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Vecchio F, Messina G, Giovenzana A, Petrelli A. New Evidence of Exocrine Pancreatopathy in Pre-symptomatic and Symptomatic Type 1 Diabetes. Curr Diab Rep 2019; 19:92. [PMID: 31471779 DOI: 10.1007/s11892-019-1223-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Type 1 diabetes (T1D) is one of the most frequent chronic autoimmune diseases in humans, characterized by the lack of insulin production resulting in high blood glucose levels and lifelong requirement of exogenous insulin administration for survival. It is now recognized that the autoimmune process begins years before the clinical onset, in a stage called pre-symptomatic T1D, in which the presence of β-cell-specific autoantibodies is detectable. Our aim is to review evidence for T1D as a "whole-pancreas disease," featured by both endocrine and exocrine pancreas alterations already at early disease stages. RECENT FINDINGS In this review, we discuss a series of recent observations indicating that in genetically predisposed individuals, structural and functional abnormalities as well as immune cell infiltration of the exocrine pancreas are already present in the pre-symptomatic stages of the disease. Despite T1D being considered a β-cell-specific disease, numerous reports point to the presence of exocrine pancreas subclinical abnormalities occurring during disease development. These observations challenge the long-standing idea that T1D exocrine damage exists as a mere consequence of disease progression and provide further explanation of mechanisms underlying T1D pathogenesis.
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Affiliation(s)
- Federica Vecchio
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Anna Giovenzana
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alessandra Petrelli
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy.
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Blanter M, Sork H, Tuomela S, Flodström-Tullberg M. Genetic and Environmental Interaction in Type 1 Diabetes: a Relationship Between Genetic Risk Alleles and Molecular Traits of Enterovirus Infection? Curr Diab Rep 2019; 19:82. [PMID: 31401790 PMCID: PMC6689284 DOI: 10.1007/s11892-019-1192-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We provide an overview of the current knowledge regarding the natural history of human type 1 diabetes (T1D) and the documented associations between virus infections (in particular the enteroviruses) and disease development. We review studies that examine whether T1D-specific risk alleles in genes involved in the function of the immune system can alter susceptibility to virus infections or affect the magnitude of the host antiviral response. We also highlight where the major gaps in our knowledge exist and consider possible implications that new insights gained from the discussed gene-environment interaction studies may bring. RECENT FINDINGS A commonality between several of the studied T1D risk variants studied is their role in modulating the host immune response to viral infection. Generally, little support exists indicating that the risk variants increase susceptibility to infection and moreover, they usually appear to predispose the immune system towards a hyper-reactive state, decrease the risk of infection, and/or favor the establishment of viral persistence. In conclusion, although the current number of studies is limited, this type of research can provide important insights into the mechanisms that are central to disease pathogenesis and further describe how genetic and environmental factors jointly influence the risk of T1D development. The latter may provide genetic markers that could be used for patient stratification and for the selection of method(s) for disease prevention.
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Affiliation(s)
- Marfa Blanter
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- 0000 0001 0668 7884grid.5596.fLaboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, EU Belgium
| | - Helena Sork
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soile Tuomela
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Flodström-Tullberg
- 0000 0000 9241 5705grid.24381.3cCenter for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Abstract
Zusammenfassung
Häufige Krankheiten, die sog. Volkskrankheiten, sind in der Regel multifaktoriell verursacht, d. h. zu ihrer Entwicklung tragen sowohl genetische Faktoren als auch nicht-genetische Umgebungseinflüsse bei. Die geschätzte Gesamterblichkeit (‑heritabilität) reicht von moderat bis vergleichsweise hoch. Die genetische Architektur ist komplex und kann das gesamte allelische Spektrum, von häufigen Varianten mit niedriger Penetranz bis hin zu seltenen Varianten mit höherer Penetranz, sowie alle möglichen Kombinationen umfassen. Während häufige Varianten seit mehreren Jahren mit großem Erfolg durch genomweite Assoziationsstudien (GWAS) identifiziert werden, war bisher die Identifizierung seltener Varianten, insbesondere aufgrund der großen Zahl beitragender Gene, nur begrenzt erfolgreich. Dies ändert sich derzeit dank der Anwendung von Hochdurchsatz-Sequenziertechnologien („next-generation sequencing“, NGS) und der daraus resultierenden zunehmenden Verfügbarkeit von exom- und genomweiten Sequenzdaten großer Kollektive. In diesem Artikel geben wir einen Überblick über die Bedeutung seltener Varianten bei häufigen Erkrankungen sowie den aktuellen Stand in Bezug auf deren Identifizierung mittels NGS. Wir betrachten insbesondere die folgenden Fragen: Bei welchen häufigen Krankheiten ist ein Beitrag seltener Varianten zu erwarten, wie können diese Varianten identifiziert werden, und welches Potenzial bieten seltene Varianten für das Verständnis biologischer Prozesse bzw. für die Translation in die klinische Praxis?
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Affiliation(s)
- Kerstin U. Ludwig
- Aff2 0000 0000 8786 803X grid.15090.3d Emmy-Noether-Gruppe „Kraniofaziale Genomik“, Institut für Humangenetik U ni ver si täts kli ni kum Bonn Venusberg-Campus 1, Gebäude 76 53127 Bonn Deutschland
| | - Franziska Degenhardt
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
| | - Markus M. Nöthen
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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105
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Motegi T, Kochi Y, Matsuda K, Kubo M, Yamamoto K, Momozawa Y. Identification of rare coding variants in TYK2 protective for rheumatoid arthritis in the Japanese population and their effects on cytokine signalling. Ann Rheum Dis 2019; 78:1062-1069. [PMID: 31118190 DOI: 10.1136/annrheumdis-2019-215062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/19/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Although genome-wide association studies (GWAS) have identified approximately 100 loci for rheumatoid arthritis (RA), the disease mechanisms are not completely understood. We evaluated the pathogenesis of RA by focusing on rare coding variants. METHODS The coding regions of 98 candidate genes identified by GWAS were sequenced in 2294 patients with RA and 4461 controls in Japan. An association analysis was performed using cases and controls for variants, genes and domains of TYK2. Cytokine responses for two associated variants (R231W, rs201917359; and R703W, rs55882956) in TYK2 as well as a previously reported risk variant (P1004A, rs34536443) for multiple autoimmune diseases were evaluated by reporter assays. RESULTS A variant in TYK2 (R703W) showed a suggestive association (p=5.47×10-8, OR=0.48). We observed more accumulation of rare coding variants in controls in TYK2 (p=3.94×10-12, OR=0.56). The four-point-one, ezrin, radixin, moesin (FERM; 2.14×10-3, OR=0.66) and pseudokinase domains (1.63×10-8, OR=0.52) of TYK2 also showed enrichment of variants in controls. R231W in FERM domain especially reduced interleukin (IL)-6 and interferon (IFN)-γ signalling, whereas P1104A in kinase domain reduced IL-12, IL-23 and IFN-α signalling. R703W in pseudokinase domain reduced cytokine signals similarly to P1104A, but the effects were weaker than those of P1104A. CONCLUSIONS The FERM and pseudokinase domains in TYK2 were associated with the risk of RA in the Japanese population. Variants in TYK2 had different effects on cytokine signalling, suggesting that the regulation of selective cytokine signalling is a target for RA treatment.
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Affiliation(s)
- Tomoki Motegi
- Veterinary Medical Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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106
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Affiliation(s)
- Erika Della Mina
- Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, Institut Imagine, Paris, France
| | - Mathieu P Rodero
- Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, Institut Imagine, Paris, France
| | - Yanick J Crow
- Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, Institut Imagine, Paris, France and Sorbonne-Paris-Cité, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris Descartes University, Paris, France, and Manchester Centre for Genomic Medicine, University of Manchester, Manchester, UK
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107
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Abstract
PURPOSE OF REVIEW Soon after the first genome-wide association study (GWAS) for type 2 diabetes (T2D) was published, it was hypothesized that rare and low-frequency variants might explain a substantial proportion of disease risk. Rare coding variants in particular were emphasized given their large expected role in disease. This review summarizes the extent to which recent T2D genetic studies provide evidence for or against this hypothesis. RECENT FINDINGS Following a comprehensive study of T2D genetic architecture using three sequencing and genotyping technologies, four even larger studies have provided a yet higher resolution view of the role of rare and low-frequency coding variation in T2D susceptibility. Empirical evidence strongly suggests that common regulatory variants are the dominant contributor to T2D heritability. However, rare coding variants may nonetheless be pervasive across T2D-relevant genes. A strategy using common variants to map disease genes, and rare coding variants to link molecular gene perturbations to cellular and phenotypic effects, may be an effective means to investigate T2D pathogenesis and potential new therapies.
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Affiliation(s)
- Jason Flannick
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- Programs in Medical and Population Genetics and Metabolism, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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108
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Qin H, Zhao J, Zhu X. Identifying Rare Variant Associations in Admixed Populations. Sci Rep 2019; 9:5458. [PMID: 30931973 PMCID: PMC6443736 DOI: 10.1038/s41598-019-41845-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 03/12/2019] [Indexed: 12/27/2022] Open
Abstract
An admixed population and its ancestral populations bear different burdens of a complex disease. The ancestral populations may have different haplotypes of deleterious alleles and thus ancestry-gene interaction can influence disease risk in the admixed population. Among admixed individuals, deleterious haplotypes and their ancestries are dependent and can provide non-redundant association information. Herein we propose a local ancestry boosted sum test (LABST) for identifying chromosomal blocks that harbor rare variants but have no ancestry switches. For such a stable ancestral block, our LABST exploits ancestry-gene interaction and the number of rare alleles therein. Under the null of no genetic association, the test statistic asymptotically follows a chi-square distribution with one degree of freedom (1-df). Our LABST properly controlled type I error rates under extensive simulations, suggesting that the asymptotic approximation was accurate for the null distribution of the test statistic. In terms of power for identifying rare variant associations, our LABST uniformly outperformed several famed methods under four important modes of disease genetics over a large range of relative risks. In conclusion, exploiting ancestry-gene interaction can boost statistical power for rare variant association mapping in admixed populations.
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Affiliation(s)
- Huaizhen Qin
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio, 44106, USA.
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109
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Johnson MB, Cerosaletti K, Flanagan SE, Buckner JH. Genetic Mechanisms Highlight Shared Pathways for the Pathogenesis of Polygenic Type 1 Diabetes and Monogenic Autoimmune Diabetes. Curr Diab Rep 2019; 19:20. [PMID: 30888520 PMCID: PMC6424922 DOI: 10.1007/s11892-019-1141-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW To highlight pathways important for the development of autoimmune diabetes by investigating shared mechanisms of disease in polygenic and monogenic diabetes. RECENT FINDINGS Genome-wide association studies have identified 57 genetic risk loci for type 1 diabetes. Progress has been made in unravelling the mechanistic effects of some of these variants, providing key insights into the pathogenesis of type 1 diabetes. Seven monogenic disorders have also been described where diabetes features as part of an autoimmune syndrome. Studying these genes in relation to polygenic risk loci provides a unique opportunity to dissect pathways important for the development of immune-mediated diabetes. Monogenic autoimmune diabetes can result from the dysregulation of multiple pathways suggesting that small effects on many immune processes are required to drive the autoimmune attack on pancreatic beta cells in polygenic type 1 diabetes. A breakdown in central and peripheral immune tolerance is a common theme in the genetic mechanisms of both monogenic and polygenic disease which highlights the importance of these checkpoints in the development and treatment of islet autoimmunity.
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Affiliation(s)
- Matthew B. Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA USA
| | - Sarah E. Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jane H. Buckner
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA USA
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110
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Qin H, Niu T, Zhao J. Identifying Multi-Omics Causers and Causal Pathways for Complex Traits. Front Genet 2019; 10:110. [PMID: 30847004 PMCID: PMC6393387 DOI: 10.3389/fgene.2019.00110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
The central dogma of molecular biology delineates a unidirectional causal flow, i.e., DNA → RNA → protein → trait. Genome-wide association studies, next-generation sequencing association studies, and their meta-analyses have successfully identified ~12,000 susceptibility genetic variants that are associated with a broad array of human physiological traits. However, such conventional association studies ignore the mediate causers (i.e., RNA, protein) and the unidirectional causal pathway. Such studies may not be ideally powerful; and the genetic variants identified may not necessarily be genuine causal variants. In this article, we model the central dogma by a mediate causal model and analytically prove that the more remote an omics level is from a physiological trait, the smaller the magnitude of their correlation is. Under both random and extreme sampling schemes, we numerically demonstrate that the proteome-trait correlation test is more powerful than the transcriptome-trait correlation test, which in turn is more powerful than the genotype-trait association test. In conclusion, integrating RNA and protein expressions with DNA data and causal inference are necessary to gain a full understanding of how genetic causal variants contribute to phenotype variations.
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Affiliation(s)
- Huaizhen Qin
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, United States
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, United States
| | - Tianhua Niu
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University School Medicine, New Orleans, LA, United States
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, United States
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111
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ONAN D, YORULMAZ A, EZGÜ FS, HAYRAN KM, KÜLCÜ S, ARTÜZ RF, YALÇIN B. The role of IFIH1 gene rs1990760 and rs2111485 single-nucleotide polymorphisms in generalized vitiligo predisposition. Turk J Med Sci 2019; 49:206-211. [PMID: 30761886 PMCID: PMC7350844 DOI: 10.3906/sag-1808-63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background/aim Interferon-induced helicase (IFIH1) is a gene locus that has been recently defined as a candidate for susceptibility to generalized vitiligo (GV). The objectives of this study were to assess the association of IFIH1 gene, rs2111485, and rs1990760 single-nucleotide polymorphisms (SNP) with susceptibility to GV and the autoimmune diseases accompanying GV. Materials and methods We prospectively studied GV patients and frequency-matched healthy controls by age and sex. The genotypes of the participants were determined for rs1990760 and rs2111485 SNPs of IFIH1. Dominant, recessive, and additive models were evaluated for each SNP adjusted for age and sex. Results The patients and their controls were observed to be in the Hardy–Weinberg equilibrium for SNP1 (2q24.2, rs1990760, IFIH1, T/C) and SNP2 (2q24.2, rs2111485, IFIH1, G/A), respectively (all P > 0.7). For SNP1, every T allel addition was significantly associated with 1.53 times protectiveness in terms of vitiligo risk (P = 0.033). As for SNP2, every G allel addition was associated with 1.42 times protectiveness, close to statistical significance (P = 0.100). Conclusions: We detected that for SNP1, each T allel and for SNP2, each G allel are protective in terms of vitiligo development. Hereby, we confirmed that IFIH1 gene locus has a role in GV susceptibility.
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Affiliation(s)
- Duru ONAN
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
- * To whom correspondence should be addressed. E-mail:
| | - Ahu YORULMAZ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Fatih Süheyl EZGÜ
- Department of Pediatric Genetics, Faculty of Medicine, Gazi University, AnkaraTurkey
| | - Kadir Mutlu HAYRAN
- Department of Preventive Oncology, Cancer Institute, Hacettepe University, AnkaraTurkey
| | - Seray KÜLCÜ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Refika Ferda ARTÜZ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Başak YALÇIN
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
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112
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Guo Y, Zhou Y. A modified association test for rare and common variants based on affected sib-pair design. J Theor Biol 2019; 467:1-6. [PMID: 30707975 DOI: 10.1016/j.jtbi.2019.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/08/2019] [Indexed: 11/18/2022]
Abstract
Current genome-wide association analysis has identified a great number of rare and common variants associated with common complex traits, however, more effective approaches for detecting associations between rare and common variants with common diseases are still demanded. Approaches for detecting rare variant association analysis will compromise the power when detecting the effects of rare and common variants simultaneously. In this paper, we extend an existing method of testing for rare variant association based on affected sib pairs (TOW-sib) and propose a variable weight test for rare and common variants association based on affected sib pairs (abbreviated as VW-TOWsib). The VW-TOWsib can be used to achieve the purpose of detecting the association of rare and common variants with complex diseases. Simulation results in various scenarios show that our proposed method is more powerful than existing methods for detecting effects of rare and common variants. At the same time, the VW-TOWsib also performs well as a method for rare variant association analysis.
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Affiliation(s)
- Yixing Guo
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University and Heilongjiang Provincial Key Laboratory of the Theory and Computation of Complex Systems, Harbin 150080, China
| | - Ying Zhou
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University and Heilongjiang Provincial Key Laboratory of the Theory and Computation of Complex Systems, Harbin 150080, China.
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113
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Fan X, Jin T. Structures of RIG-I-Like Receptors and Insights into Viral RNA Sensing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:157-188. [DOI: 10.1007/978-981-13-9367-9_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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114
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Khan S, Godfrey V, Zaki MH. Cytosolic Nucleic Acid Sensors in Inflammatory and Autoimmune Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 344:215-253. [PMID: 30798989 DOI: 10.1016/bs.ircmb.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Innate immunity employs germline-encoded pattern recognition receptors (PRRs) to sense microbial pattern molecules. Recognition of pathogen-associated molecular patterns (PAMPs) by various PPRs located on the cell membrane or in the cytosol leads to the activation of cell signaling pathways and production of inflammatory mediators. Nucleic acids including DNA, RNA, and their derivatives are potent PAMPs which can be recognized by multiple PRRs to induce inflammatory responses. While nucleic acid sensors can also sense endogenous nucleic acids, they are capable of discriminating self from non-self. However, defects in nucleic acid sensing PRRs or dysregulation of nucleic acid sensing signaling pathways may cause excessive activation of the immune system resulting in the development of inflammatory and autoimmune diseases. This review will discuss the major pathways for sensing intracellular nucleic acids and how defects in these nucleic acid sensing are associated with different kinds of autoimmune and inflammatory disorders.
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Affiliation(s)
- Shahanshah Khan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Victoria Godfrey
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Md Hasan Zaki
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States.
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115
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Burg AR, Tse HM. Redox-Sensitive Innate Immune Pathways During Macrophage Activation in Type 1 Diabetes. Antioxid Redox Signal 2018; 29:1373-1398. [PMID: 29037052 PMCID: PMC6166692 DOI: 10.1089/ars.2017.7243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SIGNIFICANCE Type 1 diabetes (T1D) is an autoimmune disease resulting in β-cell destruction mediated by islet-infiltrating leukocytes. The role of oxidative stress in human and murine models of T1D is highly significant as these noxious molecules contribute to diabetic complications and β-cell lysis, but their direct impact on dysregulated autoimmune responses is highly understudied. Pro-inflammatory macrophages play a vital role in the initiation and effector phases of T1D by producing free radicals and pro-inflammatory cytokines to facilitate β-cell destruction and to present antigen to autoreactive T cells. Recent Advances: Redox modulation of macrophage functions may play critical roles in autoimmunity. These include enhancing pro-inflammatory innate immune signaling pathways in response to environmental triggers, enforcing an M1 macrophage differentiation program, controlling antigen processing, and altering peptide recognition by oxidative post-translational modification. Therefore, an oxidative environment may act on multiple macrophage functions to orchestrate T1D pathogenesis. CRITICAL ISSUES Mechanisms involved in the initiation of T1D remain unclear, making preventive and early therapeutics difficult to develop. Although many of these advances in the redox regulation of macrophages are in their infancy, they provide insight into how oxidative stress aids in the precipitating event of autoimmune activation. FUTURE DIRECTIONS Future studies should be aimed at mechanistically determining which redox-regulated macrophage functions are pertinent in T1D pathogenesis, as well as at investigating potential targetable therapeutics to halt and/or dampen innate immune activation in T1D.
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Affiliation(s)
- Ashley R Burg
- Department of Microbiology, Comprehensive Diabetes Center, University of Alabama at Birmingham , Birmingham, Alabama
| | - Hubert M Tse
- Department of Microbiology, Comprehensive Diabetes Center, University of Alabama at Birmingham , Birmingham, Alabama
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116
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Abstract
Genome-wide association studies (GWASs) have identified thousands of loci associated with hundreds of complex diseases and traits, and progress is being made toward elucidating the causal variants and genes underlying these associations. Functional characterization of mechanisms at GWAS loci is a multi-faceted challenge. Challenges include linkage disequilibrium and allelic heterogeneity at each locus, the noncoding nature of most loci, and the time and cost needed for experimentally evaluating the potential mechanistic contributions of genes and variants. As GWAS sample sizes increase, more loci are identified, and the complexities of individual loci emerge. Loci can consist of multiple association signals, each of which can reflect the influence of multiple variants, inseparable by association analyses. Each signal within a locus can influence the same or different target genes. Experimental studies of genes and variants can differ on the basis of cell type, cellular environment, or other context-specific variables. In this review, we describe the complexity of mechanisms at GWAS loci-including multiple signals, multiple variants, and/or multiple genes-and the implications these complexities hold for experimental study design and interpretation of GWAS mechanisms.
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Affiliation(s)
- Maren E Cannon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Matz KM, Guzman RM, Goodman AG. The Role of Nucleic Acid Sensing in Controlling Microbial and Autoimmune Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 345:35-136. [PMID: 30904196 DOI: 10.1016/bs.ircmb.2018.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Innate immunity, the first line of defense against invading pathogens, is an ancient form of host defense found in all animals, from sponges to humans. During infection, innate immune receptors recognize conserved molecular patterns, such as microbial surface molecules, metabolites produces during infection, or nucleic acids of the microbe's genome. When initiated, the innate immune response activates a host defense program that leads to the synthesis proteins capable of pathogen killing. In mammals, the induction of cytokines during the innate immune response leads to the recruitment of professional immune cells to the site of infection, leading to an adaptive immune response. While a fully functional innate immune response is crucial for a proper host response and curbing microbial infection, if the innate immune response is dysfunctional and is activated in the absence of infection, autoinflammation and autoimmune disorders can develop. Therefore, it follows that the innate immune response must be tightly controlled to avoid an autoimmune response from host-derived molecules, yet still unencumbered to respond to infection. In this review, we will focus on the innate immune response activated from cytosolic nucleic acids, derived from the microbe or host itself. We will depict how viruses and bacteria activate these nucleic acid sensing pathways and their mechanisms to inhibit the pathways. We will also describe the autoinflammatory and autoimmune disorders that develop when these pathways are hyperactive. Finally, we will discuss gaps in knowledge with regard to innate immune response failure and identify where further research is needed.
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Affiliation(s)
- Keesha M Matz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - R Marena Guzman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Alan G Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.
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Vecchio F, Lo Buono N, Stabilini A, Nigi L, Dufort MJ, Geyer S, Rancoita PM, Cugnata F, Mandelli A, Valle A, Leete P, Mancarella F, Linsley PS, Krogvold L, Herold KC, Elding Larsson H, Richardson SJ, Morgan NG, Dahl-Jørgensen K, Sebastiani G, Dotta F, Bosi E, Battaglia M. Abnormal neutrophil signature in the blood and pancreas of presymptomatic and symptomatic type 1 diabetes. JCI Insight 2018; 3:122146. [PMID: 30232284 DOI: 10.1172/jci.insight.122146] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Neutrophils and their inflammatory mediators are key pathogenic components in multiple autoimmune diseases, while their role in human type 1 diabetes (T1D), a disease that progresses sequentially through identifiable stages prior to the clinical onset, is not well understood. We previously reported that the number of circulating neutrophils is reduced in patients with T1D and in presymptomatic at-risk subjects. The aim of the present work was to identify possible changes in circulating and pancreas-residing neutrophils throughout the disease course to better elucidate neutrophil involvement in human T1D. METHODS Data collected from 389 subjects at risk of developing T1D, and enrolled in 4 distinct studies performed by TrialNet, were analyzed with comprehensive statistical approaches to determine whether the number of circulating neutrophils correlates with pancreas function. To obtain a broad analysis of pancreas-infiltrating neutrophils throughout all disease stages, pancreas sections collected worldwide from 4 different cohorts (i.e., nPOD, DiViD, Siena, and Exeter) were analyzed by immunohistochemistry and immunofluorescence. Finally, circulating neutrophils were purified from unrelated nondiabetic subjects and donors at various T1D stages and their transcriptomic signature was determined by RNA sequencing. RESULTS Here, we show that the decline in β cell function is greatest in individuals with the lowest peripheral neutrophil numbers. Neutrophils infiltrate the pancreas prior to the onset of symptoms and they continue to do so as the disease progresses. Of interest, a fraction of these pancreas-infiltrating neutrophils also extrudes neutrophil extracellular traps (NETs), suggesting a tissue-specific pathogenic role. Whole-transcriptome analysis of purified blood neutrophils revealed a unique molecular signature that is distinguished by an overabundance of IFN-associated genes; despite being healthy, said signature is already present in T1D-autoantibody-negative at-risk subjects. CONCLUSIONS These results reveal an unexpected abnormality in neutrophil disposition both in the circulation and in the pancreas of presymptomatic and symptomatic T1D subjects, implying that targeting neutrophils might represent a previously unrecognized therapeutic modality. FUNDING Juvenile Diabetes Research Foundation (JDRF), NIH, Diabetes UK.
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Affiliation(s)
- Federica Vecchio
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Lo Buono
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angela Stabilini
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Nigi
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute, Seattle, Washington, USA
| | - Susan Geyer
- University of South Florida, TNCC, Tampa, Florida, USA
| | - Paola Maria Rancoita
- Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Mandelli
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Valle
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pia Leete
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Francesca Mancarella
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Peter S Linsley
- Systems Immunology Division, Benaroya Research Institute, Seattle, Washington, USA
| | - Lars Krogvold
- Pediatric Department, Oslo University Hospital HF, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kevan C Herold
- Departments of Immunobiology and Internal Medicine, Yale University, New Haven, Connecticut, USA
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital SUS, Malmo, Sweden
| | - Sarah J Richardson
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Noel G Morgan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Knut Dahl-Jørgensen
- Pediatric Department, Oslo University Hospital HF, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Emanuele Bosi
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy, and the Department of Internal Medicine, IRCCS San Raffaele Hospital, Milan, Italy.,TrialNet Clinical Center, IRCCS San Raffaele Hospital, Milan, Italy
| | | | | | - Manuela Battaglia
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy.,TrialNet Clinical Center, IRCCS San Raffaele Hospital, Milan, Italy
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Dias Junior AG, Sampaio NG, Rehwinkel J. A Balancing Act: MDA5 in Antiviral Immunity and Autoinflammation. Trends Microbiol 2018; 27:75-85. [PMID: 30201512 PMCID: PMC6319154 DOI: 10.1016/j.tim.2018.08.007] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/28/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Induction of interferons during viral infection is mediated by cellular proteins that recognise viral nucleic acids. MDA5 is one such sensor of virus presence and is activated by RNA. MDA5 is required for immunity against several classes of viruses, including picornaviruses. Recent work showed that mutations in the IFIH1 gene, encoding MDA5, lead to interferon-driven autoinflammatory diseases. Together with observations made in cancer cells, this suggests that MDA5 detects cellular RNAs in addition to viral RNAs. It is therefore important to understand the properties of the RNAs which activate MDA5. New data indicate that RNA length and secondary structure are features sensed by MDA5. We review these developments and discuss how MDA5 strikes a balance between antiviral immunity and autoinflammation. MDA5 is a pattern-recognition receptor for RNA and induces a type I interferon response. MDA5 is activated in a variety of clinically relevant settings. This includes infection with ssRNA, dsRNA, and dsDNA viruses; several autoimmune and autoinflammatory diseases, such as type 1 diabetes and Aicardi–Goutières syndrome; and some forms of cancer treatment. Synthetic, viral, and cellular RNAs can all activate MDA5. The latter may include transcripts from endogenous retroelements such as Alu repeats. Length and secondary structure are important features that determine whether an RNA molecule is detected by MDA5. Indeed, long, base-paired RNA molecules potently activate MDA5 in the test tube.
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Affiliation(s)
- Antonio Gregorio Dias Junior
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK. https://twitter.com/GregorioDias1
| | - Natalia G Sampaio
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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120
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Luce S, Guinoiseau S, Gadault A, Letourneur F, Blondeau B, Nitschke P, Pasmant E, Vidaud M, Lemonnier F, Boitard C. Humanized Mouse Model to Study Type 1 Diabetes. Diabetes 2018; 67:1816-1829. [PMID: 29967002 DOI: 10.2337/db18-0202] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
Key requirements in type 1 diabetes (T1D) are in setting up new assays as diagnostic biomarkers that will apply to prediabetes, likely T-cell assays, and in designing antigen-specific therapies to prevent T1D development. New preclinical models of T1D will be required to help with advancing both aims. By crossing mouse strains that lack either murine MHC class I and class II genes and insulin genes, we developed YES mice that instead express human HLA-A*02:01, HLA-DQ8, and insulin genes as transgenes. The metabolic and immune phenotype of YES mice is basically identical to that of the parental strains. YES mice remain insulitis and diabetes free up to 1 year of follow-up, maintain normoglycemia to an intraperitoneal glucose challenge in the long-term range, have a normal β-cell mass, and show normal immune responses to conventional antigens. This new model has been designed to evaluate adaptive immune responses to human insulin on a genetic background that recapitulates a human high-susceptibility HLA-DQ8 genetic background. Although insulitis free, YES mice develop T1D when challenged with polyinosinic-polycytidylic acid. They allow the characterization of preproinsulin epitopes recognized by CD8+ and CD4+ T cells upon immunization against human preproinsulin or during diabetes development.
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MESH Headings
- Adaptive Immunity/drug effects
- Aging
- Animals
- Autoimmune Diseases/immunology
- Autoimmune Diseases/metabolism
- Autoimmune Diseases/pathology
- Autoimmune Diseases/physiopathology
- Biomarkers/blood
- Biomarkers/metabolism
- Crosses, Genetic
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 1/physiopathology
- Disease Models, Animal
- Disease Progression
- Female
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/metabolism
- HLA-DQ Antigens/blood
- HLA-DQ Antigens/genetics
- HLA-DQ Antigens/metabolism
- Humans
- Insulin/blood
- Insulin/genetics
- Insulin/metabolism
- Islets of Langerhans/immunology
- Islets of Langerhans/metabolism
- Islets of Langerhans/pathology
- Islets of Langerhans/physiopathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Mice, Transgenic
- Poly I-C/toxicity
- Prediabetic State/immunology
- Prediabetic State/metabolism
- Prediabetic State/pathology
- Prediabetic State/physiopathology
- Protein Precursors/blood
- Protein Precursors/genetics
- Protein Precursors/metabolism
- Specific Pathogen-Free Organisms
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Affiliation(s)
- Sandrine Luce
- INSERM U1016, Institut Cochin, Paris, France
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
| | - Sophie Guinoiseau
- INSERM U1016, Institut Cochin, Paris, France
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
| | - Alexis Gadault
- INSERM U1016, Institut Cochin, Paris, France
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
| | | | | | - Patrick Nitschke
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
| | - Eric Pasmant
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
- Service de Biochimie et Génétique Moléculaire, Hôpital COCHIN, Paris, France
| | - Michel Vidaud
- Service de Biochimie et Génétique Moléculaire, Hôpital COCHIN, Paris, France
| | - François Lemonnier
- INSERM U1016, Institut Cochin, Paris, France
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
| | - Christian Boitard
- INSERM U1016, Institut Cochin, Paris, France
- Faculté de Médecine René Descartes, Université Paris Descartes, Paris, France
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121
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Gregson CL, Newell F, Leo PJ, Clark GR, Paternoster L, Marshall M, Forgetta V, Morris JA, Ge B, Bao X, Duncan Bassett JH, Williams GR, Youlten SE, Croucher PI, Davey Smith G, Evans DM, Kemp JP, Brown MA, Tobias JH, Duncan EL. Genome-wide association study of extreme high bone mass: Contribution of common genetic variation to extreme BMD phenotypes and potential novel BMD-associated genes. Bone 2018; 114:62-71. [PMID: 29883787 PMCID: PMC6086337 DOI: 10.1016/j.bone.2018.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/13/2018] [Accepted: 06/02/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND Generalised high bone mass (HBM), associated with features of a mild skeletal dysplasia, has a prevalence of 0.18% in a UK DXA-scanned adult population. We hypothesized that the genetic component of extreme HBM includes contributions from common variants of small effect and rarer variants of large effect, both enriched in an extreme phenotype cohort. METHODS We performed a genome-wide association study (GWAS) of adults with either extreme high or low BMD. Adults included individuals with unexplained extreme HBM (n = 240) from the UK with BMD Z-scores ≥+3.2, high BMD females from the Anglo-Australasian Osteoporosis Genetics Consortium (AOGC) (n = 1055) with Z-scores +1.5 to +4.0 and low BMD females also part of AOGC (n = 900), with Z-scores -1.5 to -4.0. Following imputation, we tested association between 6,379,332 SNPs and total hip and lumbar spine BMD Z-scores. For potential target genes, we assessed expression in human osteoblasts and murine osteocytes. RESULTS We observed significant enrichment for associations with established BMD-associated loci, particularly those known to regulate endochondral ossification and Wnt signalling, suggesting that part of the genetic contribution to unexplained HBM is polygenic. Further, we identified associations exceeding genome-wide significance between BMD and four loci: two established BMD-associated loci (5q14.3 containing MEF2C and 1p36.12 containing WNT4) and two novel loci: 5p13.3 containing NPR3 (rs9292469; minor allele frequency [MAF] = 0.33%) associated with lumbar spine BMD and 11p15.2 containing SPON1 (rs2697825; MAF = 0.17%) associated with total hip BMD. Mouse models with mutations in either Npr3 or Spon1 have been reported, both have altered skeletal phenotypes, providing in vivo validation that these genes are physiologically important in bone. NRP3 regulates endochondral ossification and skeletal growth, whilst SPON1 modulates TGF-β regulated BMP-driven osteoblast differentiation. Rs9292469 (downstream of NPR3) also showed some evidence for association with forearm BMD in the independent GEFOS sample (n = 32,965). We found Spon1 was highly expressed in murine osteocytes from the tibiae, femora, humeri and calvaria, whereas Npr3 expression was more variable. CONCLUSION We report the most extreme-truncate GWAS of BMD performed to date. Our findings, suggest potentially new anabolic bone regulatory pathways that warrant further study.
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Affiliation(s)
- Celia L Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Felicity Newell
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | - Paul J Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | - Graeme R Clark
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | | | - Mhairi Marshall
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | - Vincenzo Forgetta
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - John A Morris
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada; Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Xiao Bao
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Scott E Youlten
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Peter I Croucher
- The Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales Medicine, Sydney, New South Wales, Australia
| | | | - David M Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - John P Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia
| | - Jon H Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emma L Duncan
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, 37 Kent Street, Woolloongabba 4102, QLD, Australia; Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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Koba R, Shoji S, Yoshimura S, Tohya Y. Molecular characterization and immune responsive expression of feline MDA5 gene. J Vet Med Sci 2018; 80:1266-1270. [PMID: 29973480 PMCID: PMC6115252 DOI: 10.1292/jvms.17-0278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The retinoic acid-inducible gene-I-like receptor (RLR) family is a group of cytosolic RNA
helicase proteins that play an important role in sensing viral RNAs. Melanoma
differentiation-associated gene 5 (MDA5), an RLR protein, recognizes viral double-stranded
RNA and 5’-triphosphate single-stranded RNA in the cytoplasm for the expression of type I
interferon (IFN). The expression of MDA5 is also induced by type I IFN. In the present
study, we determined the complete coding sequence of the feline MDA5 gene, and analyzed
its structure. In addition, we examined tissue expression patterns, inducibilities of the
feline MDA5 by polyinosinic-polycytidylic acid and type I IFN, and a functional role of
feline MDA5 on type I IFN expression.
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Affiliation(s)
- Ryota Koba
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Sakurako Shoji
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Sawami Yoshimura
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Yukinobu Tohya
- Laboratory of Veterinary Microbiology, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
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Enteroviral infections in the pathogenesis of type 1 diabetes: new insights for therapeutic intervention. Curr Opin Pharmacol 2018; 43:11-19. [PMID: 30064099 PMCID: PMC6294842 DOI: 10.1016/j.coph.2018.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/07/2018] [Accepted: 07/16/2018] [Indexed: 12/25/2022]
Abstract
Enteroviral infection has been long-associated with type 1 diabetes in epidemiological studies. β-Cells express a specific enteroviral receptor isoform, CAR-SIV, mainly on secretory granules. β-Cells respond to enteroviruses by allowing the establishment of a persistent infection. Enteroviral vaccines are under development that might be effective in type 1 diabetes.
The development of islet autoimmunity and type 1 diabetes has long been linked with enteroviral infection but a causal relationship has proven hard to establish. This is partly because much of the epidemiological evidence derives from studies of neutralising antibody generation in blood samples while less attention has been paid to the pancreatic beta cell as a site of infection. Nevertheless, recent studies have revealed that beta cells express specific enteroviral receptors and that they can sustain a productive enteroviral infection. Importantly, they can also mount antiviral responses which attenuate viral replication and may favour the establishment of a persistent enteroviral infection. Together, these responses combine to create the Trojan horse by which enteroviruses might precipitate islet autoimmunity.
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124
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Common ground: shared risk factors for type 1 diabetes and celiac disease. Nat Immunol 2018; 19:685-695. [DOI: 10.1038/s41590-018-0130-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/27/2018] [Indexed: 02/07/2023]
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125
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Zhao C, Jia M, Song H, Yu Z, Wang W, Li Q, Zhang L, Zhao W, Cao X. The E3 Ubiquitin Ligase TRIM40 Attenuates Antiviral Immune Responses by Targeting MDA5 and RIG-I. Cell Rep 2018; 21:1613-1623. [PMID: 29117565 DOI: 10.1016/j.celrep.2017.10.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/20/2017] [Accepted: 10/04/2017] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), including melanoma differentiation-associated gene 5 (MDA5) and RIG-I, are crucial for host recognition of non-self RNAs, especially viral RNA. Thus, the expression and activation of RLRs play fundamental roles in eliminating the invading RNA viruses and maintaining immune homeostasis. However, how RLR expression is tightly regulated remains to be further investigated. In this study, we identified a major histocompatibility complex (MHC)-encoded gene, tripartite interaction motif 40 (TRIM40), as a suppressor of RLR signaling by directly targeting MDA5 and RIG-I. TRIM40 binds to MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination via its E3 ligase activity, leading to their proteasomal degradation. TRIM40 deficiency enhances RLR-triggered signaling. Consequently, TRIM40 deficiency greatly enhances antiviral immune responses and decreases viral replication in vivo. Thus, we demonstrate that TRIM40 limits RLR-triggered innate activation, suggesting TRIM40 as a potential therapeutic target for the control of viral infection.
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Affiliation(s)
- Chunyuan Zhao
- Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Mutian Jia
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China
| | - Hui Song
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China
| | - Zhongxia Yu
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China
| | - Wenwen Wang
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China
| | - Qi Li
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China
| | - Lining Zhang
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China
| | - Wei Zhao
- Department of Immunology, School of Basic Medical Science, Shandong University, Jinan, Shandong 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250012, China.
| | - Xuetao Cao
- Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China.
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Loetsch C, Warren J, Laskowski A, Vazquez-Lombardi R, Jandl C, Langley DB, Christ D, Thorburn DR, Ryugo DK, Sprent J, Batten M, King C. Cytosolic Recognition of RNA Drives the Immune Response to Heterologous Erythrocytes. Cell Rep 2018; 21:1624-1638. [PMID: 29117566 DOI: 10.1016/j.celrep.2017.10.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/07/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
The archetypal T cell-dependent antigen is sheep red blood cells (SRBCs), which have defined much of what we know about humoral immunity. Early studies using solubilized or sonicated SRBCs argued that the intact structure of SRBCs was important for optimal antibody responses. However, the reason for the requirement of intact SRBCs for the response to polyvalent protein antigen remained unknown. Here, we report that the immune response to SRBCs is driven by cytosolic recognition of SRBC RNA through the RIG-I-like receptor (RLR)-mitochondrial anti-viral signaling adaptor (MAVS) pathway. Following the uptake of SRBCs by antigen-presenting cells, the MAVS signaling complex governs the differentiation of both T follicular cells and antibody-producing B cells. Importantly, the involvement of the RLR-MAVS pathway precedes that of endosomal Toll-like receptor pathways, yet both are required for optimal effect.
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Affiliation(s)
- Claudia Loetsch
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Joanna Warren
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia
| | - Adrienne Laskowski
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia
| | - Rodrigo Vazquez-Lombardi
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Christoph Jandl
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - David B Langley
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Daniel Christ
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, The Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville VIC 3010, Australia
| | - David K Ryugo
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Jonathan Sprent
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcel Batten
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Cecile King
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Department of Medicine, University of New South Wales, Sydney, NSW 2010, Australia.
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.Robertson CC, Rich SS. Genetics of type 1 diabetes. Curr Opin Genet Dev 2018; 50:7-16. [DOI: 10.1016/j.gde.2018.01.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/20/2018] [Accepted: 01/25/2018] [Indexed: 01/14/2023]
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Amininejad L, Charloteaux B, Theatre E, Liefferinckx C, Dmitrieva J, Hayard P, Muls V, Maisin JM, Schapira M, Ghislain JM, Closset P, Talib M, Abramowicz M, Momozawa Y, Deffontaine V, Crins F, Mni M, Karim L, Cambisano N, Ornemese S, Zucchi A, Minsart C, Deviere J, Hugot JP, De Vos M, Louis E, Vermeire S, Van Gossum A, Coppieters W, Twizere JC, Georges M, Franchimont D. Analysis of Genes Associated With Monogenic Primary Immunodeficiency Identifies Rare Variants in XIAP in Patients With Crohn's Disease. Gastroenterology 2018; 154:2165-2177. [PMID: 29501442 DOI: 10.1053/j.gastro.2018.02.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 02/15/2018] [Accepted: 02/17/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS A few rare monogenic primary immunodeficiencies (PIDs) are characterized by chronic intestinal inflammation that resembles Crohn's disease (CD). We investigated whether 23 genes associated with 10 of these monogenic disorders contain common, low-frequency, or rare variants that increase risk for CD. METHODS Common and low frequency variants in 1 Mb loci centered on the candidate genes were analyzed using meta-data corresponding to genotypes of approximately 17,000 patients with CD or without CD (controls) in Europe. The contribution of rare variants was assessed by high-throughput sequencing of 4750 individuals, including 660 early-onset and/or familial cases among the 2390 patients with CD. Variants were expressed from vectors in SW480 or HeLa cells and functions of their products were analyzed in immunofluorescence, luciferase, immunoprecipitation, and immunoblot assays. RESULTS We reproduced the association of the interleukin 10 locus with CD (P = .007), although none of the significantly associated variants modified the coding sequence of interleukin 10. We found XIAP to be significantly enriched for rare coding mutations in patients with CD vs controls (P = .02). We identified 4 previously unreported missense variants associated with CD. Variants in XIAP cause the PID X-linked lymphoproliferative disease type 2, yet none of the carriers of these variants had all the clinical features of X-linked lymphoproliferative disease type 2. Identified XIAP variants S123N, R233Q, and P257A were associated with an impaired activation of NOD2 signaling after muramyl dipeptide stimulation. CONCLUSIONS In a systematic analysis of variants in 23 PID-associated genes, we confirmed the association of variants in XIAP with CD. Further screenings for CD-associated variants and analyses of their functions could increase our understanding of the relationship between PID-associated genes and CD pathogenesis.
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Affiliation(s)
- Leila Amininejad
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Benoit Charloteaux
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Emilie Theatre
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Claire Liefferinckx
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Julia Dmitrieva
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Pierre Hayard
- Department of Gastroenterology Charleroi University Hospital, Charleroi, Belgium
| | - Vincianne Muls
- Department of Gastroenterology, Saint Pierre Hospital, Brussels, Belgium
| | - Jean-Marc Maisin
- Department of Gastroenterology, Jolimont Hospital, La Louvière, Belgium
| | - Michael Schapira
- Department of Gastroenterology, Jolimont Hospital, La Louvière, Belgium
| | | | - Pierre Closset
- Department of Gastroenterology, Ixelles Hospital, Brussels, Belgium
| | - Mehdi Talib
- Department of Gastroenterology, Brugmann Hospital, Brussels, Belgium
| | - Marc Abramowicz
- Department of Human genetics, Erasme hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yukihide Momozawa
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Valerie Deffontaine
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - François Crins
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Myriam Mni
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Nadine Cambisano
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Sandra Ornemese
- Grappe Interdisciplinaire de Génoprotéomique Appliquée Imaging Platform, University of Liège, Liège, Belgium
| | - Alessandro Zucchi
- Laboratory of Parasitology, Université Libre de Bruxelles, Brussels, Belgium
| | - Charlotte Minsart
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Deviere
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Pierre Hugot
- Institut National de la Santé et de la Recherche Médicale U843, Hôpital Robert Debré, Paris, France
| | - Martine De Vos
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Edouard Louis
- Department of Gastroenterology, Sart Tilman Hospital, University of Liège, Liège, Belgium
| | - Severine Vermeire
- Department of Clinical and Experimental Medecine, Gastroenterology Section, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Andre Van Gossum
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Jean-Claude Twizere
- Laboratory of Protein Signalling and Interactions, Groupe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Denis Franchimont
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
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Sazonovs A, Barrett JC. Rare-Variant Studies to Complement Genome-Wide Association Studies. Annu Rev Genomics Hum Genet 2018; 19:97-112. [PMID: 29801418 DOI: 10.1146/annurev-genom-083117-021641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies (GWASs) have revolutionized human disease genetics by discovering tens of thousands of associations between common variants and complex diseases. In parallel, huge technological advances in DNA sequencing have made it possible to measure and analyze rare variation in populations. This review considers these two stories and how they have come together. We first review the history of GWASs and sequencing. We then consider how to understand the biological mechanisms that drive signals of strong association in the absence of rare-variant studies. We describe how rare-variant studies complement these approaches and highlight both data generation and statistical challenges in their interpretation. Finally, we consider how certain special study designs, such as those for families and isolated populations, fit in this paradigm.
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Affiliation(s)
- A Sazonovs
- Wellcome Sanger Institute, Cambridge CB10 1HH, United Kingdom;
| | - J C Barrett
- Wellcome Sanger Institute, Cambridge CB10 1HH, United Kingdom;
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Emdin CA, Khera AV, Chaffin M, Klarin D, Natarajan P, Aragam K, Haas M, Bick A, Zekavat SM, Nomura A, Ardissino D, Wilson JG, Schunkert H, McPherson R, Watkins H, Elosua R, Bown MJ, Samani NJ, Baber U, Erdmann J, Gupta N, Danesh J, Chasman D, Ridker P, Denny J, Bastarache L, Lichtman JH, D'Onofrio G, Mattera J, Spertus JA, Sheu WHH, Taylor KD, Psaty BM, Rich SS, Post W, Rotter JI, Chen YDI, Krumholz H, Saleheen D, Gabriel S, Kathiresan S. Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease. Nat Commun 2018; 9:1613. [PMID: 29691411 PMCID: PMC5915445 DOI: 10.1038/s41467-018-03911-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/21/2018] [Indexed: 02/02/2023] Open
Abstract
Less than 3% of protein-coding genetic variants are predicted to result in loss of protein function through the introduction of a stop codon, frameshift, or the disruption of an essential splice site; however, such predicted loss-of-function (pLOF) variants provide insight into effector transcript and direction of biological effect. In >400,000 UK Biobank participants, we conduct association analyses of 3759 pLOF variants with six metabolic traits, six cardiometabolic diseases, and twelve additional diseases. We identified 18 new low-frequency or rare (allele frequency < 5%) pLOF variant-phenotype associations. pLOF variants in the gene GPR151 protect against obesity and type 2 diabetes, in the gene IL33 against asthma and allergic disease, and in the gene IFIH1 against hypothyroidism. In the gene PDE3B, pLOF variants associate with elevated height, improved body fat distribution and protection from coronary artery disease. Our findings prioritize genes for which pharmacologic mimics of pLOF variants may lower risk for disease.
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Affiliation(s)
- Connor A Emdin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mark Chaffin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Derek Klarin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Krishna Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mary Haas
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Alexander Bick
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Seyedeh M Zekavat
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Computational Biology & Bioinformatics, Yale Medical School, Yale University, New Haven, MA, 06510, USA
| | - Akihiro Nomura
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, 43121, Italy
- Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, 27100, Italy
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Deutsches Zentrum für Herz-Kreislauf-Forschung, München, 80333, Germany
| | - Ruth McPherson
- University of Ottawa Heart Institute, Ottawa, ON, K1Y4W7, Canada
| | - Hugh Watkins
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, OX1 2JD, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 2JD, UK
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, Hospital del Mar Research Institute, Barcelona, 08003, Spain
- CIBER Enfermedades Cardiovasculares (CIBERCV), Barcelona, 28029, Spain
- Facultat de Medicina, Universitat de Vic-Central de Cataluña, Barcelona, VIC, 08500, Spain
| | - Matthew J Bown
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Leicester Biomedical Research Centre, Leicester, LE1 7RH, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Leicester Biomedical Research Centre, Leicester, LE1 7RH, UK
| | - Usman Baber
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck, 23562, Germany
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - John Danesh
- Department of Public Health and Primary Care, Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB2 0SR, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- National Institute of Health Research Blood and Transplant; Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Daniel Chasman
- Center for Cardiovascular Disease Prevention, Brigham and Women's Hospital, Boston, 02115, USA
| | - Paul Ridker
- Center for Cardiovascular Disease Prevention, Brigham and Women's Hospital, Boston, 02115, USA
| | - Joshua Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Judith H Lichtman
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Gail D'Onofrio
- Department of Emergency Medicine, Yale University, New Haven, CT, 06520, USA
| | - Jennifer Mattera
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, 06510, USA
| | - John A Spertus
- Department of Biomedical & Saint Luke's Mid America Heart Institute and the Health Informatics, Division of Endocrinology and Metabolism, University of Missouri-Kansas City, Kansas City, MO, 64110, USA
| | - Wayne H-H Sheu
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, 40705, Taiwan
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, 98195, WA, USA
- Cardiovascular Health Research Unit, Kaiser Permanente Washington Health Research Institute, 98101, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wendy Post
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Harlan Krumholz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, 06510, USA
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, 74800, Pakistan
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.
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Qaisar N, Jurczyk A, Wang JP. Potential role of type I interferon in the pathogenic process leading to type 1 diabetes. Curr Opin Endocrinol Diabetes Obes 2018; 25:94-100. [PMID: 29369915 PMCID: PMC5836805 DOI: 10.1097/med.0000000000000399] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Understanding the relationship between viral infections and the development of type 1 diabetes (T1D) is essential for T1D prevention. Virus-induced innate immune responses, specifically type I interferon (IFN-I) and the IFN gene signature, orchestrate early events of β-cell dysfunction preceding islet autoimmunity. We summarize recent advances in how IFN-I and the IFN gene signature can drive T1D development. RECENT FINDINGS IFN-I, particularly IFN-α, and the IFN gene signature have been detected in islets and peripheral blood of T1D patients. T1D risk genes in the IFN-I signaling pathway regulate antiviral responses in β cells driven by IFN-I and proinflammatory cytokines. Polymorphisms in these genes may cause chronic dysregulated IFN signaling in islets, characterized by hyperexpression of IFN-I, the IFN gene signature, and major histocompatibility complex class I during viral infection. Islet-cell inflammation mediated by aberrant IFN signaling drives β-cell apoptosis by initiating autoreactivity against β-cell antigens. The profound elevation in IFN-I and the IFN gene signature observed in some forms of T1D are also seen in a novel group of human autoimmune and autoinflammatory diseases called interferonopathies. SUMMARY Despite significant advances, further studies are required to functionally dissect the mechanisms by which excessive IFN-I contributes to the evolution of autoimmunity that destroys β cells.
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Affiliation(s)
- Natasha Qaisar
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Agata Jurczyk
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Corresponding author: Jennifer P. Wang, M.D., Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, Phone: 508-856-8414, Fax: 508-856-6176,
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Cetin AE, Iyidogan P, Hayashi Y, Wallen M, Vijayan K, Tu E, Nguyen M, Oliphant A. Plasmonic Sensor Could Enable Label-Free DNA Sequencing. ACS Sens 2018; 3:561-568. [PMID: 29488377 DOI: 10.1021/acssensors.7b00957] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We demonstrated a proof-of-principle concept of a label-free platform that enables nucleic acid sequencing by binding methodology. The system utilizes gold surfaces having high fidelity plasmonic nanohole arrays which are very sensitive to minute changes of local refractive indices. Our novel surface chemistry approach ensures accurate identification of correct bases at individual positions along a targeted DNA sequence on the gold surface. Binding of the correct base on the gold sensing surface triggers strong spectral variations within the nanohole optical response, which provides a high signal-to-noise ratio and accurate sequence data. Integrating our label-free sequencing platform with a lens-free imaging-based device, we reliably determined targeted DNA sequences by monitoring the changes within the plasmonic diffraction images. Consequently, this new label-free surface chemistry technique, integrated with plasmonic lens-free imaging platform, will enable monitoring multiple biomolecular binding events, which could initiate new avenues for high-throughput nucleic acid sequencing.
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Affiliation(s)
- Arif E. Cetin
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Pinar Iyidogan
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Yuki Hayashi
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Mark Wallen
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Kandaswamy Vijayan
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Eugene Tu
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Michael Nguyen
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
| | - Arnold Oliphant
- Omniome, Inc., 10575 Roselle Street, San Diego, California 92121, United States
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Wu C, Chen X, Shu J, Lee CT. Whole-genome expression analyses of type 2 diabetes in human skin reveal altered immune function and burden of infection. Oncotarget 2018; 8:34601-34609. [PMID: 28427244 PMCID: PMC5470994 DOI: 10.18632/oncotarget.16118] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
Skin disorders are among most common complications associated with type 2 diabetes mellitus (T2DM). Although T2DM patients are known to have increased risk of infections and other T2DM-related skin disorders, their molecular mechanisms are largely unknown. This study aims to identify dysregulated genes and gene networks that are associated with T2DM in human skin. We compared the expression profiles of 56,318 transcribed genes on 74 T2DM cases and 148 gender- age-, and race-matched non-diabetes controls from the Genotype-Tissue Expression (GTEx) database. RNA-Sequencing data indicates that diabetic skin is characterized by increased expression of genes that are related to immune responses (CCL20, CXCL9, CXCL10, CXCL11, CXCL13, and CCL18), JAK/STAT signaling pathway (JAK3, STAT1, and STAT2), tumor necrosis factor superfamily (TNFSF10 and TNFSF15), and infectious disease pathways (OAS1, OAS2, OAS3, and IFIH1). Genes in cell adhesion molecules pathway (NCAM1 and L1CAM) and collagen family (PCOLCE2 and COL9A3) are downregulated, suggesting structural changes in the skin of T2DM. For the first time, to the best of our knowledge, this pioneer analytic study reports comprehensive unbiased gene expression changes and dysregulated pathways in the non-diseased skin of T2DM patients. This comprehensive understanding derived from whole-genome expression profiles could advance our knowledge in determining molecular targets for the prevention and treatment of T2DM-associated skin disorders.
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Affiliation(s)
- Chun Wu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Xiaopan Chen
- Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, P.R. China
| | - Jing Shu
- Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, P.R. China
| | - Chun-Ting Lee
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
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134
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Jermendy Á, Szatmári I, Körner A, Szabó AJ, Tóth-Heyn P, Hermann R. Association between interferon-induced helicase (IFIH1) rs1990760 polymorphism and seasonal variation in the onset of type 1 diabetes mellitus. Pediatr Diabetes 2018; 19:300-304. [PMID: 28929635 DOI: 10.1111/pedi.12569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 07/18/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Infections, mostly of viral origin, may contribute to the seasonal variation in the onset of type 1 diabetes mellitus (T1DM). The rs1990760 (A>G, Ala946Thr) polymorphism (GG genotype) of the interferon induced helicase (IFIH1), a virus recognition receptor, confers a modest protection for T1DM. The aim of our study was to evaluate a possible association between this IFIH1 polymorphism and the seasonal variation in the onset of T1DM. MATERIALS AND METHODS The IFIH1 rs1990760 polymorphism was genotyped in 1055 patients of Central-Eastern European ancestry with T1DM (median age at diagnosis: 8.2 [interquartile range, IQR 4.8-11.8] years). T1DM onset was recorded in monthly intervals. RESULTS The IFIH1 genotype distribution was the following: 436 patients (41.3%) had AA genotype, 483 patients (45.8%) had AG genotype, and 136 patients (12.9%) had GG genotype. Significant seasonal variation in manifestation of T1DM (highest rate in winter and lowest rate in summer period) was observed in the total cohort (n = 1055), irrespective of gender. The disease predisposing AA genotype was more frequently found among new cases with onset in summer vs in those with onset in winter (44.3% vs 37.9%); conversely, the protective GG genotype was less frequent (9.3% vs 12.9%, respectively; P = .0268 for trend). Significant effect of genotype (P = .0418) was found on the seasonal variability of T1DM onset in the total cohort. CONCLUSIONS The IFIH1 rs1990760 polymorphism seems to be associated with the seasonal manifestation of T1DM. Our findings suggest that this virus receptor gene may contribute to T1DM manifestation primarily in the summer period.
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Affiliation(s)
- Ágnes Jermendy
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Ildikó Szatmári
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Anna Körner
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Attila J Szabó
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary.,MTA-SE, Pediatrics and Nephrology Research Group, Budapest, Hungary
| | - Péter Tóth-Heyn
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
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135
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Tarbell KV, Egen JG. Breaking self-tolerance during autoimmunity and cancer immunity: Myeloid cells and type I IFN response regulation. J Leukoc Biol 2018; 103:1117-1129. [PMID: 29393979 DOI: 10.1002/jlb.3mir1017-400r] [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: 10/08/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 02/28/2024] Open
Abstract
The generation and regulation of innate immune signals are key determinants of autoimmune pathogenesis. Emerging evidence suggests that parallel processes operating in the setting of solid tumors can similarly determine the balance between tolerance and immunity and ultimately the effectiveness of the antitumor immune response. In both contexts, self-specific responses start with innate immune cell activation that leads to the initial break in self-tolerance, which can be followed by immune response amplification and maturation through innate-adaptive crosstalk, and finally immune-mediated tissue/tumor destruction that can further potentiate inflammation. Of particular importance for these processes is type I IFN, which is induced in response to endogenous ligands, such as self-nucleic acids, and acts on myeloid cells to promote the expansion of autoreactive or tumor-specific T cells and their influx into the target tissue. Evidence from the study of human disease pathophysiology and genetics and mouse models of disease has revealed an extensive and complex network of negative regulatory pathways that has evolved to restrain type I IFN production and activity. Here, we review the overlapping features of self- and tumor-specific immune responses, including the central role that regulators of the type I IFN response and innate immune cell activation play in maintaining tolerance, and discuss how a better understanding of the pathophysiology of autoimmunity can help to identify new approaches to promote immune-mediated tumor destruction.
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Affiliation(s)
- Kristin V Tarbell
- Department of Oncology, Amgen, Inc., South San Francisco, California, USA
| | - Jackson G Egen
- Department of Oncology, Amgen, Inc., South San Francisco, California, USA
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136
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Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel) 2018; 9:E61. [PMID: 29370075 PMCID: PMC5852557 DOI: 10.3390/genes9020061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
A plethora of genetic association analyses have identified several genetic risk loci. Technological and statistical advancements have now led to the identification of not only common genetic variants, but also low-frequency variants, structural variants, and environmental factors, as well as multi-omics variations that affect the phenotypic variance of complex traits in a population, thus referred to as complex trait architecture. The concept of heritability, or the proportion of phenotypic variance due to genetic inheritance, has been studied for several decades, but its application is mainly in addressing the narrow sense heritability (or additive genetic component) from Genome-Wide Association Studies (GWAS). In this commentary, we reflect on our perspective on the complexity of understanding heritability for human traits in comparison to model organisms, highlighting another round of clues beyond GWAS and an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.
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Affiliation(s)
- Shefali Setia Verma
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marylyn D Ritchie
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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137
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Paschou SA, Papadopoulou-Marketou N, Chrousos GP, Kanaka-Gantenbein C. On type 1 diabetes mellitus pathogenesis. Endocr Connect 2018; 7:R38-R46. [PMID: 29191919 PMCID: PMC5776665 DOI: 10.1530/ec-17-0347] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Abstract
Type 1 diabetes mellitus (T1DM) results from the autoimmune destruction of β cells of the endocrine pancreas. Pathogenesis of T1DM is different from that of type 2 diabetes mellitus, where both insulin resistance and reduced secretion of insulin by the β cells play a synergistic role. We will present genetic, environmental and immunologic factors that destroy β cells of the endocrine pancreas and lead to insulin deficiency. The process of autoimmune destruction takes place in genetically susceptible individuals under the triggering effect of one or more environmental factors and usually progresses over a period of many months to years, during which period patients are asymptomatic and euglycemic, but positive for relevant autoantibodies. Symptomatic hyperglycemia and frank diabetes occur after a long latency period, which reflects the large percentage of β cells that need to be destroyed before overt diabetes become evident.
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Affiliation(s)
- Stavroula A Paschou
- Division of EndocrinologyMetabolism and Diabetes, First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nektaria Papadopoulou-Marketou
- Division of EndocrinologyMetabolism and Diabetes, First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Chrousos
- Division of EndocrinologyMetabolism and Diabetes, First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Christina Kanaka-Gantenbein
- Division of EndocrinologyMetabolism and Diabetes, First Department of Pediatrics, 'Aghia Sophia' Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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138
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Bansal V, Gassenhuber J, Phillips T, Oliveira G, Harbaugh R, Villarasa N, Topol EJ, Seufferlein T, Boehm BO. Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6888 individuals. BMC Med 2017; 15:213. [PMID: 29207974 PMCID: PMC5717832 DOI: 10.1186/s12916-017-0977-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/11/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diagnosis of monogenic as well as atypical forms of diabetes mellitus has important clinical implications for their specific diagnosis, prognosis, and targeted treatment. Single gene mutations that affect beta-cell function represent 1-2% of all cases of diabetes. However, phenotypic heterogeneity and lack of family history of diabetes can limit the diagnosis of monogenic forms of diabetes. Next-generation sequencing technologies provide an excellent opportunity to screen large numbers of individuals with a diagnosis of diabetes for mutations in disease-associated genes. METHODS We utilized a targeted sequencing approach using the Illumina HiSeq to perform a case-control sequencing study of 22 monogenic diabetes genes in 4016 individuals with type 2 diabetes (including 1346 individuals diagnosed before the age of 40 years) and 2872 controls. We analyzed protein-coding variants identified from the sequence data and compared the frequencies of pathogenic variants (protein-truncating variants and missense variants) between the cases and controls. RESULTS A total of 40 individuals with diabetes (1.8% of early onset sub-group and 0.6% of adult onset sub-group) were carriers of known pathogenic missense variants in the GCK, HNF1A, HNF4A, ABCC8, and INS genes. In addition, heterozygous protein truncating mutations were detected in the GCK, HNF1A, and HNF1B genes in seven individuals with diabetes. Rare missense mutations in the GCK gene were significantly over-represented in individuals with diabetes (0.5% carrier frequency) compared to controls (0.035%). One individual with early onset diabetes was homozygous for a rare pathogenic missense variant in the WFS1 gene but did not have the additional phenotypes associated with Wolfram syndrome. CONCLUSION Targeted sequencing of genes linked with monogenic diabetes can identify disease-relevant mutations in individuals diagnosed with type 2 diabetes not suspected of having monogenic forms of the disease. Our data suggests that GCK-MODY frequently masquerades as classical type 2 diabetes. The results confirm that MODY is under-diagnosed, particularly in individuals presenting with early onset diabetes and clinically labeled as type 2 diabetes; thus, sequencing of all monogenic diabetes genes should be routinely considered in such individuals. Genetic information can provide a specific diagnosis, inform disease prognosis and may help to better stratify treatment plans.
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Affiliation(s)
- Vikas Bansal
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | | | - Tierney Phillips
- Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Rebecca Harbaugh
- Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Nikki Villarasa
- Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Eric J Topol
- Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Thomas Seufferlein
- Department of Internal Medicine I, Ulm University Medical Centre, Ulm, Germany
| | - Bernhard O Boehm
- Department of Internal Medicine I, Ulm University Medical Centre, Ulm, Germany. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore. .,Imperial College London, London, UK.
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139
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Pociot F. Type 1 diabetes genome-wide association studies: not to be lost in translation. Clin Transl Immunology 2017; 6:e162. [PMID: 29333267 PMCID: PMC5750451 DOI: 10.1038/cti.2017.51] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic studies have identified >60 loci associated with the risk of developing type 1 diabetes (T1D). The vast majority of these are identified by genome-wide association studies (GWAS) using large case-control cohorts of European ancestry. More than 80% of the heritability of T1D can be explained by GWAS data in this population group. However, with few exceptions, their individual contribution to T1D risk is low and understanding their function in disease biology remains a huge challenge. GWAS on its own does not inform us in detail on disease mechanisms, but the combination of GWAS data with other omics-data is beginning to advance our understanding of T1D etiology and pathogenesis. Current knowledge supports the notion that genetic variation in both pancreatic β cells and in immune cells is central in mediating T1D risk. Advances, perspectives and limitations of GWAS are discussed in this review.
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Affiliation(s)
- Flemming Pociot
- Department of Pediatrics, Herlev and Gentofte Hospital, Herlev, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Steno Diabetes Center Copenhagen, Gentofte, Denmark
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140
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Agrawal PB, Wang R, Li HL, Schmitz-Abe K, Simone-Roach C, Chen J, Shi J, Louie T, Sheng S, Towne MC, Brainson CF, Matthay MA, Kim CF, Bamshad M, Emond MJ, Gerard NP, Kleyman TR, Gerard C. The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated with F508del CFTR Mutations. Am J Respir Cell Mol Biol 2017; 57:711-720. [PMID: 28708422 PMCID: PMC5765421 DOI: 10.1165/rcmb.2017-0166oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) remains the most lethal genetic disease in the Caucasian population. However, there is great variability in clinical phenotypes and survival times, even among patients harboring the same genotype. We identified five patients with CF and a homozygous F508del mutation in the CFTR gene who were in their fifth or sixth decade of life and had shown minimal changes in lung function over a longitudinal period of more than 20 years. Because of the rarity of this long-term nonprogressive phenotype, we hypothesized these individuals may carry rare genetic variants in modifier genes that ameliorate disease severity. Individuals at the extremes of survival time and lung-function trajectory underwent whole-exome sequencing, and the sequencing data were filtered to include rare missense, stopgain, indel, and splicing variants present with a mean allele frequency of <0.2% in general population databases. Epithelial sodium channel (ENaC) mutants were generated via site-directed mutagenesis and expressed for Xenopus oocyte assays. Four of the five individuals carried extremely rare or never reported variants in the SCNN1D and SCNN1B genes of the ENaC. Separately, an independently enriched rare variant in SCNN1D was identified in the Exome Variant Server database associated with a milder pulmonary disease phenotype. Functional analysis using Xenopus oocytes revealed that two of the three variants in δ-ENaC encoded by SCNN1D exhibited hypomorphic channel activity. Our data suggest a potential role for δ-ENaC in controlling sodium reabsorption in the airways, and advance the plausibility of ENaC as a therapeutic target in CF.
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Affiliation(s)
- Pankaj B. Agrawal
- Divisions of Newborn Medicine
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | - Hongmei Lisa Li
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Department of Genetics, and
| | - Klaus Schmitz-Abe
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | | | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Tin Louie
- Biostatistics and Center for Biomedical Statistics
| | | | - Meghan C. Towne
- Genetics and Genomics
- Gene Discovery Core, Manton Center for Orphan Disease Research
| | | | - Michael A. Matthay
- Departments of Medicine and
- Anesthesia, Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California
| | - Carla F. Kim
- Pulmonary and Respiratory Diseases, and
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Department of Genetics, and
| | - Michael Bamshad
- Pediatrics and Genome Sciences, University of Washington, Seattle, Washington
| | | | - Norma P. Gerard
- Pulmonary and Respiratory Diseases, and
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Thomas R. Kleyman
- Departments of Medicine
- Cell Biology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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141
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McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Del Amo J, Gill MJ, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Wolinsky SM, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the Impact of Functional Genetic Variation on HIV-1 Control. J Infect Dis 2017; 216:1063-1069. [PMID: 28968755 PMCID: PMC5853944 DOI: 10.1093/infdis/jix470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.
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Affiliation(s)
- Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Laboratory, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Deepti Gurdasani
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York
| | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Elizabeth H Young
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Julia Del Amo
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M John Gill
- Department of Medicine, University of Calgary, Canada
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, United Kingdom
| | - Paul Kellam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago
| | - Robert Zangerle
- Department of Dermatology and Venereology, Medical University Innsbruck, Austria
| | | | - Martin Fisher
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston
- Howard Hughes Medical Institute, Chevy Chase
| | | | | | - Manjinder S Sandhu
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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142
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Abstract
PURPOSE OF REVIEW In this paper, we review the progress made thus far in research related to the genetics of peripheral arterial disease (PAD) by detailing efforts to date in heritability, linkage analyses, and candidate gene studies. We further summarize more contemporary genome-wide association studies (GWAS) and epigenetic studies of PAD. Finally, we review current challenges and future avenues of advanced research in PAD genetics including whole genome sequencing studies. RECENT FINDINGS Studies have estimated the heritability of PAD to be moderate, though the contribution to this heritability that is independent of traditional cardiovascular risk factors remains unclear. Recent efforts have identified SNPs associated with PAD in GWAS analyses, but these have yet to be replicated in independent studies. Much remains to be discovered in the field of PAD genetics. An improved understanding of the genetic foundation for PAD will allow for earlier diagnosis of disease and a more complete pathophysiological understanding of the mechanisms of the disease leading to novel therapeutic interventions. Future avenues for success will likely arise from very large-scale GWAS, whole genome sequencing, and epigenetic studies involving very well-characterized cohorts.
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Affiliation(s)
- Nathan Belkin
- Division of Vascular and Endovascular Surgery, Hospital of the University of Pennsylvania, 3400 Spruce Street, 4 Maloney, Philadelphia, PA, 19104, USA
| | - Scott M Damrauer
- Division of Vascular and Endovascular Surgery, Hospital of the University of Pennsylvania, 3400 Spruce Street, 4 Maloney, Philadelphia, PA, 19104, USA. .,Department of Surgery, Corporal Michael Crescenz VA Medical Center, 3900 Woodland Ave., Philadelphia, PA, 19104, USA.
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143
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Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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144
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Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease. Nat Genet 2017; 49:1722-1730. [PMID: 29083407 PMCID: PMC5899829 DOI: 10.1038/ng.3978] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Most genome-wide association studies have been conducted in European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we examined protein-coding genetic variants in 47,532 East Asian individuals using an exome array. We identified 255 variants at 41 loci reaching chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After meta-analysis with > 300,000 European samples, we identified an additional 9 novel loci. The same 16 genes were identified by the protein-altering variants in both East Asians and Europeans, likely pointing to the functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population-specific, and that examining genomic data across diverse ancestries may facilitate the identification of functional genes at associated loci.
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145
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Dou J, Sun B, Sim X, Hughes JD, Reilly DF, Tai ES, Liu J, Wang C. Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data. PLoS Genet 2017; 13:e1007021. [PMID: 28961250 PMCID: PMC5636172 DOI: 10.1371/journal.pgen.1007021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022] Open
Abstract
Knowledge of biological relatedness between samples is important for many genetic studies. In large-scale human genetic association studies, the estimated kinship is used to remove cryptic relatedness, control for family structure, and estimate trait heritability. However, estimation of kinship is challenging for sparse sequencing data, such as those from off-target regions in target sequencing studies, where genotypes are largely uncertain or missing. Existing methods often assume accurate genotypes at a large number of markers across the genome. We show that these methods, without accounting for the genotype uncertainty in sparse sequencing data, can yield a strong downward bias in kinship estimation. We develop a computationally efficient method called SEEKIN to estimate kinship for both homogeneous samples and heterogeneous samples with population structure and admixture. Our method models genotype uncertainty and leverages linkage disequilibrium through imputation. We test SEEKIN on a whole exome sequencing dataset (WES) of Singapore Chinese and Malays, which involves substantial population structure and admixture. We show that SEEKIN can accurately estimate kinship coefficient and classify genetic relatedness using off-target sequencing data down sampled to ~0.15X depth. In application to the full WES dataset without down sampling, SEEKIN also outperforms existing methods by properly analyzing shallow off-target data (~0.75X). Using both simulated and real phenotypes, we further illustrate how our method improves estimation of trait heritability for WES studies. Inference of genetic relatedness from molecular markers has broad applications in many areas, including quantitative genetics, forensics, evolution and ecology. Classic estimators, however, are not suitable for low-coverage sequencing data, which have high levels of genotype uncertainty and missing data. We evaluate existing methods and describe a new method for kinship estimation using sparse sequencing data. Our method leverages correlations between neighboring markers and models genotype uncertainty in kinship estimators for both homogeneous populations and admixed populations. We show that our method can accurately estimate kinship coefficient even when the sequencing depth is as low as ~0.15X, while existing methods have strong downward bias. Our method can be applied to estimate kinship using sparse off-target data and thus enables control of family structure and estimation of heritability in target sequencing studies, in which the deeply sequenced target regions are often too small to infer genetic relatedness. Even for whole exome sequencing, we show that our method can improve kinship and heritability estimation by including off-target data, compared to conventional analyses solely based on the target regions.
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Affiliation(s)
- Jinzhuang Dou
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Baoluo Sun
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jason D. Hughes
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States of America
| | - Dermot F. Reilly
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States of America
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianjun Liu
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Chaolong Wang
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- * E-mail:
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146
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Zaki M, Thoenes M, Kawalia A, Nürnberg P, Kaiser R, Heller R, Bolz HJ. Recurrent and Prolonged Infections in a Child with a Homozygous IFIH1 Nonsense Mutation. Front Genet 2017; 8:130. [PMID: 29018476 PMCID: PMC5614965 DOI: 10.3389/fgene.2017.00130] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/04/2017] [Indexed: 01/02/2023] Open
Abstract
In an Egyptian girl born to consanguineous parents, whole-exome sequencing (WES) identified a homozygous mutation in PHGDH, c.1273G>A (p.Val425Met), indicating 3-phosphoglycerate dehydrogenase deficiency. This diagnosis was compatible with the patient's microcephaly, severe psychomotor retardation, seizures and cataracts. However, she additionally suffered from recurrent (at least monthly) episodes of prolonged and severe chest infections requiring hospitalization, suggesting a secondary, predisposing and potentially Mendelian, condition. A local reactivation of an EBV infection in the respiratory tract was detected after a recent chest infection, likely representing an opportunistic infection based on a compromised immune system. Further inspection of WES data revealed a homozygous nonsense mutation, c.2665A>T (p.Lys889∗), in IFIH1, encoding MDA5. MDA5 detects long viral double-stranded RNA that is generated during replication of picorna viruses, and thereby activates the type I interferon signaling pathway. The results of Western blot analysis of protein from cultured fibroblasts of the patient indicates absence of wild type MDA5/IFIH1, compatible with NMD. We propose that, analogous to the severe course of primary influenza infection due to biallelic deficiency of a downstream effector, IRF7, homozygous loss of IFIH1 defines a novel Mendelian immunodeficiency disorder that increases susceptibility to severe viral infections. This is contrasted to heterozygous gain-of-function IFIH1 mutations in autoimmune diseases. Our findings highlight the potential of comprehensive genomic investigations in patients from consanguineous families to identify monogenic predispositions to severe infections.
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Affiliation(s)
- Maha Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research CentreCairo, Egypt
| | - Michaela Thoenes
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of CologneCologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of CologneCologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of CologneCologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Hospital of CologneCologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
| | - Hanno J Bolz
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
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147
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Lu C, MacDougall M. RIG-I-Like Receptor Signaling in Singleton-Merten Syndrome. Front Genet 2017; 8:118. [PMID: 28955379 PMCID: PMC5600918 DOI: 10.3389/fgene.2017.00118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Singleton-Merten syndrome (SMS) is an autosomal dominant, multi-system innate immune disorder characterized by early and severe aortic and valvular calcification, dental and skeletal abnormalities, psoriasis, glaucoma, and other varying clinical findings. Recently we identified a specific gain-of-function mutation in IFIH1, interferon induced with helicase C domain 1, segregated with this disease. SMS disease without hallmark dental anomalies, termed atypical SMS, has recently been reported caused by variants in DDX58, DEXD/H-box helicase 58. IFIH1 and DDX58 encode retinoic acid-inducible gene I (RIG-I)-like receptors family members melanoma differentiation-associated gene 5 and RIG-I, respectively. These cytosolic pattern recognition receptors function in viral RNA detection initiating an innate immune response through independent pathways that promote type I and type III interferon expression and proinflammatory cytokines. In this review, we focus on SMS as an innate immune disorder summarizing clinical features, molecular aspects of the pathogenetic pathway and discussing underlying mechanisms of the disease.
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Affiliation(s)
- Changming Lu
- Institute of Oral Health Research, School of Dentistry, University of Alabama at Birmingham, BirminghamAL, United States
| | - Mary MacDougall
- Faculty of Dentistry, University of British Columbia, VancouverBC, Canada
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148
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Analysis of population-specific pharmacogenomic variants using next-generation sequencing data. Sci Rep 2017; 7:8416. [PMID: 28871186 PMCID: PMC5583360 DOI: 10.1038/s41598-017-08468-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/11/2017] [Indexed: 02/03/2023] Open
Abstract
Functional rare variants in drug-related genes are believed to be highly differentiated between ethnic- or racial populations. However, knowledge of population differentiation (PD) of rare single-nucleotide variants (SNVs), remains widely lacking, with the highest fixation indices, (Fst values), from both rare and common variants annotated to specific genes, having only been marginally used to understand PD at the gene level. In this study, we suggest a new, gene-based PD method, PD of Rare and Common variants (PDRC), for analyzing rare variants, as inspired by Generalized Cochran-Mantel-Haenszel (GCMH) statistics, to identify highly population-differentiated drug response-related genes (“pharmacogenes”). Through simulation studies, we reveal that PDRC adequately summarizes rare and common variants, due to PD, over a specific gene. We also applied the proposed method to a real whole-exome sequencing dataset, consisting of 10,000 datasets, from the Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) initiative, and 3,000 datasets from the Genetics of Type 2 diabetes (Go-T2D) repository. Among the 48 genes annotated with Very Important Pharmacogenetic summaries (VIPgenes), in the PharmGKB database, our PD method successfully identified candidate genes with high PD, including ACE, CYP2B6, DPYD, F5, MTHFR, and SCN5A.
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149
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Wen Y, Burt A, Lu Q. Risk Prediction Modeling on Family-Based Sequencing Data Using a Random Field Method. Genetics 2017; 207:63-73. [PMID: 28679544 PMCID: PMC5586386 DOI: 10.1534/genetics.117.199752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/27/2017] [Indexed: 01/08/2023] Open
Abstract
Family-based design is one of the most popular designs in genetic studies and has many unique features for risk-prediction research. It is robust against genetic heterogeneity, and the relatedness among family members can be informative for predicting an individual's risk for disease with polygenic and shared environmental components of risk. Despite these strengths, family-based designs have been used infrequently in current risk-prediction studies, and their related statistical methods have not been well developed. In this article, we developed a generalized random field (GRF) method for family-based risk-prediction modeling on sequencing data. In GRF, subjects' phenotypes are viewed as stochastic realizations of a random field in a space, and a subject's phenotype is predicted by adjacent subjects, where adjacencies between subjects are determined by their genetic and within-family similarities. Different from existing methods that adjust for familial correlations, the GRF uses this information to form surrogates to further improve prediction accuracy. It also uses within-family information to capture predictors (e.g., rare mutations) that are homogeneous in families. Through simulations, we have demonstrated that the GRF method attained better performance than an existing method by considering additional information from family members and accounting for genetic heterogeneity. We further provided practical recommendations for designing family-based risk prediction studies. Finally, we illustrated the GRF method with an application to a whole-genome exome data set from the Michigan State University Twin Registry study.
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Affiliation(s)
- Yalu Wen
- Institute of Cancer Stem Cell, Dalian Medical University, Liaoning, 116044, China
- Department of Statistics, University of Auckland, 1010, New Zealand
| | - Alexandra Burt
- Department of Psychology, Michigan State University, East Lansing, Michigan 48824
| | - Qing Lu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan 48824
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150
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Jerram ST, Leslie RD. The Genetic Architecture of Type 1 Diabetes. Genes (Basel) 2017; 8:genes8080209. [PMID: 28829396 PMCID: PMC5575672 DOI: 10.3390/genes8080209] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/07/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022] Open
Abstract
Type 1 diabetes (T1D) is classically characterised by the clinical need for insulin, the presence of disease-associated serum autoantibodies, and an onset in childhood. The disease, as with other autoimmune diseases, is due to the interaction of genetic and non-genetic effects, which induce a destructive process damaging insulin-secreting cells. In this review, we focus on the nature of this interaction, and how our understanding of that gene-environment interaction has changed our understanding of the nature of the disease. We discuss the early onset of the disease, the development of distinct immunogenotypes, and the declining heritability with increasing age at diagnosis. Whilst Human Leukocyte Antigens (HLA) have a major role in causing T1D, we note that some of these HLA genes have a protective role, especially in children, whilst other non-HLA genes are also important. In adult-onset T1D, the disease is often not insulin-dependent at diagnosis, and has a dissimilar immunogenotype with reduced genetic predisposition. Finally, we discuss the putative nature of the non-genetic factors and how they might interact with genetic susceptibility, including preliminary studies of the epigenome associated with T1D.
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Affiliation(s)
- Samuel T Jerram
- Bart's and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK.
| | - Richard David Leslie
- Bart's and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK.
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