based cohort study of 347 individuals with Hailey-Hailey disease was performed to assess the risks of type 1 diabetes and type 2 diabetes, using Swedish nationwide registries. Pedigrees from 2 Swedish families with Hailey-Hailey disease were also investigated: 1 with concurrent type 1 diabetes and HLA-DQ3, the other with type 2 diabetes. Lastly, a clinical cohort with 23 individuals with Hailey-Hailey disease and matched healthy controls was evaluated regarding diabetes. In the register data males with Hailey-Hailey disease had a 70% elevated risk of type 2 diabetes, whereas no excess risk among women could be confirmed. In both pedigrees an unusually high inheritance for diabetes was observed. In the clinical cohort, individuals with Hailey-Hailey disease displayed a metabolic phenotype indicative of type 2 diabetes. Hailey-Hailey disease seems to act as a synergistic risk factor for diabetes. This study indicates, for the first time, an association between Hailey-Hailey disease and diabetes and represents human evidence that SPCA1 and the Golgi apparatus may be implicated in diabetes pathophysiology.
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Affiliation(s)
- Philip Curman
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - William Jebril
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Carmella Evans-Molina
- Departments of Anatomy, Cell Biology, and Physiology; Biochemistry and Molecular Biology; Medicine; Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202; The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202; Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Etty Bachar-Wikstrom
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Cederlöf
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
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Nousiainen S, Kuismin O, Reinikka S, Manninen R, Khamaiseh S, Kuivalainen M, Terho A, Koivurova S, Niinimäki M, Salokas K, Varjosalo M, Ahtikoski A, Bützow R, Lindgren O, Uimari O, Vahteristo P. Whole-exome sequencing reveals candidate high-risk susceptibility genes for endometriosis. Hum Genomics 2023; 17:88. [PMID: 37789421 PMCID: PMC10546785 DOI: 10.1186/s40246-023-00538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Endometriosis is a common, chronic disease among fertile-aged women. Disease course may be highly invasive, requiring extensive surgery. The etiology of endometriosis remains elusive, though a high level of heritability is well established. Several low-penetrance predisposing loci have been identified, but high-risk susceptibility remains undetermined. Endometriosis is known to increase the risk of epithelial ovarian cancers, especially of endometrioid and clear cell types. Here, we have analyzed a Finnish family where four women have been diagnosed with surgically verified, severely symptomatic endometriosis and two of the patients also with high-grade serous carcinoma. RESULTS Whole-exome sequencing revealed three rare candidate predisposing variants segregating with endometriosis. The variants were c.1238C>T, p.(Pro413Leu) in FGFR4, c.5065C>T, p.(Arg1689Trp) in NALCN, and c.2086G>A, p.(Val696Met) in NAV2. The only variant predicted deleterious by in silico tools was the one in FGFR4. Further screening of the variants in 92 Finnish endometriosis and in 19 endometriosis-ovarian cancer patients did not reveal additional carriers. Histopathology, positive p53 immunostaining, and genetic analysis supported the high-grade serous subtype of the two tumors in the family. CONCLUSIONS Here, we provide FGFR4, NALCN, and NAV2 as novel high-risk candidate genes for familial endometriosis. Our results also support the association of endometriosis with high-grade serous carcinoma. Further studies are required to validate the findings and to reveal the exact pathogenesis mechanisms of endometriosis. Elucidating the genetic background of endometriosis defines the etiology of the disease and provides opportunities for expedited diagnostics and personalized treatments.
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Affiliation(s)
- Susanna Nousiainen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Siiri Reinikka
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Roosa Manninen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
| | - Sara Khamaiseh
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Mari Kuivalainen
- Department of Obstetrics and Gynecology, Kainuu Central Hospital, Kajaani, Finland
| | - Anna Terho
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
| | - Sari Koivurova
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
| | - Maarit Niinimäki
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
| | - Kari Salokas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anne Ahtikoski
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Ralf Bützow
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Helsinki, Finland
- Department of Pathology, Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Outi Lindgren
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Pathology, Oulu University Hospital, Oulu, Finland
| | - Outi Uimari
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Pia Vahteristo
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Helsinki, Finland.
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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Chandra A, Yoon S, Michieletto MF, Goldman N, Ferrari EK, Abedi M, Johnson I, Fasolino M, Pham K, Joannas L, Kee BL, Henao-Mejia J, Vahedi G. Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. Immunity 2023; 56:1451-1467.e12. [PMID: 37263273 PMCID: PMC10979463 DOI: 10.1016/j.immuni.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.
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Affiliation(s)
- Aditi Chandra
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sora Yoon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michaël F Michieletto
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Naomi Goldman
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily K Ferrari
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maryam Abedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabelle Johnson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria Fasolino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth Pham
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leonel Joannas
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara L Kee
- Department of Pathology, Committees on Cancer Biology and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Jorge Henao-Mejia
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Yao Q, Gorevic P, Shen B, Gibson G. Genetically transitional disease: a new concept in genomic medicine. Trends Genet 2023; 39:98-108. [PMID: 36564319 DOI: 10.1016/j.tig.2022.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Traditional classification of genetic diseases as monogenic and polygenic has lagged far behind scientific progress. In this opinion article, we propose and define a new terminology, genetically transitional disease (GTD), referring to cases where a large-effect mutation is necessary, but not sufficient, to cause disease. This leads to a working disease nosology based on gradients of four types of genetic architecture: monogenic, polygenic, GTD, and mixed. We present four scenarios under which GTD may occur; namely, subsets of traditionally Mendelian disease, modifiable Tier 1 monogenic conditions, variable penetrance, and situations where a genetic mutational spectrum produces qualitatively divergent pathologies. The implications of the new nosology in precision medicine are discussed, in which therapeutic options may target the molecular cause or the disease phenotype.
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Affiliation(s)
- Qingping Yao
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA.
| | - Peter Gorevic
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA
| | - Bo Shen
- Center for Inflammatory Bowel Diseases, New York-Presbyterian/Columbia University Irving Medical Center, New York, NY, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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7
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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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8
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Huang M, Xu H. Genetic susceptibility to autoimmunity-Current status and challenges. Adv Immunol 2022; 156:25-54. [PMID: 36410874 DOI: 10.1016/bs.ai.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.
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Affiliation(s)
| | - Huji Xu
- School of Medicine, Tsinghua University, Beijing, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Navel Medical University, Shanghai, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
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9
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Nazarenko MS, Sleptcov AA, Puzyrev VP. “Mendelian Code” in the Genetic Structure of Common Multifactorial Diseases. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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11
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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12
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Koromani F, Alonso N, Alves I, Brandi ML, Foessl I, Formosa MM, Morgenstern MF, Karasik D, Kolev M, Makitie O, Ntzani E, Pietsch BO, Ohlsson C, Rauner M, Soe K, Soldatovic I, Teti A, Valjevac A, Rivadeneira F. The "GEnomics of Musculo Skeletal Traits TranslatiOnal NEtwork": Origins, Rationale, Organization, and Prospects. Front Endocrinol (Lausanne) 2021; 12:709815. [PMID: 34484122 PMCID: PMC8415473 DOI: 10.3389/fendo.2021.709815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/15/2021] [Indexed: 02/01/2023] Open
Abstract
Musculoskeletal research has been enriched in the past ten years with a great wealth of new discoveries arising from genome wide association studies (GWAS). In addition to the novel factors identified by GWAS, the advent of whole-genome and whole-exome sequencing efforts in family based studies has also identified new genes and pathways. However, the function and the mechanisms by which such genes influence clinical traits remain largely unknown. There is imperative need to bring multidisciplinary expertise together that will allow translating these genomic discoveries into useful clinical applications with the potential of improving patient care. Therefore "GEnomics of MusculoSkeletal traits TranslatiOnal NEtwork" (GEMSTONE) aims to set the ground for the: 1) functional characterization of discovered genes and pathways; 2) understanding of the correspondence between molecular and clinical assessments; and 3) implementation of novel methodological approaches. This research network is funded by The European Cooperation in Science and Technology (COST). GEMSTONE includes six working groups (WG), each with specific objectives: WG1-Study populations and expertise groups: creating, maintaining and updating an inventory of experts and resources (studies and datasets) participating in the network, helping to assemble focus groups defined by phenotype, functional and methodological expertise. WG2-Phenotyping: describe ways to decompose the phenotypes of the different functional studies into meaningful components that will aid the interpretation of identified biological pathways. WG3 Monogenic conditions - human KO models: makes an inventory of genes underlying musculoskeletal monogenic conditions that aids the assignment of genes to GWAS signals and prioritizing GWAS genes as candidates responsible for monogenic presentations, through biological plausibility. WG4 Functional investigations: creating a roadmap of genes and pathways to be prioritized for functional assessment in cell and organism models of the musculoskeletal system. WG5 Bioinformatics seeks the integration of the knowledge derived from the distinct efforts, with particular emphasis on systems biology and artificial intelligence applications. Finally, WG6 Translational outreach: makes a synopsis of the knowledge derived from the distinct efforts, allowing to prioritize factors within biological pathways, use refined disease trait definitions and/or improve study design of future investigations in a potential therapeutic context (e.g. clinical trials) for musculoskeletal diseases.
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Affiliation(s)
- Fjorda Koromani
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Nerea Alonso
- Rheumatology and Bone Disease Unit, CGEM-IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Maria Luisa Brandi
- Department of Surgery and Translational Medicine (M.L.B.), University of Florence, Florence, Italy
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrinology Lab Platform, Medical University Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | | | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
| | - Mikhail Kolev
- Department of Mathematics, South-West University Neofit Rilski, Blagoevgrad, Bulgaria
| | - Outi Makitie
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Evangelia Ntzani
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Ioannina, Greece
- Department of Health Services, Policy and Practice, Center for Research Synthesis in Health, School of Public Health, Brown University, Providence, RI, United States
| | - Barbara Obermayer Pietsch
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrinology Lab Platform, Medical University Graz, Graz, Austria
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Martina Rauner
- Department of Medicine III, Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Kent Soe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Clinical Cell Biology, Pathology Research Unit, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Ivan Soldatovic
- Institute of Biostatistics, University of Belgrade, Belgrade, Serbia
| | - Anna Teti
- Department of Biotechnological and Applied Clinical Sciences, L’Aquila, Italy
| | - Amina Valjevac
- Department of Physiology, Medical Faculty University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
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13
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Lebedeva IV, Wagner MV, Sahdeo S, Lu YF, Anyanwu-Ofili A, Harms MB, Wadia JS, Rajagopal G, Boland MJ, Goldstein DB. Precision genetic cellular models identify therapies protective against ER stress. Cell Death Dis 2021; 12:770. [PMID: 34354042 PMCID: PMC8342410 DOI: 10.1038/s41419-021-04045-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/08/2022]
Abstract
Rare monogenic disorders often share molecular etiologies involved in the pathogenesis of common diseases. Congenital disorders of glycosylation (CDG) and deglycosylation (CDDG) are rare pediatric disorders with symptoms that range from mild to life threatening. A biological mechanism shared among CDG and CDDG as well as more common neurodegenerative diseases such as Alzheimer's disease and amyotrophic lateral sclerosis, is endoplasmic reticulum (ER) stress. We developed isogenic human cellular models of two types of CDG and the only known CDDG to discover drugs that can alleviate ER stress. Systematic phenotyping confirmed ER stress and identified elevated autophagy among other phenotypes in each model. We screened 1049 compounds and scored their ability to correct aberrant morphology in each model using an agnostic cell-painting assay based on >300 cellular features. This primary screen identified multiple compounds able to correct morphological phenotypes. Independent validation shows they also correct cellular phenotypes and alleviate each of the ER stress markers identified in each model. Many of the active compounds are associated with microtubule dynamics, which points to new therapeutic opportunities for both rare and more common disorders presenting with ER stress, such as Alzheimer's disease and amyotrophic lateral sclerosis.
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Affiliation(s)
- Irina V Lebedeva
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Michelle V Wagner
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA, USA
- Janssen R&D US, San Diego, CA, USA
| | - Sunil Sahdeo
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA, USA
- Janssen R&D US, San Diego, CA, USA
| | - Yi-Fan Lu
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Matthew B Harms
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jehangir S Wadia
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA, USA
- Janssen R&D US, San Diego, CA, USA
| | | | - Michael J Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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14
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Tukker AM, Royal CD, Bowman AB, McAllister KA. The Impact of Environmental Factors on Monogenic Mendelian Diseases. Toxicol Sci 2021; 181:3-12. [PMID: 33677604 PMCID: PMC8599782 DOI: 10.1093/toxsci/kfab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Environmental factors and gene-environment interactions modify the variable expressivity, progression, severity, and onset of some classic (monogenic) Mendelian-inherited genetic diseases. Cystic fibrosis, Huntington disease, Parkinson's disease, and sickle cell disease are examples of well-known Mendelian disorders that are influenced by exogenous exposures. Environmental factors may act by direct or indirect mechanisms to modify disease severity, timing, and presentation, including through epigenomic influences, protein misfolding, miRNA alterations, transporter activity, and mitochondrial effects. Because pathological features of early-onset Mendelian diseases can mimic later onset complex diseases, we propose that studies of environmental exposure vulnerabilities using monogenic model systems of rare Mendelian diseases have high potential to provide insight into complex disease phenotypes arising from multi-genetic/multi-toxicant interactions. Mendelian disorders can be modeled by homologous mutations in animal model systems with strong recapitulation of human disease etiology and natural history, providing an important advantage for study of these diseases. Monogenic high penetrant mutations are ideal for toxicant challenge studies with a wide variety of environmental stressors, because background genetic variability may be less able to alter the relatively strong phenotype driving disease-causing mutations. These models promote mechanistic understandings of gene-environment interactions and biological pathways relevant to both Mendelian and related sporadic complex disease outcomes by creating a sensitized background for relevant environmental risk factors. Additionally, rare disease communities are motivated research participants, creating the potential of strong research allies among rare Mendelian disease advocacy groups and disease registries and providing a variety of translational opportunities that are under-utilized in genetic or environmental health science.
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Affiliation(s)
- Anke M Tukker
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Charmaine D Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health and Center on Genomics, Race, Identity, Difference, Duke University, Durham, North Carolina 27708
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Kimberly A McAllister
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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15
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Abstract
Congenital heart disease is the most common congenital defect observed in newborns. Within the spectrum of congenital heart disease are left‐sided obstructive lesions (LSOLs), which include hypoplastic left heart syndrome, aortic stenosis, bicuspid aortic valve, coarctation of the aorta, and interrupted aortic arch. These defects can arise in isolation or as a component of a defined syndrome; however, nonsyndromic defects are often observed in multiple family members and associated with high sibling recurrence risk. This clear evidence for a heritable basis has driven a lengthy search for disease‐causing variants that has uncovered both rare and common variants in genes that, when perturbed in cardiac development, can result in LSOLs. Despite advancements in genetic sequencing platforms and broadening use of exome sequencing, the currently accepted LSOL‐associated genes explain only 10% to 20% of patients. Further, the combinatorial effects of common and rare variants as a cause of LSOLs are emerging. In this review, we highlight the genes and variants associated with the different LSOLs and discuss the strengths and weaknesses of the present genetic associations. Furthermore, we discuss the research avenues needed to bridge the gaps in our current understanding of the genetic basis of nonsyndromic congenital heart disease.
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Affiliation(s)
- Lauren E Parker
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC
| | - Andrew P Landstrom
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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16
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Kim SS, Dey KK, Weissbrod O, Márquez-Luna C, Gazal S, Price AL. Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease. Nat Commun 2020; 11:6258. [PMID: 33288751 PMCID: PMC7721881 DOI: 10.1038/s41467-020-20087-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Despite considerable progress on pathogenicity scores prioritizing variants for Mendelian disease, little is known about the utility of these scores for common disease. Here, we assess the informativeness of Mendelian disease-derived pathogenicity scores for common disease and improve upon existing scores. We first apply stratified linkage disequilibrium (LD) score regression to evaluate published pathogenicity scores across 41 common diseases and complex traits (average N = 320K). Several of the resulting annotations are informative for common disease, even after conditioning on a broad set of functional annotations. We then improve upon published pathogenicity scores by developing AnnotBoost, a machine learning framework to impute and denoise pathogenicity scores using a broad set of functional annotations. AnnotBoost substantially increases the informativeness for common disease of both previously uninformative and previously informative pathogenicity scores, implying that Mendelian and common disease variants share similar properties. The boosted scores also produce improvements in heritability model fit and in classifying disease-associated, fine-mapped SNPs. Our boosted scores may improve fine-mapping and candidate gene discovery for common disease.
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Affiliation(s)
- Samuel S Kim
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Kushal K Dey
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Carla Márquez-Luna
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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17
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Li C, Wang N, Schäffer AA, Liu X, Zhao Z, Elliott G, Garrett L, Choi NT, Wang Y, Wang Y, Wang C, Wang J, Chan D, Su P, Cui S, Yang Y, Gao B. Mutations in COMP cause familial carpal tunnel syndrome. Nat Commun 2020; 11:3642. [PMID: 32686688 PMCID: PMC7371736 DOI: 10.1038/s41467-020-17378-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/21/2020] [Indexed: 02/06/2023] Open
Abstract
Carpal tunnel syndrome (CTS) is the most common peripheral nerve entrapment syndrome, affecting a large proportion of the general population. Genetic susceptibility has been implicated in CTS, but the causative genes remain elusive. Here, we report the identification of two mutations in cartilage oligomeric matrix protein (COMP) that segregate with CTS in two large families with or without multiple epiphyseal dysplasia (MED). Both mutations impair the secretion of COMP by tenocytes, but the mutation associated with MED also perturbs its secretion in chondrocytes. Further functional characterization of the CTS-specific mutation reveals similar histological and molecular changes of tendons/ligaments in patients’ biopsies and the mouse models. The mutant COMP fails to oligomerize properly and is trapped in the ER, resulting in ER stress-induced unfolded protein response and cell death, leading to inflammation, progressive fibrosis and cell composition change in tendons/ligaments. The extracellular matrix (ECM) organization is also altered. Our studies uncover a previously unrecognized mechanism in CTS pathogenesis. Familial carpal tunnel syndrome (CTS) is common, but causal genes are not characterized. Here the authors report two CTS-related mutations in two large families that impair secretion of COMP in tenocytes, leading to ER stress-induced unfolded protein response, inflammation and fibrosis in patients and mouse models.
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Affiliation(s)
- Chunyu Li
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Ni Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alejandro A Schäffer
- National Center for Biotechnology Information and National Cancer Institute, National Institutes of Health, Bethesda, MD, US
| | - Xilin Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhuo Zhao
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Gene Elliott
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Lisa Garrett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US
| | - Nga Ting Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yueshu Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yufa Wang
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Cheng Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peiqiang Su
- Department of Orthopaedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shusen Cui
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
| | - Yingzi Yang
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US. .,Department of Developmental Biology, Harvard School of Dental Medicine, Harvard Stem Cell Institute, Harvard University, Boston, MA, US.
| | - Bo Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. .,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, US.
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18
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Fischer TT, Ehrlich BE. Wolfram Syndrome: a Monogenic Model to Study Diabetes Mellitus and Neurodegeneration. CURRENT OPINION IN PHYSIOLOGY 2020; 17:115-123. [PMID: 32864536 DOI: 10.1016/j.cophys.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Wolfram syndrome (WS) is a rare, progressive disorder characterized by childhood-onset diabetes mellitus, optic nerve atrophy, hearing loss, diabetes insipidus, and neurodegeneration. Currently, there is no effective treatment for WS, and patients typically die between 30 and 40 years of age. WS is primarily caused by autosomal recessive mutations in the Wolfram syndrome 1 (WFS1) gene (OMIM 222300), which encodes for wolframin (WFS1). This disorder is therefore a valuable monogenic model for prevalent diseases, particularly diabetes mellitus and neurodegeneration. Whereas reduced survival and secretion are known cellular impairments causing WS, the underlying molecular pathways and the physiological function of WFS1 remain incompletely described. Here, we characterize WFS1 as a regulator of intracellular calcium homeostasis, review our current understanding of the disease mechanism of WS, and discuss candidate treatment approaches. These insights will facilitate identification of new therapeutic strategies not only for WS but also for diabetes mellitus and neurodegeneration.
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Affiliation(s)
- Tom T Fischer
- Department of Pharmacology, Yale University, New Haven, CT-06520, USA.,Institute of Pharmacology, University of Heidelberg, Germany
| | - Barbara E Ehrlich
- Department of Pharmacology, Yale University, New Haven, CT-06520, USA.,Department of Molecular Physiology, Yale University, New Haven, CT-06520, USA
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19
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Kajikawa T, Wang B, Li X, Wang H, Chavakis T, Moutsopoulos NM, Hajishengallis G. Frontline Science: Activation of metabolic nuclear receptors restores periodontal tissue homeostasis in mice with leukocyte adhesion deficiency-1. J Leukoc Biol 2020; 108:1501-1514. [PMID: 32421906 DOI: 10.1002/jlb.5hi0420-648r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/14/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
β2 Integrins mediate neutrophil-endothelial adhesion and recruitment of neutrophils to sites of inflammation. The diminished expression of β2 integrins in patients with mutations in the ITGB2 (CD18) gene (leukocyte adhesion deficiency-Type 1; LAD1) results in few or no neutrophils in peripheral tissues. In the periodontium, neutrophil paucity is associated with up-regulation of IL-23 and IL-17, which drive inflammatory bone loss. Using a relevant mouse model, we investigated whether diminished efferocytosis (owing to neutrophil scarcity) is associated with LAD1 periodontitis pathogenesis and aimed to develop approaches to restore the missing efferocytosis signals. We first showed that CD18-/- mice phenocopied human LAD1 in terms of IL-23/IL-17-driven inflammatory bone loss. Ab-mediated blockade of c-Mer tyrosine kinase (Mer), a major efferocytic receptor, mimicked LAD1-associated up-regulation of gingival IL-23 and IL-17 mRNA expression in wild-type (WT) mice. Consistently, soluble Mer-Fc reversed the inhibitory effect of efferocytosis on IL-23 expression in LPS-activated Mϕs. Adoptive transfer of WT neutrophils to CD18-/- mice down-regulated IL-23 and IL-17 expression to normal levels, but not when CD18-/- mice were treated with blocking anti-Mer Ab. Synthetic agonist-induced activation of liver X receptors (LXR) and peroxisome proliferator-activated receptors (PPAR), which link efferocytosis to generation of homeostatic signals, inhibited the expression of IL-23 and IL-17 and favorably affected the bone levels of CD18-/- mice. Therefore, our data link diminished efferocytosis-associated signaling due to impaired neutrophil recruitment to dysregulation of the IL-23-IL-17 axis and, moreover, suggest LXR and PPAR as potential therapeutic targets for treating LAD1 periodontitis.
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Affiliation(s)
- Tetsuhiro Kajikawa
- School of Dental Medicine, Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Baomei Wang
- School of Dental Medicine, Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaofei Li
- School of Dental Medicine, Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hui Wang
- School of Dental Medicine, Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Triantafyllos Chavakis
- Faculty of Medicine, Institute for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - George Hajishengallis
- School of Dental Medicine, Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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20
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Ross JP, Dion PA, Rouleau GA. Exome sequencing in genetic disease: recent advances and considerations. F1000Res 2020; 9:F1000 Faculty Rev-336. [PMID: 32431803 PMCID: PMC7205110 DOI: 10.12688/f1000research.19444.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, exome sequencing (ES) has allowed significant advancements to the field of disease research. By targeting the protein-coding regions of the genome, ES combines the depth of knowledge on protein-altering variants with high-throughput data generation and ease of analysis. New discoveries continue to be made using ES, and medical science has benefitted both theoretically and clinically from its continued use. In this review, we describe recent advances and successes of ES in disease research. Through selected examples of recent publications, we explore how ES continues to be a valuable tool to find variants that might explain disease etiology or provide insight into the biology underlying the disease. We then discuss shortcomings of ES in terms of variant discoveries made by other sequencing technologies that would be missed because of the scope and techniques of ES. We conclude with a brief outlook on the future of ES, suggesting that although newer and more thorough sequencing methods will soon supplant ES, its results will continue to be useful for disease research.
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Affiliation(s)
- Jay P. Ross
- Department of Human Genetics, McGill University, 3640 University, Montréal, QC, H3A 0C7, Canada
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
| | - Patrick A. Dion
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, 3640 University, Montréal, QC, H3A 0C7, Canada
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
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21
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Claussnitzer M, Cho JH, Collins R, Cox NJ, Dermitzakis ET, Hurles ME, Kathiresan S, Kenny EE, Lindgren CM, MacArthur DG, North KN, Plon SE, Rehm HL, Risch N, Rotimi CN, Shendure J, Soranzo N, McCarthy MI. A brief history of human disease genetics. Nature 2020; 577:179-189. [PMID: 31915397 PMCID: PMC7405896 DOI: 10.1038/s41586-019-1879-7] [Citation(s) in RCA: 331] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022]
Abstract
A primary goal of human genetics is to identify DNA sequence variants that influence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition.
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Affiliation(s)
- Melina Claussnitzer
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, 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
| | - Rory Collins
- Nuffield Department of Population Health (NDPH), University of Oxford, Oxford, UK
- UK Biobank, Stockport, UK
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Health 2030 Genome Center, Geneva, Switzerland
| | | | - Sekar Kathiresan
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - Eimear E Kenny
- Charles Bronfman Institute for Personalized Medicine, 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
- Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cecilia M Lindgren
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel G MacArthur
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn N North
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
| | - Sharon E Plon
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Magnuson Health Sciences Building, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
- Human Genetics, Genentech, South San Francisco, CA, USA.
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22
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Hajishengallis G. New developments in neutrophil biology and periodontitis. Periodontol 2000 2019; 82:78-92. [DOI: 10.1111/prd.12313] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- George Hajishengallis
- Department of Microbiology Penn Dental Medicine University of Pennsylvania Philadelphia Pennsylvania, USA
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23
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Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Modern high-throughput experiments provide us with numerous potential associations between genes and diseases. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. To facilitate the discovery of causative genes, various approaches for prioritization of genes according to their relevance for a given disease have been developed. In this article, we explain the gene prioritization problem and provide an overview of computational tools for gene prioritization. Among about a hundred of published gene prioritization tools, we select and briefly describe 14 most up-to-date and user-friendly. Also, we discuss the advantages and disadvantages of existing tools, challenges of their validation, and the directions for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, Faculty of Technology and Center for Biotechnology, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Universitätsstraße 25, Bielefeld, Germany
| | - Maren Kleine
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Universitätsstraße 25, Bielefeld, Germany
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24
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Koster KP, Francesconi W, Berton F, Alahmadi S, Srinivas R, Yoshii A. Developmental NMDA receptor dysregulation in the infantile neuronal ceroid lipofuscinosis mouse model. eLife 2019; 8:40316. [PMID: 30946007 PMCID: PMC6464704 DOI: 10.7554/elife.40316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 03/31/2019] [Indexed: 12/20/2022] Open
Abstract
Protein palmitoylation and depalmitoylation alter protein function. This post-translational modification is critical for synaptic transmission and plasticity. Mutation of the depalmitoylating enzyme palmitoyl-protein thioesterase 1 (PPT1) causes infantile neuronal ceroid lipofuscinosis (CLN1), a pediatric neurodegenerative disease. However, the role of protein depalmitoylation in synaptic maturation is unknown. Therefore, we studied synapse development in Ppt1-/- mouse visual cortex. We demonstrate that the developmental N-methyl-D-aspartate receptor (NMDAR) subunit switch from GluN2B to GluN2A is stagnated in Ppt1-/- mice. Correspondingly, Ppt1-/- neurons exhibit immature evoked NMDAR currents and dendritic spine morphology in vivo. Further, dissociated Ppt1-/- cultured neurons show extrasynaptic, diffuse calcium influxes and enhanced vulnerability to NMDA-induced excitotoxicity, reflecting the predominance of GluN2B-containing receptors. Remarkably, Ppt1-/- neurons demonstrate hyperpalmitoylation of GluN2B as well as Fyn kinase, which regulates surface retention of GluN2B. Thus, PPT1 plays a critical role in postsynapse maturation by facilitating the GluN2 subunit switch and proteostasis of palmitoylated proteins.
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Affiliation(s)
- Kevin P Koster
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States
| | - Walter Francesconi
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States
| | - Fulvia Berton
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States
| | - Sami Alahmadi
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States
| | - Roshan Srinivas
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, United States
| | - Akira Yoshii
- Department of Pediatrics, University of Illinois at Chicago, Chicago, United States.,Department of Neurology, University of Illinois at Chicago, Chicago, United States
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25
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Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics. Sci Rep 2018; 8:16583. [PMID: 30409984 PMCID: PMC6224454 DOI: 10.1038/s41598-018-34815-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Consanguineous populations of the Arabian Peninsula have been underrepresented in global efforts that catalogue human exome variability. We sequenced 291 whole exomes of unrelated, healthy native Arab individuals from Kuwait to a median coverage of 45X and characterised 170,508 single-nucleotide variants (SNVs), of which 21.7% were ‘personal’. Up to 12% of the SNVs were novel and 36% were population-specific. Half of the SNVs were rare and 54% were missense variants. The study complemented the Greater Middle East Variome by way of reporting many additional Arabian exome variants. The study corroborated Kuwaiti population genetic substructures previously derived using genome-wide genotype data and illustrated the genetic relatedness among Kuwaiti population subgroups, Middle Eastern, European and Ashkenazi Jewish populations. The study mapped 112 rare and frequent functional variants relating to pharmacogenomics and disorders (recessive and common) to the phenotypic characteristics of Arab population. Comparative allele frequency data and carrier distributions of known Arab mutations for 23 disorders seen among Arabs, of putative OMIM-listed causal mutations for 12 disorders observed among Arabs but not yet characterized for genetic basis in Arabs, and of 17 additional putative mutations for disorders characterized for genetic basis in Arab populations are presented for testing in future Arab studies.
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26
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Mortezaei Z, Cazier JB, Mehrabi AA, Cheng C, Masoudi-Nejad A. Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. J Cell Biochem 2018; 120:5459-5471. [PMID: 30302804 DOI: 10.1002/jcb.27825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
Understanding the genetic causes of neurodegenerative disease (ND) can be useful for their prevention and treatment. Among the genetic variations responsible for ND, heritable germline variants have been discovered in genome-wide association studies (GWAS), and nonheritable somatic mutations have been discovered in sequencing projects. Distinguishing the important initiating genes in ND and comparing the importance of heritable and nonheritable genetic variants for treating ND are important challenges. In this study, we analysed GWAS results, somatic mutations and drug targets of ND from large databanks by performing directed network-based analysis considering a randomised network hypothesis testing procedure. A disease-associated biological network was created in the context of the functional interactome, and the nonrandom topological characteristics of directed-edge classes were interpreted. Hierarchical network analysis indicated that drug targets tend to lie upstream of somatic mutations and germline variants. Furthermore, using directed path length information and biological explanations, we provide information on the most important genes in these created node classes and their associated drugs. Finally, we identified nine germline variants overlapping with drug targets for ND, seven somatic mutations close to drug targets from the hierarchical network analysis and six crucial genes in controlling other genes from the network analysis. Based on these findings, some drugs have been proposed for treating ND via drug repurposing. Our results provide new insights into the therapeutic actionability of GWAS results and somatic mutations for ND. The interesting properties of each node class and the existing relationships between them can broaden our knowledge of ND.
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Affiliation(s)
- Zahra Mortezaei
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, Haworth Building, University of Birmingham, Birmingham, UK
| | - Ali Ashraf Mehrabi
- Department of Biometry and Plant Genetics, University of Ilam, Ilam, Iran
| | - Chao Cheng
- Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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27
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Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. Am J Hum Genet 2018; 103:535-552. [PMID: 30290150 DOI: 10.1016/j.ajhg.2018.08.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/28/2018] [Indexed: 01/29/2023] Open
Abstract
Although recent studies provide evidence for a common genetic basis between complex traits and Mendelian disorders, a thorough quantification of their overlap in a phenotype-specific manner remains elusive. Here, we have quantified the overlap of genes identified through large-scale genome-wide association studies (GWASs) for 62 complex traits and diseases with genes containing mutations known to cause 20 broad categories of Mendelian disorders. We identified a significant enrichment of genes linked to phenotypically matched Mendelian disorders in GWAS gene sets; of the total 1,240 comparisons, a higher proportion of phenotypically matched or related pairs (n = 50 of 92 [54%]) than phenotypically unmatched pairs (n = 27 of 1,148 [2%]) demonstrated significant overlap, confirming a phenotype-specific enrichment pattern. Further, we observed elevated GWAS effect sizes near genes linked to phenotypically matched Mendelian disorders. Finally, we report examples of GWAS variants localized at the transcription start site or physically interacting with the promoters of genes linked to phenotypically matched Mendelian disorders. Our results are consistent with the hypothesis that genes that are disrupted in Mendelian disorders are dysregulated by non-coding variants in complex traits and demonstrate how leveraging findings from related Mendelian disorders and functional genomic datasets can prioritize genes that are putatively dysregulated by local and distal non-coding GWAS variants.
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28
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Loss-of-function mutations in caspase recruitment domain-containing protein 14 (CARD14) are associated with a severe variant of atopic dermatitis. J Allergy Clin Immunol 2018; 143:173-181.e10. [PMID: 30248356 DOI: 10.1016/j.jaci.2018.09.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is a highly prevalent chronic inflammatory skin disease that is known to be, at least in part, genetically determined. Mutations in caspase recruitment domain-containing protein 14 (CARD14) have been shown to result in various forms of psoriasis and related disorders. OBJECTIVE We aimed to identify rare DNA variants conferring a significant risk for AD through genetic and functional studies in a cohort of patients affected with severe AD. METHODS Whole-exome and direct gene sequencing, immunohistochemistry, real-time PCR, ELISA, and functional assays in human keratinocytes were used. RESULTS In a cohort of patients referred with severe AD, DNA sequencing revealed in 4 patients 2 rare heterozygous missense mutations in the gene encoding CARD14, a major regulator of nuclear factor κB (NF-κB). A dual luciferase reporter assay demonstrated that both mutations exert a dominant loss-of-function effect and result in decreased NF-κB signaling. Accordingly, immunohistochemistry staining showed decreased expression of CARD14 in patients' skin, as well as decreased levels of activated p65, a surrogate marker for NF-κB activity. CARD14-deficient or mutant-expressing keratinocytes displayed abnormal secretion of key mediators of innate immunity. CONCLUSIONS Although dominant gain-of-function mutations in CARD14 are associated with psoriasis and related diseases, loss-of-function mutations in the same gene are associated with a severe variant of AD.
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29
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Wu H, Shen X, Huang L, Zeng Y, Gao Y, Shao L, Lu B, Zhong Y, Miao B, Xu Y, Wang Y, Li Y, Xiong L, Lu S, Xie XS, Zhou C. Genotyping single-sperm cells by universal MARSALA enables the acquisition of linkage information for combined pre-implantation genetic diagnosis and genome screening. J Assist Reprod Genet 2018; 35:1071-1078. [PMID: 29790070 DOI: 10.1007/s10815-018-1158-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/08/2018] [Indexed: 12/29/2022] Open
Abstract
PURPOSE This paper aims to investigate the feasibility of performing pre-implantation genetic diagnosis (PGD) and pre-implantation genetic screening (PGS) simultaneously by a universal strategy without the requirement of genotyping relevant affected family members or lengthy preliminary work on linkage analysis. METHODS By utilizing a universal Mutated Allele Revealed by Sequencing with Aneuploidy and Linkage Analyses (MARSALA) strategy based on low depth whole genome sequencing (~3x), not involving specific primers' design nor the enrichment of SNP markers for haplotype construction. Single-sperm cells and trephectoderm cells from in vitro fertilized embryos from a couple carrying HBB mutations were genotyped. Haplotypes of paternal alleles were constructed and investigated in embryos, and the chromosome copy number profiles were simultaneously analyzed. RESULTS The universal MARSALA strategy allows the selection of a euploid embryo free of disease mutations for in uterus transfer and successful pregnancy. A follow-up amniocentesis was performed at 17 weeks of gestation to confirm the PGD/PGS results. CONCLUSION We present the first successful PGD procedure based on genotyping multiple single-sperm cells to obtain SNP linkage information. Our improved PGD/PGS procedure does not require genotyping the proband or relevant family members and therefore can be applicable to a wider population of patients when conducting PGD for monogenic disorders.
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Affiliation(s)
- Haitao Wu
- Reproductive Medicine Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, 529030, China.,Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Xiaoting Shen
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 01238, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Yanhong Zeng
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yumei Gao
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - Lin Shao
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - Baomin Lu
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yiping Zhong
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Benyu Miao
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yanwen Xu
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yali Wang
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yubin Li
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Luoxing Xiong
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Sijia Lu
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 01238, USA.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China
| | - Canquan Zhou
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China.
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30
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Bowman P, Flanagan SE, Hattersley AT. Future Roadmaps for Precision Medicine Applied to Diabetes: Rising to the Challenge of Heterogeneity. J Diabetes Res 2018; 2018:3061620. [PMID: 30599002 PMCID: PMC6288579 DOI: 10.1155/2018/3061620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Precision medicine, the concept that specific treatments can be targeted to groups of individuals with specific genetic, cellular, or molecular features, is a key aspect of modern healthcare, and its use is rapidly expanding. In diabetes, the application of precision medicine has been demonstrated in monogenic disease, where sulphonylureas are used to treat patients with neonatal diabetes due to mutations in ATP-dependent potassium (KATP) channel genes. However, diabetes is highly heterogeneous, both between and within polygenic and monogenic subtypes. Making the correct diagnosis and using the correct treatment from diagnosis can be challenging for clinicians, but it is crucial to prevent long-term morbidity and mortality. To facilitate precision medicine in diabetes, research is needed to develop a better understanding of disease heterogeneity and its impact on potential treatments for specific subtypes. Animal models have been used in diabetes research, but they are not translatable to humans in the majority of cases. Advances in molecular genetics and functional laboratory techniques and availability and sharing of large population data provide exciting opportunities for human studies. This review will map the key elements of future diabetes research in humans and its potential for clinical translation to promote precision medicine in all diabetes subtypes.
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Affiliation(s)
- P. Bowman
- University of Exeter Medical School, Exeter, UK
- Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - A. T. Hattersley
- University of Exeter Medical School, Exeter, UK
- Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits. Am J Hum Genet 2017; 100:865-884. [PMID: 28552196 PMCID: PMC5473732 DOI: 10.1016/j.ajhg.2017.04.014] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/21/2017] [Indexed: 01/05/2023] Open
Abstract
Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. 71% of signals reside within genes and fine mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically relevant discoveries across the frequency spectrum.
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Affiliation(s)
- Ioanna Tachmazidou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Dániel Süveges
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Graham R S Ritchie
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh EH16 4UX, UK; MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Julia Steinberg
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Klaudia Walter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Valentina Iotchkova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | | | - Jie Huang
- Boston VA Research Institute, Boston, MA 02130, USA
| | - Yasin Memari
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Shane McCarthy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrew A Crawford
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Cristina Bombieri
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Massimiliano Cocca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34100, Italy
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Pekka Jousilahti
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Marjolein N Kooijman
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Giovanni Malerba
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Angela Matchan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Sarah J Metrustry
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Nigel W Rayner
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - William R Scott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Lorraine Southam
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; Max Planck Institute for Psycholinguistics, Nijmegen 6500, the Netherlands
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Katerina Trajanoska
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Gialuigi Zaza
- Renal Unit, Department of Medicine, Verona University Hospital, Verona 37126, Italy
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK
| | - María S Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Narinder Bansal
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Marianne Benn
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Zhongsheng Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Petr Danecek
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Wei-Yu Lin
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Alisa K Manning
- Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Harvard University Medical School, Boston, MA 02115, USA
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy; Università degli Studi di Sassari, Sassari 07100, Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy
| | - Anne Tybjaerg-Hansen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Anette Varbo
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | | | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London WC1E 6BT, UK
| | | | - Audrey E Hendricks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - John P Kemp
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK; University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD 4072, Australia
| | - Alireza Moayyeri
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; Institute of Health Informatics, University College London, London NW1 2DA, UK
| | | | - Michal Szpak
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Scott G Wilson
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; School of Medicine and Pharmacology, The University of Western Australia, Crawley, WA 6009, Australia; Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB-CNR), Cagliari 09100, Italy; Università degli Studi di Sassari, Sassari 07100, Italy
| | - Emanuele Di Angelantonio
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Cecilia Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Li Ka Shing Centre for Health Information and Discovery, The Big Data Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Department of Biostatistics, University of Liverpool, Liverpool L69 3GL, UK; Estonian Genome Center, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | | | | | - Paul Burton
- D2K Research Group, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK; Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | - Janine F Felix
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Giovanni Gambaro
- Division of Nephrology and Dialysis, Columbus-Gemelli University Hospital, Catholic University, Rome 00168, Italy
| | - Paolo Gasparini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34100, Italy; Medical Genetics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste 34100, Italy
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Marcus Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Middlesex UB1 3EU, UK; Imperial College Healthcare NHS Trust, London W2 1NY, UK; National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland; Estonian Genome Center, University of Tartu, Tartu, Tartumaa 51010, Estonia; Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan 20132, Italy
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam 3000 CA, the Netherlands
| | | | | | | | - Inês Barroso
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; University of Cambridge Metabolic Research Laboratories, and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada; Department of Oncology, McGill University, Montréal, QC H2W 1S6, Canada
| | - John R B Perry
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK; MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Brian R Walker
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Adam S Butterworth
- Cardiovascular Epidemiology Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicole Soranzo
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Eleftheria Zeggini
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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Pranavchand R, Reddy BM. Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers. J Postgrad Med 2016; 62:188-98. [PMID: 27424552 PMCID: PMC4970347 DOI: 10.4103/0022-3859.186390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Human Genome Project (HGP) has identified millions of single nucleotide polymorphisms (SNPs) and their association with several diseases, apart from successfully characterizing the Mendelian/monogenic diseases. However, the dissection of precise etiology of complex genetic disorders still poses a challenge for human geneticists. This review outlines the landmark results of genome-wide association studies (GWAS) with respect to major complex diseases - Coronary artery disease (CAD), type 2 diabetes mellitus (T2DM), and predominant cancers. A brief account on the current Indian scenario is also given. All the relevant publications till mid-2015 were accessed through web databases such as PubMed and Google. Several databases providing genetic information related to these diseases were tabulated and in particular, the list of the most significant SNPs identified through GWAS was made, which may be useful for designing studies in functional validation. Post-GWAS implications and emerging concepts such as epigenomics and pharmacogenomics were also discussed.
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Affiliation(s)
- R Pranavchand
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Andhra Pradesh, India
| | - B M Reddy
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Andhra Pradesh, India
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Hirota K, Akagawa H, Onda H, Yoneyama T, Kawamata T, Kasuya H. Association of Rare Nonsynonymous Variants in PKD1 and PKD2 with Familial Intracranial Aneurysms in a Japanese Population. J Stroke Cerebrovasc Dis 2016; 25:2900-2906. [DOI: 10.1016/j.jstrokecerebrovasdis.2016.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/18/2016] [Accepted: 08/03/2016] [Indexed: 01/01/2023] Open
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Rivadeneira F, Mäkitie O. Osteoporosis and Bone Mass Disorders: From Gene Pathways to Treatments. Trends Endocrinol Metab 2016; 27:262-281. [PMID: 27079517 DOI: 10.1016/j.tem.2016.03.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 12/28/2022]
Abstract
Genomic technologies have evolved rapidly contributing to the understanding of diseases. Genome-wide association studies (GWAS) and whole-exome sequencing have aided the identification of the genetic determinants of monogenic and complex conditions including osteoporosis and bone mass disorders. Overlap exists between the genes implicated in monogenic and complex forms of bone mass disorders, largely explained by the clustering of genes encoding factors in signaling pathways crucial for mesenchymal cell differentiation, skeletal development, and bone remodeling and metabolism. Numerous of the remaining discovered genes merit functional follow-up studies to elucidate their role in bone biology. The insight provided by genetic studies is serving the identification of biomarkers predictive of disease, redefining disease, response to treatment, and discovery of novel drug targets for skeletal disorders.
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Affiliation(s)
- Fernando Rivadeneira
- Musculoskeletal Genomics, Health and Metabolism, Departments of Internal Medicine and Epidemiology, Erasmus University Medical Center, 3000CA Rotterdam, The Netherlands.
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Molecular Medicine and Surgery, Karolinska Institutet, and Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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Immune and regulatory functions of neutrophils in inflammatory bone loss. Semin Immunol 2016; 28:146-58. [PMID: 26936034 DOI: 10.1016/j.smim.2016.02.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/06/2016] [Accepted: 02/14/2016] [Indexed: 02/06/2023]
Abstract
Although historically viewed as merely anti-microbial effectors in acute infection or injury, neutrophils are now appreciated to be functionally versatile with critical roles also in chronic inflammation. Periodontitis, a chronic inflammatory disease that destroys the tooth-supporting gums and bone, is particularly affected by alterations in neutrophil numbers or function, as revealed by observations in monogenic disorders and relevant mouse models. Besides being a significant debilitating disease and health burden in its own right, periodontitis is thus an attractive model to dissect uncharted neutrophil-associated (patho)physiological pathways. Here, we summarize recent evidence that neutrophils can contribute to inflammatory bone loss not only through the typical bystander injury dogma but intriguingly also through their absence from the affected tissue, where they normally perform important immunomodulatory functions. Moreover, we discuss recent advances in the interactions of neutrophils with the vascular endothelium and - upon extravasation - with bacteria, and how the dysregulation of these interactions leads to inflammatory tissue damage. Overall, neutrophils have both protective and destructive roles in periodontitis, as they are involved in both the maintenance of periodontal tissue homeostasis and the induction of inflammatory bone loss. This highlights the importance of developing approaches that promote or sustain a fine balance between homeostatic immunity and inflammatory pathology.
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Hajishengallis G, Moutsopoulos NM. Role of bacteria in leukocyte adhesion deficiency-associated periodontitis. Microb Pathog 2015; 94:21-6. [PMID: 26375893 DOI: 10.1016/j.micpath.2015.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 12/29/2022]
Abstract
Leukocyte adhesion deficiency Type I (LAD-I)-associated periodontitis is an aggressive form of inflammatory bone loss that has been historically attributed to lack of neutrophil surveillance of the periodontal infection. However, this form of periodontitis has proven unresponsive to antibiotics and/or mechanical removal of the tooth-associated biofilm. Recent studies in LAD-I patients and relevant animal models have shown that the fundamental cause of LAD-I periodontitis involves dysregulation of a granulopoietic cytokine cascade. This cascade includes interleukin IL-23 (IL-23) and IL-17 that drive inflammatory bone loss in LAD-I patients and animal models and, moreover, foster a nutritionally favorable environment for bacterial growth and development of a compositionally unique microbiome. Although the lack of neutrophil surveillance in the periodontal pockets might be expected to lead to uncontrolled bacterial invasion of the underlying connective tissue, microbiological analyses of gingival biopsies from LAD-I patients did not reveal tissue-invasive infection. However, bacterial lipopolysaccharide was shown to translocate into the lesions of LAD-I periodontitis. It is concluded that the bacteria serve as initial triggers for local immunopathology through translocation of bacterial products into the underlying tissues where they unleash the dysregulated IL-23-IL-17 axis. Subsequently, the IL-23/IL-17 inflammatory response sustains and shapes a unique local microbiome which, in turn, can further exacerbate inflammation and bone loss in the susceptible host.
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Affiliation(s)
- George Hajishengallis
- Department of Microbiology, University of Pennsylvania Penn Dental Medicine, Philadelphia, PA 19104, USA.
| | - Niki M Moutsopoulos
- Oral Immunity and Inflammation Unit, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD 20892, USA.
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De Vilder EYG, Hosen MJ, Vanakker OM. The ABCC6 Transporter as a Paradigm for Networking from an Orphan Disease to Complex Disorders. BIOMED RESEARCH INTERNATIONAL 2015; 2015:648569. [PMID: 26356190 PMCID: PMC4555454 DOI: 10.1155/2015/648569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/15/2015] [Accepted: 06/23/2015] [Indexed: 01/16/2023]
Abstract
The knowledge on the genetic etiology of complex disorders largely results from the study of rare monogenic disorders. Often these common and rare diseases show phenotypic overlap, though monogenic diseases generally have a more extreme symptomatology. ABCC6, the gene responsible for pseudoxanthoma elasticum, an autosomal recessive ectopic mineralization disorder, can be considered a paradigm gene with relevance that reaches far beyond this enigmatic orphan disease. Indeed, common traits such as chronic kidney disease or cardiovascular disorders have been linked to the ABCC6 gene. While during the last decade the awareness of the wide ramifications of ABCC6 has increased significantly, the gene itself and the transmembrane transporter it encodes have not unveiled all of the mysteries that surround them. To gain more insights, multiple approaches are being used including next-generation sequencing, computational methods, and various "omics" technologies. Much effort is made to place the vast amount of data that is gathered in an integrated system-biological network; the involvement of ABCC6 in common disorders provides a good view on the wide implications and potential of such a network. In this review, we summarize the network approaches used to study ABCC6 and the role of this gene in several complex diseases.
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Affiliation(s)
- Eva Y. G. De Vilder
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Mohammad Jakir Hosen
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Moutsopoulos NM, Lionakis MS, Hajishengallis G. Inborn errors in immunity: unique natural models to dissect oral immunity. J Dent Res 2015; 94:753-8. [PMID: 25900229 DOI: 10.1177/0022034515583533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In recent years, the study of genetic defects arising from inborn errors in immunity has resulted in the discovery of new genes involved in the function of the immune system and in the elucidation of the roles of known genes whose importance was previously unappreciated. With the recent explosion in the field of genomics and the increasing number of genetic defects identified, the study of naturally occurring mutations has become a powerful tool for gaining mechanistic insight into the functions of the human immune system. In this concise perspective, we discuss emerging evidence that inborn errors in immunity constitute real-life models that are indispensable both for the in-depth understanding of human biology and for obtaining critical insights into common diseases, such as those affecting oral health. In the field of oral mucosal immunity, through the study of patients with select gene disruptions, the interleukin-17 (IL-17) pathway has emerged as a critical element in oral immune surveillance and susceptibility to inflammatory disease, with disruptions in the IL-17 axis now strongly linked to mucosal fungal susceptibility, whereas overactivation of the same pathways is linked to inflammatory periodontitis.
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Affiliation(s)
- N M Moutsopoulos
- Oral Immunity and Inflammation Unit, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - M S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - G Hajishengallis
- Department of Microbiology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
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Crabtree GW, Gogos JA. Synaptic plasticity, neural circuits, and the emerging role of altered short-term information processing in schizophrenia. Front Synaptic Neurosci 2014; 6:28. [PMID: 25505409 PMCID: PMC4243504 DOI: 10.3389/fnsyn.2014.00028] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/22/2014] [Indexed: 01/01/2023] Open
Abstract
Synaptic plasticity alters the strength of information flow between presynaptic and postsynaptic neurons and thus modifies the likelihood that action potentials in a presynaptic neuron will lead to an action potential in a postsynaptic neuron. As such, synaptic plasticity and pathological changes in synaptic plasticity impact the synaptic computation which controls the information flow through the neural microcircuits responsible for the complex information processing necessary to drive adaptive behaviors. As current theories of neuropsychiatric disease suggest that distinct dysfunctions in neural circuit performance may critically underlie the unique symptoms of these diseases, pathological alterations in synaptic plasticity mechanisms may be fundamental to the disease process. Here we consider mechanisms of both short-term and long-term plasticity of synaptic transmission and their possible roles in information processing by neural microcircuits in both health and disease. As paradigms of neuropsychiatric diseases with strongly implicated risk genes, we discuss the findings in schizophrenia and autism and consider the alterations in synaptic plasticity and network function observed in both human studies and genetic mouse models of these diseases. Together these studies have begun to point toward a likely dominant role of short-term synaptic plasticity alterations in schizophrenia while dysfunction in autism spectrum disorders (ASDs) may be due to a combination of both short-term and long-term synaptic plasticity alterations.
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Affiliation(s)
- Gregg W. Crabtree
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia UniversityNew York, NY, USA
| | - Joseph A. Gogos
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia UniversityNew York, NY, USA
- Department of Neuroscience, College of Physicians and Surgeons, Columbia UniversityNew York, NY, USA
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Esplin ED, Oei L, Snyder MP. Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Pharmacogenomics 2014; 15:1771-1790. [PMID: 25493570 DOI: 10.2217/pgs.14.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The potential for personalized sequencing to individually optimize medical treatment in diseases such as cancer and for pharmacogenomic application is just beginning to be realized, and the utility of sequencing healthy individuals for managing health is also being explored. The data produced requires additional advancements in interpretation of variants of unknown significance to maximize clinical benefit. Nevertheless, personalized sequencing, only recently applied to clinical medicine, has already been broadly applied to the discovery and study of disease. It is poised to enable the earlier and more accurate diagnosis of disease risk and occurrence, guide prevention and individualized intervention as well as facilitate monitoring of healthy and treated patients, and play a role in the prevention and recurrence of future disease. This article documents the advancing capacity of personalized sequencing, reviews its impact on disease-oriented scientific discovery and anticipates its role in the future of medicine.
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Affiliation(s)
- Edward D Esplin
- 300 Pasteur Drive, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D. A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources. Drug Discov Today 2013; 19:882-9. [PMID: 24201223 DOI: 10.1016/j.drudis.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/24/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
In the Semantic Enrichment of the Scientific Literature (SESL) project, researchers from academia and from life science and publishing companies collaborated in a pre-competitive way to integrate and share information for type 2 diabetes mellitus (T2DM) in adults. This case study exposes benefits from semantic interoperability after integrating the scientific literature with biomedical data resources, such as UniProt Knowledgebase (UniProtKB) and the Gene Expression Atlas (GXA). We annotated scientific documents in a standardized way, by applying public terminological resources for diseases and proteins, and other text-mining approaches. Eventually, we compared the genetic causes of T2DM across the data resources to demonstrate the benefits from the SESL triple store. Our solution enables publishers to distribute their content with little overhead into remote data infrastructures, such as into any Virtual Knowledge Broker.
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Affiliation(s)
- Dietrich Rebholz-Schuhmann
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Computerlinguistik, Universität Zürich, Binzmühlestrasse 14, 8050 Zürich, Switzerland.
| | - Christoph Grabmüller
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Silvestras Kavaliauskas
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samuel Croset
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Woollard
- GlaxoSmithKline, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Rolf Backofen
- Albert-Ludwigs-University Freiburg, Fahnenbergplatz, D-79085 Freiburg, Germany
| | - Wendy Filsell
- Unilever R&D, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Dominic Clark
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Slim R, Wallace EP. NLRP7 and the Genetics of Hydatidiform Moles: Recent Advances and New Challenges. Front Immunol 2013; 4:242. [PMID: 23970884 PMCID: PMC3747449 DOI: 10.3389/fimmu.2013.00242] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/05/2013] [Indexed: 01/09/2023] Open
Abstract
NOD-like receptor proteins (NLRPs) are emerging key players in several inflammatory pathways in Mammals. The first identified gene coding for a protein from this family is Nlrp5 and was originally called Mater for “Maternal Antigen That Mouse Embryos Require” for normal development beyond the two-cell stage. This important discovery was followed by the identification of other NLRPs playing roles in inflammatory disorders and of the first maternal-effect gene in humans, NLRP7, which is responsible for an aberrant form of human pregnancy called hydatidiform mole (HM). In this review, we recapitulate the various aspects of the pathology of HM, highlight recent advances regarding NLRP7 and its role in HM and related forms of reproductive losses, and expand our discussion to other NLRPs with a special emphasis on those with known roles in mammalian reproduction. Our aim is to facilitate the genetic complexity of recurrent fetal loss in humans and encourage interdisciplinary collaborations in the fields of NLRPs and reproductive loss.
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Affiliation(s)
- Rima Slim
- Department of Human Genetics, McGill University Health Centre , Montreal, QC , Canada ; Department of Obstetrics and Gynecology, McGill University Health Centre , Montreal, QC , Canada
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Cannistraci CV, Ogorevc J, Zorc M, Ravasi T, Dovc P, Kunej T. Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. BMC Med Genomics 2013; 6:5. [PMID: 23410028 PMCID: PMC3626861 DOI: 10.1186/1755-8794-6-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 02/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approach was employed to elucidate genetic factors and molecular pathways underlying testis descent. METHODS Literature mining was performed to collect genomic loci associated with cryptorchidism in seven mammalian species. Information regarding the collected candidate genes was stored in MySQL relational database. Genomic view of the loci was presented using Flash GViewer web tool (http://gmod.org/wiki/Flashgviewer/). DAVID Bioinformatics Resources 6.7 was used for pathway enrichment analysis. Cytoscape plug-in PiNGO 1.11 was employed for protein-network-based prediction of novel candidate genes. Relevant protein-protein interactions were confirmed and visualized using the STRING database (version 9.0). RESULTS The developed cryptorchidism gene atlas includes 217 candidate loci (genes, regions involved in chromosomal mutations, and copy number variations) identified at the genomic, transcriptomic, and proteomic level. Human orthologs of the collected candidate loci were presented using a genomic map viewer. The cryptorchidism gene atlas is freely available online: http://www.integratomics-time.com/cryptorchidism/. Pathway analysis suggested the presence of twelve enriched pathways associated with the list of 179 literature-derived candidate genes. Additionally, a list of 43 network-predicted novel candidate genes was significantly associated with four enriched pathways. Joint pathway analysis of the collected and predicted candidate genes revealed the pivotal importance of the muscle-contraction pathway in cryptorchidism and evidence for genomic associations with cardiomyopathy pathways in RASopathies. CONCLUSIONS The developed gene atlas represents an important resource for the scientific community researching genetics of cryptorchidism. The collected data will further facilitate development of novel genetic markers and could be of interest for functional studies in animals and human. The proposed network-based systems biology approach elucidates molecular mechanisms underlying co-presence of cryptorchidism and cardiomyopathy in RASopathies. Such approach could also aid in molecular explanation of co-presence of diverse and apparently unrelated clinical manifestations in other syndromes.
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Affiliation(s)
- Carlo V Cannistraci
- Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University for Science and Technology, Thuwal, Saudi Arabia.
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Rabbani B, Mahdieh N, Hosomichi K, Nakaoka H, Inoue I. Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders. J Hum Genet 2012; 57:621-32. [DOI: 10.1038/jhg.2012.91] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ochagavía ME, Miranda J, Nazábal M, Martin A, Novoa LI, Bringas R, Fernández-DE-Cossío J, Camacho H. A methodology based on molecular interactions and pathways to find candidate genes associated to diseases: its application to schizophrenia and Alzheimer's disease. J Bioinform Comput Biol 2011; 9:541-57. [PMID: 21776608 DOI: 10.1142/s0219720011005392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/20/2010] [Accepted: 01/21/2011] [Indexed: 12/13/2022]
Abstract
Experimental techniques for the identification of genes associated with diseases are expensive and have certain limitations. In this scenario, computational methods are useful tools to identify lists of promising genes for further experimental verification. This paper describes a flexible methodology for the in silico prediction of genes associated with diseases combining the use of available tools for gene enrichment analysis, gene network generation and gene prioritization. A set of reference genes, with a known association to a disease, is used as bait to extract candidate genes from molecular interaction networks and enriched pathways. In a second step, prioritization methods are applied to evaluate the similarities between previously selected candidates and the set of reference genes. The top genes obtained by these programs are grouped into a single list sorted by the number of methods that have selected each gene. As a proof of concept, top genes reported a few years ago in SzGene and AlzGene databases were used as references to predict genes associated to schizophrenia and Alzheimer's disease, respectively. In both cases, we were able to predict a statistically significant amount of genes belonging to the updated lists.
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Affiliation(s)
- María Elena Ochagavía
- Bioinformatics Department, Center for Genetic Engineering and Biotechnology, Ave. 31 e/ 158 y 190 Havana, P.O. Box 6162, Cuba.
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Carr IM, Diggle CP, Touqan N, Anwar R, Sheridan EG, Bonthron DT, Johnson CA, Ali M, Markham AF. Identification of autosomal recessive disease loci using out-bred nuclear families. Hum Mutat 2011; 33:338-42. [PMID: 22052625 DOI: 10.1002/humu.21645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/18/2011] [Indexed: 11/05/2022]
Abstract
Autozygosity mapping has been a powerful method for the identification of autosomal recessive disease genes. However, the approach is limited by the availability of suitable consanguineous pedigrees. While rare autosomal recessive diseases are overrepresented in consanguineous families, a significant proportion of affected patients nonetheless originate in families where the parents are apparently unrelated. However, due to their relative rarity and the heterogeneity of disease alleles, it has proved difficult to use these patients to identify disease loci. Therefore, we developed "Phaser," a computer application that is able to infer the phase of SNP alleles and so haplotype entire chromosomes in small nuclear families (http://dna.leeds.ac.uk/Phaser). Once the index case's chromosomes have been haplotyped, it is then possible to deduce those of the parents and subsequently identify the parental origin of all the siblings' DNA. By combining information from a small number of nuclear families, it may then be possible to identify linkage to the recessive disease locus, in both in-bred and out-bred families. We have illustrated the program's utility by using it to correctly identify both the cystic fibrosis locus (using two unrelated compound heterozygous CEPH families) and a new gene mutated in early-onset myopathy with respiratory distress and dysphagia locus in a single consanguineous pedigree.
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Affiliation(s)
- Ian M Carr
- School of Medicine, University of Leeds, Leeds, United Kingdom.
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Carr IM, Markham SAF, Pena SDJ. Estimating the degree of identity by descent in consanguineous couples. Hum Mutat 2011; 32:1350-8. [DOI: 10.1002/humu.21584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/26/2011] [Indexed: 11/09/2022]
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Carr IM, Johnson CA, Markham AF, Toomes C, Bonthron DT, Sheridan EG. DominantMapper: rule-based analysis of SNP data for rapid mapping of dominant diseases in related nuclear families. Hum Mutat 2011; 32:1359-66. [PMID: 21905167 DOI: 10.1002/humu.21597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/11/2011] [Indexed: 11/10/2022]
Abstract
With the advent of cheap rapid methods for whole-genome SNP genotyping and the completion of the Human Genome Project, mapping disease loci has become primarily a bioinformatic rather than a laboratory problem. Here, we describe DominantMapper, a computer program that implements a rule-based analysis algorithm for the detection of dominant disease loci in either a small number of nuclear families or a single large nuclear family. To demonstrate its utility, we present the successful analysis of two pedigrees in which the affected individuals carry either APC or TSPAN12 mutations.
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Affiliation(s)
- Ian M Carr
- Leeds Institute of Molecular Medicine, University of Leeds, UK.
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Abstract
Exome sequencing is revolutionizing Mendelian disease gene identification. This results in improved clinical diagnosis, more accurate genotype-phenotype correlations and new insights into the role of rare genomic variation in disease.
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Affiliation(s)
- Christian Gilissen
- Department of Human Genetics, Institute for Genetic and Metabolic Disorders, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
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Kuhlenbäumer G, Hullmann J, Appenzeller S. Novel genomic techniques open new avenues in the analysis of monogenic disorders. Hum Mutat 2011; 32:144-51. [DOI: 10.1002/humu.21400] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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