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Nakazawa-Ueji YE, Valencia-Pacheco G, González-Herrera LJ, Chan-Chalé L, Velasco-Cárdenas RMH, Carreño-Gonzalez MJ, Pérez-Mendoza G, Amaro-Adrián GI, Rodríguez-Dzul EA, Quintal-Ortiz IG, Angulo-Ramírez AV, López-Villanueva RF. Association of the polymorphisms rs179008 ( TLR7), rs2004640 ( IRF5), rs1800795 ( IL-6) and rs2280788 ( CCL5) with systemic lupus erythematosus in women of Mayan ethnicity from Yucatan. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-17. [PMID: 38459707 DOI: 10.1080/15257770.2024.2325438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/24/2024] [Indexed: 03/10/2024]
Abstract
Introduction: IFN-α is the main cytokine in SLE, and single nucleotide polymorphisms (SNP) in different genes could induce it. Aim: To determine the association of rs2004640 (IRF5), rs179008 (TLR7), rs1800795 (IL-6) and rs2280788 (CCL5) with SLE in Mexican women with Mayan ethnicity. Methods: DNA and RNA were isolated from the peripheral blood of 110 patients and 200 healthy control subjects. SNP genotyping and gene expression analysis of IRF5, TLR7, IL-6 and IFN-α were determined by real-time PCR and analyzed with SNP Stat, Stata 10.1 and Graph Pad Prism v5. Results: rs2004640, rs179008, and rs1800795 in both groups were according to Hardy-Weinberg equilibrium. Risk alleles rs179008T and rs2004640T frequencies were higher in controls (p = 0.015 and p = 0.028, respectively), whereas rs179008A frequency was higher in patients (p = 0.015). Allelic combination AGT frequency was higher in patients (p = 0.001). IL-6 rs1800795C > G and CCL5 rs2280788G > C frequencies did not show significant differences (p > 0.05), being rs2280788G (CCL5) monomorphic in controls. SLE patients showed higher TLR7, IRF5, IL6, and IFN-α mRNA levels. IRF5 expression was higher in SLE patients homozygous for rs2004640T (IRF5). Conclusion: This work showed the contribution of TLR7 and IRF5 in SLE pathogenesis in Mayan females from Yucatan.
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Affiliation(s)
- Yumi Elena Nakazawa-Ueji
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
| | | | | | - Laureano Chan-Chalé
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
| | | | | | - Gerardo Pérez-Mendoza
- Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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3
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Mustafa R, Ghanbari M, Karhunen V, Evangelou M, Dehghan A. Phenome-wide association study on miRNA-related sequence variants: the UK Biobank. Hum Genomics 2023; 17:104. [PMID: 37996941 PMCID: PMC10668386 DOI: 10.1186/s40246-023-00553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Genetic variants in the coding region could directly affect the structure and expression levels of genes and proteins. However, the importance of variants in the non-coding region, such as microRNAs (miRNAs), remain to be elucidated. Genetic variants in miRNA-related sequences could affect their biogenesis or functionality and ultimately affect disease risk. Yet, their implications and pleiotropic effects on many clinical conditions remain unknown. METHODS Here, we utilised genotyping and hospital records data in the UK Biobank (N = 423,419) to investigate associations between 346 genetic variants in miRNA-related sequences and a wide range of clinical diagnoses through phenome-wide association studies. Further, we tested whether changes in blood miRNA expression levels could affect disease risk through colocalisation and Mendelian randomisation analysis. RESULTS We identified 122 associations for six variants in the seed region of miRNAs, nine variants in the mature region of miRNAs, and 27 variants in the precursor miRNAs. These included associations with hypertension, dyslipidaemia, immune-related disorders, and others. Nineteen miRNAs were associated with multiple diagnoses, with six of them associated with multiple disease categories. The strongest association was reported between rs4285314 in the precursor of miR-3135b and celiac disease risk (odds ratio (OR) per effect allele increase = 0.37, P = 1.8 × 10-162). Colocalisation and Mendelian randomisation analysis highlighted potential causal role of miR-6891-3p in dyslipidaemia. CONCLUSIONS Our study demonstrates the pleiotropic effect of miRNAs and offers insights to their possible clinical importance.
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Affiliation(s)
- Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ville Karhunen
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- UK Dementia Research Institute, Imperial College London, London, UK.
- MRC Centre for Environment and Health, Imperial College London, London, UK.
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4
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Naito T, Okada Y. HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases. Semin Immunopathol 2021; 44:15-28. [PMID: 34786601 PMCID: PMC8837514 DOI: 10.1007/s00281-021-00901-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.
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Affiliation(s)
- Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan.
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
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5
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Zouali M. DNA methylation signatures of autoimmune diseases in human B lymphocytes. Clin Immunol 2020; 222:108622. [PMID: 33188932 DOI: 10.1016/j.clim.2020.108622] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Accepted: 11/07/2020] [Indexed: 12/15/2022]
Abstract
B lymphocytes play key roles in adaptive and innate immunity. In autoimmune diseases, their participation in disease instigation and/or progression has been demonstrated in both experimental models and clinical trials. Recent epigenetic investigations of human B lymphocyte subsets revealed the importance of DNA methylation in exquisitely regulating the cellular activation and differentiation programs. This review discusses recent advances on the potential of DNA methylation to shape events that impart generation of plasma cells and memory B cells, providing novel insight into homeostatic regulation of the immune system. In parallel, epigenetic profiling of B cells from patients with systemic or organo-specific autoimmune diseases disclosed distinctive differential methylation regions that, in some cases, could stratify patients from controls. Development of tools for editing DNA methylation in the mammalian genome could be useful for future functional studies of epigenetic regulation by offering the possibility to edit locus-specific methylation, with potential translational applications.
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Affiliation(s)
- Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, No. 91, Xueshi Road, North District, Taichung City, Taïwan 404, Taichung, Taiwan.
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Cytokine genes multi-locus analysis reveals synergistic influence on genetic susceptibility in Indian SLE - A multifactor-dimensionality reduction approach. Cytokine 2020; 135:155240. [PMID: 32795905 DOI: 10.1016/j.cyto.2020.155240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/21/2020] [Accepted: 08/04/2020] [Indexed: 01/05/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with unclear etiology. Several loci associated with genetic susceptibility for lupus have been described. However, it lacks reports on cytokine gene-gene interactions among SLE patients from Asian population. Epistasis interaction among single nucleotide polymorphisms (SNPs) of cytokine genes in Indian SLE patients was tested using multifactor-dimensionality reduction (MDR) analysis. A total of fourteen SNPs lacking linkage disequilibrium among different cytokines genes were genotyped in a cohort of 200 SLE patients and 201 healthy individuals as controls of Indian origin. A high degree of synergism among Lymphotoxin-α (LT-α), Interleukin-1β (IL-1β) and Interleukin-10 (IL-10) gene polymorphisms was detected in our SLE patients. Furthermore, by virtue of biological inter-relations among different cytokines, a high strength of interactions was observed among pro-inflammatory (IL-1β, IL-6) and anti-inflammatory (IL-10) cytokine gene SNPs. Also, among studied pro-inflammatory cytokines and chemokines, a strong synergistic effect among Tumor Necrosis Factor-α (TNF-α), LT-α and Monocyte Chemo-attractant Protein-1 (MCP-1) SNPs was occurred. A nature of strong interaction among the candidate cytokine genes may speculate a proactive role in causing genetic susceptibility to the disease in SLE patients with Indian origin.
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7
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Kasai S, Itonaga H, Niino D, Miyoshi H, Kato T, Imanishi D, Fujioka M, Furumoto T, Sato S, Sawayama Y, Taguchi J, Imaizumi Y, Hata T, Yoshida S, Moriuchi Y, Ohshima K, Miyazaki Y. Programmed death 1 ligand (PD-L1) in solid cancers after allogeneic hematopoietic stem cell transplantation: a retrospective analysis by the Nagasaki Transplant Group. Int J Hematol 2020; 112:524-534. [PMID: 32588395 DOI: 10.1007/s12185-020-02926-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Programmed death 1 ligand (PD-L1) is an immunomodulatory molecule expressed by cancer cells, and it has been widely demonstrated to inhibit host antitumor responses. The aim of the present study was to identify clinicopathological features associated with PD-L1 expression in the secondary solid cancers of patients after allogeneic hematopoietic stem cell transplantation. In this database of 530 patients who received allo-HSCT between 1990 and 2017, 15 developed solid cancers with a median interval of 3487 days after transplantation. Three patients had 2 different solid cancers. Eighteen solid cancer cases were identified. A multivariate analysis showed that chronic graft-versus-host disease (GVHD) was associated with an increased risk of solid cancer. The presence of chronic GVHD was observed in 8 out of 18 cases at the diagnosis of secondary malignancies. PD-L1 expression levels in cancers were significantly higher in patients with active chronic GVHD than in those without chronic GVHD (P = 0.020). Five cases of cancer that developed in the involved organs of chronic GVHD showed 30% or higher PD-L1 positivity. The present results revealed distinct PD-L1 expression in the secondary solid cancers of post-transplant patients with chronic GVHD.
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Affiliation(s)
- Sachie Kasai
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hidehiro Itonaga
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4, Sakamoto, Nagasaki city, Nagasaki, Japan.
| | - Daisuke Niino
- Department of Pathology, Sasebo City General Hospital, Sasebo, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Takeharu Kato
- Department of Hematology, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Daisuke Imanishi
- Department of Hematology, Nagasaki Prefecture Gotochuoh Hospital, Goto, Japan
| | - Machiko Fujioka
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Hematology, Nagasaki University Hospital, Nagasaki, Japan
| | - Takafumi Furumoto
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - Shinya Sato
- Department of Hematology, Nagasaki University Hospital, Nagasaki, Japan
| | - Yasushi Sawayama
- Department of Hematology, Nagasaki University Hospital, Nagasaki, Japan
| | - Jun Taguchi
- Department of Hematology, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | | | - Tomoko Hata
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4, Sakamoto, Nagasaki city, Nagasaki, Japan
| | - Shinichiro Yoshida
- Department of Hematology, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | | | - Koichi Ohshima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, 1-12-4, Sakamoto, Nagasaki city, Nagasaki, Japan.,Department of Hematology, Nagasaki University Hospital, Nagasaki, Japan
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8
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Grzegorzewska AE, Frycz BA, Świderska M, Niepolski L, Mostowska A, Jagodziński PP. Calcium-sensing receptor gene (CASR) polymorphisms and CASR transcript level concerning dyslipidemia in hemodialysis patients: a cross-sectional study. BMC Nephrol 2019; 20:436. [PMID: 31775661 PMCID: PMC6882244 DOI: 10.1186/s12882-019-1619-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is scarce data on CASR associations with dyslipidemia. We investigated in hemodialysis (HD) patients whether CASR single nucleotide polymorphisms (SNPs) rs7652589 and rs1801725 have associations with dyslipidemia and show epistatic interactions with SNPs of the energy homeostasis-associated gene (ENHO), retinoid X receptor α gene (RXRA), and liver X receptor α gene (LXRA). METHODS The study included 1208 HD subjects. For diagnosis of dyslipidemia, both K/DOQI criteria and atherogenic index ≥3.8 were used. CASR rs1801725 was genotyped by TaqMan SNP Genotyping Assay, other SNPs - by high-resolution melting curve analysis or polymerase chain reaction-restriction fragment length polymorphism, as appropriate. Relative transcript levels of CASR, ENHO, RXRA, and LXRA were measured in peripheral blood mononuclear cells. The occurrence of dyslipidemic phenotypes concerning tested polymorphisms was compared using models of inheritance. Haplotypes were estimated using the Haploview 4.2 software. Epistatic interactions between tested SNPs were analyzed using the logistic regression and epistasis option in the PLINK software. RESULTS Rs7652589 indicated a greater probability of atherogenic dyslipidemia in the dominant inheritance model (OR 1.4, 95%CI 1.0-2.0, P = 0.026), principally because of increased triglyceride (TG) levels. The rs1801725 variant allele was associated with a decreased probability of dyslipidemia characterized by non-HDL-cholesterol ≥130 mg/dL and TG ≥200 mg/dL (OR 0.6, 0.4-0.9, P = 0.012). There were no epistatic interactions between CASR and RXRA, LXRA, and ENHO regarding dyslipidemia. Both rs7652589 and rs1801725 SNPs were not in linkage disequilibrium (D' = 0.091, r2 = 0.003 for the entire HD group) and their haplotypes did not correlate with dyslipidemia. Relative CASR transcript was lower at a borderline significance level in patients harboring the rs1801725 variant allele compared with homozygotes of the major allele (0.20, 0.06-7.80 vs. 0.43, 0.04-5.06, P = 0.058). CASR transcript correlated positively with RXRA transcript (adjusted P = 0.001), LXRA transcript (adjusted P = 0.0009), ENHO transcript (borderline significance, adjusted P = 0.055), dry body weight (adjusted P = 0.035), and renal replacement therapy duration (adjusted P = 0.013). CONCLUSIONS CASR polymorphisms (rs7652589, rs1801725) are associated with dyslipidemia in HD patients. CASR correlates with RXRA, LXRA, and ENHO at the transcript level. Further investigations may elucidate whether other CASR SNPs contribute to associations shown in this study.
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Affiliation(s)
- Alicja E Grzegorzewska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland.
| | - Bartosz A Frycz
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781, Poznań, Poland
| | - Monika Świderska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland
| | - Leszek Niepolski
- B.Braun Avitum Poland, Dialysis Center, Sienkiewicza 3, 64-300, Nowy Tomyśl, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781, Poznań, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781, Poznań, Poland
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Affiliation(s)
- Tetsuji Sawada
- Department of Rheumatology, Tokyo Medical University Hospital, Tokyo, Japan
| | - Daiki Fujimori
- Department of Rheumatology, Tokyo Medical University Hospital, Tokyo, Japan
| | - Yusuke Yamamoto
- Department of Rheumatology, Tokyo Medical University Hospital, Tokyo, Japan
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10
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11
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Unravelling the Roles of Susceptibility Loci for Autoimmune Diseases in the Post-GWAS Era. Genes (Basel) 2018; 9:genes9080377. [PMID: 30060490 PMCID: PMC6115971 DOI: 10.3390/genes9080377] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022] Open
Abstract
Although genome-wide association studies (GWAS) have identified several hundred loci associated with autoimmune diseases, their mechanistic insights are still poorly understood. The human genome is more complex than single nucleotide polymorphisms (SNPs) that are interrogated by GWAS arrays. Apart from SNPs, it also comprises genetic variations such as insertions-deletions, copy number variations, and somatic mosaicism. Although previous studies suggest that common copy number variations do not play a major role in autoimmune disease risk, it is possible that certain rare genetic variations with large effect sizes are relevant to autoimmunity. In addition, other layers of regulations such as gene-gene interactions, epigenetic-determinants, gene and environmental interactions also contribute to the heritability of autoimmune diseases. This review focuses on discussing why studying these elements may allow us to gain a more comprehensive understanding of the aetiology of complex autoimmune traits.
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12
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Murayama G, Furusawa N, Chiba A, Yamaji K, Tamura N, Miyake S. Enhanced IFN-α production is associated with increased TLR7 retention in the lysosomes of palasmacytoid dendritic cells in systemic lupus erythematosus. Arthritis Res Ther 2017; 19:234. [PMID: 29052537 PMCID: PMC5649081 DOI: 10.1186/s13075-017-1441-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/21/2017] [Indexed: 01/04/2023] Open
Abstract
Background Interferon-α (IFN-α) is increased and plays an important role in the pathogenesis of systemic lupus erythematosus (SLE). Plasmacytoid dendritic cells (pDCs) are the main producer of IFN-α, but their IFN-α producing capacity has been shown to be unchanged or reduced when stimulated with a Toll-like receptor 9 (TLR9) agonist in patients with SLE compared to in healthy individuals. In this study, we investigated the IFN-α-producing capacity of lupus pDCs under different stimulation. Methods pDCs from patients with SLE and healthy controls (HC) were stimulated with TLR9 or TLR7 agonist, and their IFN-α producing capacity was examined by intracellular cytokine staining and flow cytometry. The correlation of IFN-α-producing capacity with serum IFN-α levels and disease activity was assessed. The effect of in vitro IFN-α exposure on IFN-α production by pDCs was examined. Localization of TLR7 in cellular compartments in pDCs was investigated. Results The IFN-α producing capacity of pDCs was reduced after TLR9 stimulation, but increased when stimulated with a TLR7 agonist in SLE compared to in HC. IFN-α production by pDCs upon TLR9 stimulation was reduced and the percentage of IFN-α+pDC was inversely correlated with disease activity and serum IFN-α levels. However, the TLR7 agonist-induced IFN-α producing capacity of lupus pDCs was enhanced and correlated with disease activity and serum IFN-α. Exposure to IFN-α enhanced IFN-α production of TLR7-stimulated pDCs, but reduced that of pDCs activated with a TLR9 agonist. TLR7 localization was increased in late endosome/lysosome compartments in pDCs from SLE patients. Conclusions These findings indicate that enhanced TLR7 responses of lupus pDCs, owing to TLR7 retention in late endosome/lysosome and exposure to IFN-α, are associated with the pathogenesis of SLE. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1441-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goh Murayama
- Department of Immunology, Juntendo University School of Medicine, 2-2-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Nanako Furusawa
- Department of Immunology, Juntendo University School of Medicine, 2-2-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Asako Chiba
- Department of Immunology, Juntendo University School of Medicine, 2-2-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Ken Yamaji
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Naoto Tamura
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Sachiko Miyake
- Department of Immunology, Juntendo University School of Medicine, 2-2-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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13
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017. [PMID: 28449694 DOI: 10.1186/s13059-017-1207-1.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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14
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017; 18:76. [PMID: 28449694 PMCID: PMC5406920 DOI: 10.1186/s13059-017-1207-1] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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15
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Evidence for gene-gene epistatic interactions between susceptibility genes for Mycobacterium avium subsp. paratuberculosis infection in cattle. Livest Sci 2017. [DOI: 10.1016/j.livsci.2016.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder with complex genetic underpinnings. This review attempts to assemble the myriad of genomic findings to build a clearer picture of the pathobiology of SLE to serve as a guide for therapeutics. Over 100 genes are now known for SLE, and several more penetrant ones have led to the emergence of more defined lupus phenotypes. Also discussed here are the targeted therapies that have come up on the horizon and the specific biologic mechanisms of more traditional therapies which have only recently been explored. The diagnostic toolbox has been enhanced by the addition of new antibodies, gene expression signatures, and mutation panels. This provides an opportunity to piece together the lupus puzzle and even revisit the clinical classification of SLE.
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17
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Zamani MR, Aslani S, Salmaninejad A, Javan MR, Rezaei N. PD-1/PD-L and autoimmunity: A growing relationship. Cell Immunol 2016; 310:27-41. [PMID: 27660198 DOI: 10.1016/j.cellimm.2016.09.009] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022]
Abstract
Programmed death 1 (PD-1) and its ligands, namely PD-L1 and PD-L2, are one of the key factors responsible for inhibitory T cell signaling, mediating the mechanisms of tolerance and providing immune homeostasis. Mounting evidence demonstrates that impaired PD-1:PD-L function plays an important role in a variety of autoimmune diseases such as Type 1 diabetes (T1D), encephalomyelitis, inflammatory bowel diseases (IBD), Rheumatoid Arthritis (RA), autoimmune hepatitis (AIH), Behcet's disease (BD), myasthenia gravis (MG), autoimmune uveitis (AU), Sjögren's syndrome (SjS), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), myocarditis, and ankylosing spondylitis (AS). By investigating the candidate genes, genome-wide association studies, and identification of single nucleotide polymorphisms (SNPs) in PD-1 gene in humans, it has been shown that there is a higher risk in relevant genetic associations with developing autoimmune diseases in certain ethnic groups. In this review we have tried to present a comprehensive role of PD-1:PD-L in all recently studied autoimmune diseases.
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Affiliation(s)
- Mohammad Reza Zamani
- Department of Immunology and Biology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Saeed Aslani
- Department of Immunology and Biology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Salmaninejad
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Student Research Committee, Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Javan
- Department of Immunology, Faculty of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Nima Rezaei
- Department of Immunology and Biology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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18
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Cai TT, Zhang J, Wang X, Song RH, Qin Q, Muhali FS, Zhou JZ, Xu J, Zhang JA. Gene-gene and gene-sex epistatic interactions of DNMT1, DNMT3A and DNMT3B in autoimmune thyroid disease. Endocr J 2016; 63:643-53. [PMID: 27237591 DOI: 10.1507/endocrj.ej15-0596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to investigate the associations of DNA methyltransferases (DNMTs) polymorphisms with susceptibility to autoimmune thyroid diseases (AITDs) and to test gene-gene/gene-sex epistasis interactions. Eight single-nucleotide polymorphisms (SNPs) in DNMT1, DNMT3A and DNMT3B were selected and genotyped by multiplex polymerase chain reaction combined with ligase detection reaction method (PCR-LDR). A total of 685 Graves' disease (GD) patients, 353 Hashimoto's thyroiditis (HT) patients and 909 healthy controls were included in the final analysis. Epistasis was tested by additive model, multiplicative model and general multifactor dimensionality reduction (general MDR). Rs2424913 (DNMT3B) and rs2228611 (DNMT1) were associated with susceptibility to AITD and GD in the dominant and overdominant model, respectively (rs2424913: P=0.009 for AITD, P=0.0041 for GD; rs2228611: P=0.035 for AITD, P=0.043 for GD). Multiplicative and multiple high dimensional gene-gene or gene-sex interactions were also observed in this study. We have found evidence for a potential role of rs2424913 (DNMT3B) and rs2228611 (DNMT1) in AITD susceptibility and identified novel gene-gene/gene-sex interactions in AITD. Our study may highlight sex and genes of DNMTs family as contributors to the pathogenesis of AITD.
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Affiliation(s)
- Tian-Tian Cai
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
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19
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Leng RX, Pan HF, Liu J, Yang XK, Zhang C, Tao SS, Wang DG, Li XM, Li XP, Yang W, Ye DQ. Evidence for genetic association of TBX21 and IFNG with systemic lupus erythematosus in a Chinese Han population. Sci Rep 2016; 6:22081. [PMID: 26916970 PMCID: PMC4768161 DOI: 10.1038/srep22081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/05/2016] [Indexed: 01/21/2023] Open
Abstract
TBX21 recode T-bet which is an important transcription factor that drives the Th1 immune response primarily by promoting expression of the interferon-gamma (IFNG) gene. Recent studies have shown that genetic variants in TBX21 and IFNG are connected with risk of systemic lupus erythematosus (SLE). The aim of the present study was to replicate these genetic associations with SLE in Anhui Chinese population. Genotyping of 3 variants (rs4794067 in TBX21, rs2069705 and rs2069718 in IFNG) was performed. A total of 3732 subjects were included in the final analysis. The study only identified the association of rs2069705 with SLE susceptibility (T vs. C: odds ratio [OR] = 1.12, 95% confidence interval [CI] = 1.00–1.26, P = 0.046). Combined analysis with Hong Kong GWAS showed that the OR for rs2069705 was 1.10 (95% CI: 1.01–1.21, P = 0.027). Further pooled analysis with Korean populations involving 10498 subjects showed a more significant association between rs2069705 and SLE (T vs. C: OR = 1.11, 95%CI = 1.04–1.19, P = 0.002; TT + TC vs. CC: OR = 1.11, 95%CI = 1.02–1.21, P = 0.012; TT vs. TC + CC: OR = 1.28, 95%CI = 1.07–1.54, P = 0.008; TT vs. CC: OR = 1.33, 95%CI = 1.10–1.60, P = 0.003). In addition, we also identified a significant genetic interaction between rs2069705 and rs4794067 in Anhui Chinese population. Our study suggests that IFNG and IFNG-TBX21 interaction are involved in SLE susceptibility.
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Affiliation(s)
- Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - Juan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ke Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - Chao Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - Sha-Sha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
| | - De-Guang Wang
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Mei Li
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Xiang-Pei Li
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Anhui Provincial Laboratory of Population Health and Major Disease Screening and Diagnosis, Anhui Medical University, Hefei, Anhui, China
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20
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Scarbrough PM, Weber RP, Iversen ES, Brhane Y, Amos CI, Kraft P, Hung RJ, Sellers TA, Witte JS, Pharoah P, Henderson BE, Gruber SB, Hunter DJ, Garber JE, Joshi AD, McDonnell K, Easton DF, Eeles R, Kote-Jarai Z, Muir K, Doherty JA, Schildkraut JM. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer. Cancer Epidemiol Biomarkers Prev 2016; 25:193-200. [PMID: 26637267 PMCID: PMC4713268 DOI: 10.1158/1055-9965.epi-15-0649] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/05/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND DNA damage is an established mediator of carcinogenesis, although genome-wide association studies (GWAS) have identified few significant loci. This cross-cancer site, pooled analysis was performed to increase the power to detect common variants of DNA repair genes associated with cancer susceptibility. METHODS We conducted a cross-cancer analysis of 60,297 single nucleotide polymorphisms, at 229 DNA repair gene regions, using data from the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) Network. Our analysis included data from 32 GWAS and 48,734 controls and 51,537 cases across five cancer sites (breast, colon, lung, ovary, and prostate). Because of the unavailability of individual data, data were analyzed at the aggregate level. Meta-analysis was performed using the Association analysis for SubSETs (ASSET) software. To test for genetic associations that might escape individual variant testing due to small effect sizes, pathway analysis of eight DNA repair pathways was performed using hierarchical modeling. RESULTS We identified three susceptibility DNA repair genes, RAD51B (P < 5.09 × 10(-6)), MSH5 (P < 5.09 × 10(-6)), and BRCA2 (P = 5.70 × 10(-6)). Hierarchical modeling identified several pleiotropic associations with cancer risk in the base excision repair, nucleotide excision repair, mismatch repair, and homologous recombination pathways. CONCLUSIONS Only three susceptibility loci were identified, which had all been previously reported. In contrast, hierarchical modeling identified several pleiotropic cancer risk associations in key DNA repair pathways. IMPACT Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria.
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Affiliation(s)
- Peter M Scarbrough
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina. Cancer Prevention, Detection, and Control Research Program, Duke Cancer Institute, Durham, North Carolina. Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina. Cancer Prevention, Detection, and Control Research Program, Duke Cancer Institute, Durham, North Carolina
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - John S Witte
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Paul Pharoah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom. Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amit D Joshi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts
| | - Kevin McDonnell
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California. Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Doug F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Ros Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom. Royal Marsden NHS Foundation Trust, London and Sutton, United Kingdom
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom. Royal Marsden NHS Foundation Trust, London and Sutton, United Kingdom
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, United Kingdom. Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina. Cancer Prevention, Detection, and Control Research Program, Duke Cancer Institute, Durham, North Carolina. Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia.
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21
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Cassiano GC, Santos EJM, Maia MHT, Furini ADC, Storti-Melo LM, Tomaz FMB, Trindade PCA, Capobianco MP, Amador MAT, Viana GMR, Póvoa MM, Santos SEB, Machado RLD. Impact of population admixture on the distribution of immune response co-stimulatory genes polymorphisms in a Brazilian population. Hum Immunol 2015; 76:836-42. [PMID: 26429313 DOI: 10.1016/j.humimm.2015.09.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 09/08/2014] [Accepted: 09/27/2015] [Indexed: 12/21/2022]
Abstract
Co-stimulatory molecules are essential in the orchestration of immune response and polymorphisms in their genes are associated with various diseases. However, in the case of variable allele frequencies among continental populations, this variation can lead to biases in genetic studies conducted in admixed populations such as those from Brazil. The aim of this study was to evaluate the influence of genomic ancestry on distributions of co-stimulatory genes polymorphisms in an admixed Brazilian population. A total of 273 individuals from the north of Brazil participated in this study. Nine single nucleotide polymorphisms in 7 genes (CD28, CTLA4, ICOS, CD86, CD40, CD40L and BLYS) were determined by polymerase chain reaction-restriction fragment length polymorphism. We also investigated 48 insertion/deletion ancestry markers to characterize individual African, European and Amerindian ancestry proportions in the samples. The analysis showed that the main contribution was European (43.9%) but also a significant contribution of African (31.6%) and Amerindian (24.5%) ancestry. ICOS, CD40L and CD86 polymorphisms were associated with genomic ancestry. However there were no significant differences in the proportions of ancestry for the other SNPs and haplotypes studied. Our findings reinforce the need to apply AIMs in genetic association studies involving these polymorphisms in the Brazilian population.
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Affiliation(s)
- Gustavo Capatti Cassiano
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil.
| | | | | | - Adriana da Cruz Furini
- Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Franciele Maira Batista Tomaz
- Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Marcela Petrolini Capobianco
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Giselle Maria Rachid Viana
- Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
| | - Marinete Marins Póvoa
- Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
| | | | - Ricardo Luiz Dantas Machado
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
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22
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Leon Rodriguez DA, Serrano Lopera A, Cordero-Coma M, Márquez A, Fonollosa A, Ruiz-Arruza I, Callejas JL, García Serrano JL, Díaz Valle D, Pato E, Cañal J, del Rio MJ, Capella MJ, Blanco A, Olea JL, Cordero Y, Martín-Villa JM, Gorroño-Echebarría MB, Molins B, Adán A, Martin J. Study of association of CTLA4 gene variants to non-anterior uveitis. ACTA ACUST UNITED AC 2015; 86:373-6. [PMID: 26373706 DOI: 10.1111/tan.12668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/31/2015] [Accepted: 08/25/2015] [Indexed: 11/26/2022]
Abstract
This study was undertaken to investigate the possible genetic association of functional CTLA4 polymorphisms with susceptibility to non-anterior uveitis. Four hundred and seventeen patients with endogenous non-anterior uveitis and 1517 healthy controls of Spanish Caucasian origin were genotyped for the CTLA4 polymorphisms rs733618, rs5742909 and rs231775, using predesigned TaqMan(©) allele discrimination assays. PLINK software was used for the statistical analyses. No significant associations between the CTLA4 polymorphisms and susceptibility to global non-anterior uveitis were found. It was also the case when the potential association of these genetic variants with the anatomical localization of the disease, such as intermediate, posterior or panuveitis, was assessed. Our results do not support a relevant role of these CTLA4 polymorphisms in the non-anterior uveitis genetic predisposition.
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Affiliation(s)
- D A Leon Rodriguez
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, P.T.S, Granada, Spain
| | - A Serrano Lopera
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, P.T.S, Granada, Spain
| | - M Cordero-Coma
- Ophthalmology Department, Hospital de León, IBIOMED, Universidad de León, León, Spain
| | - A Márquez
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, P.T.S, Granada, Spain.,Systemic Autoimmune Diseases Unit, Hospital Clínico San Cecilio, Granada, Spain
| | - A Fonollosa
- Ophthalmology Department, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - I Ruiz-Arruza
- Autoimmune Diseases Research Unit, Internal Medicine Department, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - J L Callejas
- Systemic Autoimmune Diseases Unit, Hospital Clínico San Cecilio, Granada, Spain
| | | | - D Díaz Valle
- Ophthalmology Department, Hospital Clínico San Carlos, Madrid, Spain
| | - E Pato
- Rheumatology Department, Hospital Clínico San Carlos, Madrid, Spain
| | - J Cañal
- Ophthalmology Department, Hospital Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - M J del Rio
- Ophthalmology Department, Hospital Carlos Haya, Málaga, Spain
| | - M J Capella
- Institut Universitari Barraquer, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Blanco
- Ophthalmology Department, Hospital Donostia, San Sebastián, Spain
| | - J L Olea
- Ophthalmology Department, Hospital Son Espases, Palma de Mallorca, Spain
| | - Y Cordero
- Ophthalmology Department, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - J M Martín-Villa
- Immunology Department, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - M B Gorroño-Echebarría
- Ophthalmology Department, Hospital Universitario Principe de Asturias, Alcalá de Henares, Spain
| | - B Molins
- Ophthalmology Department, Hospital Clinic, Barcelona, Spain
| | - A Adán
- Ophthalmology Department, Hospital Clinic, Barcelona, Spain
| | - J Martin
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, P.T.S, Granada, Spain
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23
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Li Y, Chen S, Li P, Wu Z, Li J, Liu B, Zhang F, Li Y. Association of the IRF5 rs2070197 polymorphism with systemic lupus erythematosus: a meta-analysis. Clin Rheumatol 2015; 34:1495-501. [PMID: 26233721 DOI: 10.1007/s10067-015-3036-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/16/2015] [Accepted: 07/22/2015] [Indexed: 02/08/2023]
Abstract
The aim of this study was to explore whether the interferon regulatory factor 5 (IRF5) gene rs2070197 polymorphism was associated with systemic lupus erythematosus (SLE) in multiple ethic populations. A meta-analysis was conducted on the C allele of the IRF5 rs2070197 polymorphism. A total of 7 published case-control studies with 12 comparisons involving 8171 SLE patients and 8904 controls were available for this meta-analysis. This meta-analysis demonstrated the IRF5 rs2070197 polymorphism conferred susceptibility to SLE in all subjects (odds ratio (OR) = 2.128, 95 % confidence interval (CI): 1.856-2.441, P < 0.001) without inter-study heterogeneity. The IRF5 rs2070197 polymorphism was identified as risk factors for SLE in Caucasian populations (OR 1.82, 95 % CI 1.70-1.96), but it had no effects (monomorphic) in Asians. Large-scale multicenter epidemiological studies in selected populations with other risk factors were urgently required.
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Affiliation(s)
- Yuan Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
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24
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Relle M, Weinmann-Menke J, Scorletti E, Cavagna L, Schwarting A. Genetics and novel aspects of therapies in systemic lupus erythematosus. Autoimmun Rev 2015; 14:1005-18. [PMID: 26164648 DOI: 10.1016/j.autrev.2015.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
Abstract
Autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, autoimmune hepatitis and inflammatory bowel disease, have complex pathogeneses and the factors which cause these disorders are not well understood. But all have in common that they arise from a dysfunction of the immune system, interpreting self components as foreign antigens. Systemic lupus erythematosus (SLE) is one of these complex inflammatory disorders that mainly affects women and can lead to inflammation and severe damage of virtually any tissue and organ. Recently, the application of advanced techniques of genome-wide scanning revealed more genetic information about SLE than previously possible. These case-control or family-based studies have provided evidence that SLE susceptibility is based (with a few exceptions) on an individual accumulation of various risk alleles triggered by environmental factors and also help to explain the discrepancies in SLE susceptibility between different populations or ethnicities. Moreover, during the past years new therapies (autologous stem cell transplantation, B cell depletion) and improved conventional treatment options (corticosteroids, traditional and new immune-suppressants like mycophenolate mofetile) changed the perspective in SLE therapeutic approaches. Thus, this article reviews genetic aspects of this autoimmune disease, summarizes clinical aspects of SLE and provides a general overview of conventional and new therapeutic approaches in SLE.
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Affiliation(s)
- Manfred Relle
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Julia Weinmann-Menke
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Eva Scorletti
- Division of Rheumatology, IRCCS Fondazione Policlinico San Matteo, Lombardy, Pavia, Italy
| | - Lorenzo Cavagna
- Division of Rheumatology, IRCCS Fondazione Policlinico San Matteo, Lombardy, Pavia, Italy
| | - Andreas Schwarting
- First Department of Medicine, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany; Acura Centre of Rheumatology Rhineland-Palatinate, Bad Kreuznach, Germany.
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Akkad DA, Olischewsky A, Reiner F, Hellwig K, Esser S, Epplen JT, Curk T, Gold R, Haghikia A. Combinations of susceptibility genes are associated with higher risk for multiple sclerosis and imply disease course specificity. PLoS One 2015; 10:e0127632. [PMID: 26011527 PMCID: PMC4444291 DOI: 10.1371/journal.pone.0127632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/16/2015] [Indexed: 11/26/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system that predominantly affects young adults. The genetic contributions to this multifactorial disease were underscored by a genome wide association study (GWAS) conducted by the International Multiple Sclerosis Genetic Consortium in a multinational cohort prompting the discovery of 57 non-MHC MS-associated common genetic variants. Hitherto, few of these newly reported variants have been replicated in larger independent patient cohorts. We genotyped a cohort of 1033 MS patients and 644 healthy controls with a consistent genetic background for the 57 non-MHC variants reported to be associated with MS by the first large GWAS as well as the HLA DRB1*1501 tagging SNP rs3135388. We robustly replicated three of the 57 non-MHC reported MS-associated single nucleotide polymorphisms (SNPs). In addition, our study revealed several genotype-genotype combinations with an evidently higher degree of disease association than the genotypes of the single SNPs. We further correlated well-defined clinical phenotypes, i.e. ataxia, visual impairment due to optic neuritis and paresis with single SNPs and genotype combinations, and identified several associations. The results may open new avenues for clinical implications of the MS associated genetic variants reported from large GWAS.
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Affiliation(s)
- Denis A. Akkad
- Department of Human Genetics, Ruhr-University Bochum, Bochum, Germany
- * E-mail: (DAA); (AH)
| | - Alexandra Olischewsky
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Franziska Reiner
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Kerstin Hellwig
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Sarika Esser
- Department of Human Genetics, Ruhr-University Bochum, Bochum, Germany
| | - Jörg T. Epplen
- Department of Human Genetics, Ruhr-University Bochum, Bochum, Germany
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Ralf Gold
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Aiden Haghikia
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Bochum, Germany
- * E-mail: (DAA); (AH)
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Zhang Y, Yang J, Zhang J, Sun L, Hirankarn N, Pan HF, Lau CS, Chan TM, Lee TL, Leung AMH, Mok CC, Zhang L, Wang Y, Shen JJ, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Wong CM, Ng IOL, Garcia-Barcelo MM, Cherny SS, Cui Y, Sham PC, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Genome-wide search followed by replication reveals genetic interaction of CD80 and ALOX5AP associated with systemic lupus erythematosus in Asian populations. Ann Rheum Dis 2015; 75:891-8. [PMID: 25862617 DOI: 10.1136/annrheumdis-2014-206367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Genetic interaction has been considered as a hallmark of the genetic architecture of systemic lupus erythematosus (SLE). Based on two independent genome-wide association studies (GWAS) on Chinese populations, we performed a genome-wide search for genetic interactions contributing to SLE susceptibility. METHODS The study involved a total of 1 659 cases and 3 398 controls in the discovery stage and 2 612 cases and 3 441 controls in three cohorts for replication. Logistic regression and multifactor dimensionality reduction were used to search for genetic interaction. RESULTS Interaction of CD80 (rs2222631) and ALOX5AP (rs12876893) was found to be significantly associated with SLE (OR_int=1.16, P_int_all=7.7E-04 at false discovery rate<0.05). Single nuclear polymorphism rs2222631 was found associated with SLE with genome-wide significance (P_all=4.5E-08, OR=0.86) and is independent of rs6804441 in CD80, whose association was reported previously. Significant correlation was observed between expression of these two genes in healthy controls and SLE cases, together with differential expression of these genes between cases and controls, observed from individuals from the Hong Kong cohort. Genetic interactions between BLK (rs13277113) and DDX6 (rs4639966), and between TNFSF4 (rs844648) and PXK (rs6445975) were also observed in both GWAS data sets. CONCLUSIONS Our study represents the first genome-wide evaluation of epistasis interactions on SLE and the findings suggest interactions and independent variants may help partially explain missing heritability for complex diseases.
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Affiliation(s)
- Yan Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jing Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Liangdan Sun
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Nattiya Hirankarn
- Lupus Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Chak Sing Lau
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tak Mao Chan
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tsz Leung Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, New Territory, Hong Kong, Hong Kong
| | - Lu Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yongfei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sik Nin Wong
- Department of Paediatrics and Adolescent Medicine, Tuen Mun Hospital, Hong Kong, Hong Kong
| | - Ka Wing Lee
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong
| | - Marco Hok Kung Ho
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Pamela Pui Wah Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chun Yin Chong
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Raymond Woon Sing Wong
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mo Yin Mok
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wilfred Hing Sang Wong
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Kwok Lung Tong
- Department of Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Niko Kei Chiu Tse
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Xiang-Pei Li
- Department of Rheumatology, Anhui Provincial Hospital, Hefei, China
| | - Yingyos Avihingsanon
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pornpimol Rianthavorn
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Kanya Suphapeetiporn
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Wai Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Irene Oi Lin Ng
- Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Stacey S Cherny
- Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yong Cui
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong LKS Faculty of Medicine, Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sen Yang
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Dong-Qing Ye
- Lupus Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Xue-Jun Zhang
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong LKS Faculty of Medicine, Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, Hong Kong
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Lee YH, Bae SC. Association between the functional ITGAM rs1143679 G/A polymorphism and systemic lupus erythematosus/lupus nephritis or rheumatoid arthritis: an update meta-analysis. Rheumatol Int 2014; 35:815-23. [PMID: 25315704 DOI: 10.1007/s00296-014-3156-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
The aim of this study was to determine whether the functional integrin-α-M (ITGAM) rs1143679 polymorphism is associated with susceptibility to systemic lupus erythematosus (SLE), lupus nephritis (LN), and rheumatoid arthritis (RA). A series of meta-analyses were conducted to test for associations between the ITGAM rs1143679 polymorphism and SLE, LN, or RA. A total of 24 comparisons involving 7,738 patients and 8,309 controls for SLE, and 2,663 patients and 2,694 controls in RA were considered. Meta-analysis showed a significant association between the ITGAM rs1143679 A allele and SLE in all subjects (OR 1.773, 95 % CI 1.656, 1.901, p < 1.0 × 10(-9)). After stratification by ethnicity, the A allele was found to be significantly associated with SLE in European, Latin American, and Asian. A significant association was also found between the ITGAM A allele and lupus nephritis in Europeans (OR 2.131, 95 % CI 1.565, 2.903, p = 1.6 × 10(-7)). However, no association was found between RA and the ITGAM rs1143679 polymorphism. Our meta-analyses confirm that the ITGAM rs1143679 polymorphism is associated with SLE susceptibility in different ethnic groups and demonstrate that the polymorphism is associated with LN in European.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 126-1, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-705, Korea,
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Genetics, environment, and gene-environment interactions in the development of systemic rheumatic diseases. Rheum Dis Clin North Am 2014; 40:637-57. [PMID: 25437282 DOI: 10.1016/j.rdc.2014.07.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rheumatic diseases offer distinct challenges to researchers because of heterogeneity in disease phenotypes, low disease incidence, and geographic variation in genetic and environmental factors. Emerging research areas, including epigenetics, metabolomics, and the microbiome, may provide additional links between genetic and environmental risk factors in the pathogenesis of rheumatic disease. This article reviews the methods used to establish genetic and environmental risk factors and studies gene-environment interactions in rheumatic diseases, and provides specific examples of successes and challenges in identifying gene-environment interactions in rheumatoid arthritis, systemic lupus erythematosus, and ankylosing spondylitis. Emerging research strategies and future challenges are discussed.
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Singh N, Traisak P, Martin KA, Kaplan MJ, Cohen PL, Denny MF. Genomic alterations in abnormal neutrophils isolated from adult patients with systemic lupus erythematosus. Arthritis Res Ther 2014; 16:R165. [PMID: 25107306 PMCID: PMC4262380 DOI: 10.1186/ar4681] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/18/2014] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Patients with systemic lupus erythematosus (SLE) have an abnormal population of neutrophils, called low-density granulocytes (LDGs), that express the surface markers of mature neutrophils, yet their nuclear morphology resembles an immature cell. Because a similar discrepancy in maturation status is observed in myelodysplasias, and disruption of neutrophil development is frequently associated with genomic alterations, genomic DNA isolated from autologous pairs of LDGs and normal-density neutrophils was compared for genomic changes. METHODS Alterations in copy number and losses of heterozygosity (LOH) were detected by cytogenetic microarray analysis. Microsatellite instability (MSI) was detected by capillary gel electrophoresis of fluorescently labeled PCR products. RESULTS Control neutrophils and normal-density SLE neutrophils had similar levels of copy number variations, while the autologous SLE LDGs had an over twofold greater number of copy number alterations per genome. The additional copy number alterations found in LDGs were prevalent in six of the thirteen SLE patients, and occurred preferentially on chromosome 19, 17, 8, and X. These same SLE patients also displayed an increase in LOH. Several SLE patients had a common LOH on chromosome 5q that includes several cytokine genes and a DNA repair enzyme. In addition, three SLE patients displayed MSI. Two patients displayed MSI in greater than one marker, and one patient had MSI and increased copy number alterations. No correlations between genomic instability and immunosuppressive drugs, disease activity or disease manifestations were apparent. CONCLUSIONS The increased level of copy number alterations and LOH in the LDG samples relative to autologous normal-density SLE neutrophils suggests somatic alterations that are consistent with DNA strand break repair, while MSI suggests a replication error-prone status. Thus, the LDGs isolated have elevated levels of somatic alterations that are consistent with genetic damage or genomic instability. This suggests that the LDGs in adult SLE patients are derived from cell progenitors that are distinct from the autologous normal-density neutrophils, and may reflect a role for genomic instability in the disease.
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Affiliation(s)
- Namrata Singh
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
| | - Pamela Traisak
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
| | - Kayla A Martin
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
| | - Mariana J Kaplan
- />Systemic Autoimmunity Branch, Intramural Research Program, NIAMS/NIH, 10 Center Drive, Bethesda, MD 20892 USA
| | - Philip L Cohen
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
- />Temple Autoimmunity Center, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
| | - Michael F Denny
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
- />Temple Autoimmunity Center, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
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Chance, genetics, and the heterogeneity of disease and pathogenesis in systemic lupus erythematosus. Semin Immunopathol 2014; 36:495-517. [PMID: 25102991 DOI: 10.1007/s00281-014-0440-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 06/30/2014] [Indexed: 12/30/2022]
Abstract
Systemic lupus erythematosus (SLE) is a remarkably complex and heterogeneous systemic autoimmune disease. Disease complexity within individuals and heterogeneity among individuals, even genetically identical individuals, is driven by stochastic execution of a complex inherited program. Genome-wide association studies (GWAS) have progressively improved understanding of which genes are most critical to the potential for SLE and provided illuminating insight about the immune mechanisms that are engaged in SLE. What initiates expression of the genetic program to cause SLE within an individual and how that program is initiated remains poorly understood. If we extrapolate from all of the different experimental mouse models for SLE, we can begin to appreciate why SLE is so heterogeneous and consequently why prediction of disease outcome is so difficult. In this review, we critically evaluate extrinsic versus intrinsic cellular functions in the clearance and elimination of cellular debris and how dysfunction in that system may promote autoimmunity to nuclear antigens. We also examine several mouse models genetically prone to SLE either because of natural inheritance or inheritance of induced mutations to illustrate how different immune mechanisms may initiate autoimmunity and affect disease pathogenesis. Finally, we describe the heterogeneity of disease manifestations in SLE and discuss the mechanisms of disease pathogenesis with emphasis on glomerulonephritis. Particular attention is given to discussion of how anti-DNA autoantibody initiates experimental lupus nephritis (LN) in mice.
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Shan S, Dang J, Li J, Yang Z, Zhao H, Xin Q, Ma X, Liu Y, Bian X, Gong Y, Liu Q. ETS1 variants confer susceptibility to ankylosing spondylitis in Han Chinese. Arthritis Res Ther 2014; 16:R87. [PMID: 24708692 PMCID: PMC4060494 DOI: 10.1186/ar4530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/25/2014] [Indexed: 12/21/2022] Open
Abstract
Introduction ETS1 is a negative regulator of the Th17 differentiation gene and plays a central role in the pathogenesis of autoimmune diseases. We aimed to investigate whether polymorphisms in ETS1 confer susceptibility to ankylosing spondylitis (AS) in Han Chinese. Methods We selected seven single nucleotide polymorphisms (SNPs) within ETS1 based on HapMap data and previous genome-wide association study. Genotyping involved the TaqMan method in 1,015 patients with AS and 1,132 healthy controls from Shandong Province, and 352 AS patients and 400 healthy controls from Ningxia, a northwest region in China. Gene expression was determined by real-time PCR. Results The SNP rs1128334 was strongly associated with AS (odds ratio 1.204, 95% confidence interval 1.06-1.37; P = 0.005). This association was confiexrmed in the Ningxia population (P = 0.015). Carriers of the haplotype TAT for rs12574073, rs1128334 and rs4937333 were associated with increased risk of AS and haplotype CGC with reduced risk as compared to controls. In addition, ETS1 expression was lower in AS patients than controls. The risk allele A of rs1128334 and haplotype A-T of rs1128334 and rs4937333 were associated with decreased expression of ETS1. Conclusions Common variants in ETS1 may contribute to AS susceptibility in Han Chinese people.
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Clark N, Wu X, Her C. MutS Homologues hMSH4 and hMSH5: Genetic Variations, Functions, and Implications in Human Diseases. Curr Genomics 2013; 14:81-90. [PMID: 24082819 PMCID: PMC3637681 DOI: 10.2174/1389202911314020002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/19/2013] [Accepted: 01/21/2013] [Indexed: 12/01/2022] Open
Abstract
The prominence of the human mismatch repair (MMR) pathway is clearly reflected by the causal link between MMR gene mutations and the occurrence of Lynch syndrome (or HNPCC). The MMR family of proteins also carries out a plethora of diverse cellular functions beyond its primary role in MMR and homologous recombination. In fact, members of the MMR family of proteins are being increasingly recognized as critical mediators between DNA damage repair and cell survival. Thus, a better functional understanding of MMR proteins will undoubtedly aid the development of strategies to effectively enhance apoptotic signaling in response to DNA damage induced by anti-cancer therapeutics. Among the five known human MutS homologs, hMSH4 and hMSH5 form a unique heterocomplex. However, the expression profiles of the two genes are not correlated in a number of cell types, suggesting that they may function independently as well. Consistent with this, these two proteins are promiscuous and thought to play distinct roles through interacting with different binding partners. Here, we describe the gene and protein structures of eukaryotic MSH4 and MSH5 with a particular emphasis on their human homologues, and we discuss recent findings of the roles of these two genes in DNA damage response and repair. Finally, we delineate the potential links of single nucleotide polymorphism (SNP) loci of these two genes with several human diseases.
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Affiliation(s)
- Nicole Clark
- STARS Program, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7520, USA ; School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7520, USA
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Cen H, Zhou M, Leng RX, Wang W, Feng CC, Li BZ, Zhu Y, Yang XK, Yang M, Zhai Y, Zhang M, Hu LF, Li R, Chen GM, Chen H, Pan HF, Li XP, Ye DQ. Genetic interaction between genes involved in NF-κB signaling pathway in systemic lupus erythematosus. Mol Immunol 2013; 56:643-8. [PMID: 23911423 DOI: 10.1016/j.molimm.2013.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/29/2013] [Accepted: 07/08/2013] [Indexed: 01/14/2023]
Abstract
Recently, multiple genetic associations have been found between genes involved in nuclear factor-kappaB (NF-κB) signaling pathway and systemic lupus erythematosus (SLE) or other autoimmune diseases. This study was undertaken to replicate some of these associations and further test for genetic interactions among these genes in SLE in a Chinese population. Ten single-nucleotide polymorphisms (SNPs) in NFKB1, REL, inhibitor of κB-like (IκBL), IκB kinase β (IKBKB), tumor necrosis factor receptor associated factor 6 (TRAF6), tumor necrosis factor a-induced protein 3 (TNFAIP3), TNFAIP3 interacting protein 1 (TNIP1) were genotyped in 898 Chinese patients with SLE and 988 healthy controls by Sequenom MassArray technology. Single-marker genetic association analysis was performed, and additive and multiplicative interactions were analyzed. Associations of TNFAIP3 rs2230926 (p=1.43 × 10(-3)) and TNIP1 rs10036748 (p=4.33 × 10(-3)) with SLE were replicated in our study. Two other SNPs, NFKB1 rs28362491 and IκBL rs2071592, showed nominal evidence for association (p=4.70 × 10(-2) and p=5.90 × 10(-3), respectively) but these were not significant after applying Bonferroni correction. Additive interaction analysis revealed significant interaction between NFKB1 rs28362491 and TNFAIP3 rs2230926 (RERI=0.98, 95%CI=0.02-1.93; AP=43.2%, 95%CI=0.12-0.74). Significant multiplicative interaction was observed between NFKB1 rs28362491 and TNIP1 rs3792783 (p=0.03). Our results provide evidence for gene-gene interactions, which further support the important role of NF-κB signaling pathway in the genetic basis of SLE and the notion of genetic interactions accounting for missing heritability.
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Affiliation(s)
- Han Cen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, PR China; Anhui Provincial Laboratory of Population Health & Major Disease Screening and Diagnosis, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, PR China
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Abstract
Genetic studies in immune-mediated diseases have yielded a large number of disease-associated loci. Here we review the progress being made in 12 such diseases, for which 199 independently associated non-HLA loci have been identified by genome-wide association studies since 2007. It is striking that many of the loci are not unique to a single disease but shared between different immune-mediated diseases. The challenge now is to understand how the unique and shared genetic factors can provide insight into the underlying disease biology. We annotated disease-associated variants using the Encyclopedia of DNA Elements (ENCODE) database and demonstrate that, of the predisposing disease variants, the majority have the potential to be regulatory. We also demonstrate that many of these variants affect the expression of nearby genes. Furthermore, we summarize results from the Immunochip, a custom array, which allows a detailed comparison between five of the diseases that have so far been analyzed using this platform.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands;
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Sun F, Li P, Chen H, Wu Z, Xu J, Shen M, Leng X, Shi Q, Zhang W, Tian X, Li Y, Zhang F. Association studies of TNFSF4, TNFAIP3 and FAM167A-BLK polymorphisms with primary Sjogren’s syndrome in Han Chinese. J Hum Genet 2013; 58:475-9. [DOI: 10.1038/jhg.2013.26] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/19/2013] [Accepted: 03/01/2013] [Indexed: 12/21/2022]
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Co-stimulatory molecules as targets for treatment of lupus. Clin Immunol 2013; 148:369-75. [PMID: 23680362 DOI: 10.1016/j.clim.2013.04.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 11/22/2022]
Abstract
Co-stimulatory molecules help to regulate interactions between T cells and antigen-presenting cells and may play an important role in the pathogenesis of lupus. Both work in murine models and some early studies in human lupus support further examination of these molecules as therapeutic targets. Complexities of lupus clinical trial variables may have hampered progress in this area but recent developments in the field may make interventional trials more feasible in the near future. To date biologics which provide direct blockade of interactions between CD40 and CD154, B7RP-1 and ICOS, and CD80 or CD86 with CD28 have been assessed in multicenter clinical trials. These data will be reviewed and critiqued.
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Zhang J, Zhang Y, Zhang L, Yang J, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Lau YL, Yang W. Epistatic interaction between genetic variants in susceptibility gene ETS1 correlates with IL-17 levels in SLE patients. Ann Hum Genet 2013; 77:344-50. [PMID: 23614478 DOI: 10.1111/ahg.12018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 12/14/2012] [Indexed: 02/02/2023]
Abstract
T-helper cells that produce IL-17 (Th17 cells) are a subset of CD4(+) T-cells with pathological roles in autoimmune diseases including systemic lupus erythematosus (SLE), and ETS1 is a negative regulator of Th17 cell differentiation. Our previous work on genome-wide association study (GWAS) identified two variants in the ETS1 gene (rs10893872 and rs1128334) as being associated with SLE. However, like many other risk alleles for complex diseases, little is known on how these genetic variants might affect disease pathogenesis. In this study, we examined serum IL-17 levels from 283 SLE cases and observed a significant correlation between risk variants in ETS1 and serum IL-17 concentration in patients, which suggests a potential mechanistic link between these variants and the disease. Furthermore, we found that the two variants act synergistically in influencing IL-17 production, with evidence of significant genetic interaction between them as well as higher correlation between the haplotype formed by the risk alleles and IL-17 level in patient serum. In addition, the correlation between ETS1 variants and IL-17 level seems to be more significant in SLE patients manifesting renal involvement, dsDNA autoantibody production or early-onset.
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Affiliation(s)
- Jing Zhang
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong
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Rullo OJ, Tsao BP. Recent insights into the genetic basis of systemic lupus erythematosus. Ann Rheum Dis 2012; 72 Suppl 2:ii56-61. [PMID: 23253915 DOI: 10.1136/annrheumdis-2012-202351] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Many identified genetic risk factors for systemic lupus erythematosus (SLE) contribute to the function of the immune system, which has expanded our understanding of disease pathogenesis. We outline the genetic variants in recently identified SLE-associated loci, the immunological pathways affected by these gene products and the disease manifestations linked to these loci. Pathways potentially influenced by SLE risk variants include: apoptosis, DNA degradation and clearance of cellular debris; antigen presentation; type I interferon, Toll-like receptor and nuclear factor kappa κB activation; defective clearance of immune complexes containing nuclear antigens; B and T-cell function and signalling; and monocyte and neutrophil function and signalling. These identified SLE susceptibility loci are predominantly common variants that have been confirmed among multiple ancestries, suggesting shared mechanisms in disease aetiology. Ongoing genetic studies continue the investigation of specific functional variants, and their potential consequences on immune dysregulation, enhancing our understanding of links between genotypes and specific disease manifestations. The next generation of sequencing explores the identification of causal rare variants that may contribute robust genetic effects to developing SLE. Novel insights coming from genetic studies of SLE provide the opportunity to elucidate pathogenic mechanisms as well as contribute to the development of innovative therapeutic targets for this complex disease.
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Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease of diverse manifestations, with onset usually in young women in the third to fourth decade of life. The chronic nature of this relapsing remitting disease leads to organ damage accrual over time. Mortality and morbidity are increased in patients with SLE compared with the general population. Therapeutic advances over the last few decades have led to significant improvements in patient outcomes. Five-year survival has improved to over 90% from a low of 50% in the 1950s. However, multiple aspects of the management of SLE patients are still far from optimal. Early diagnosis remains a challenge; diagnostic delays leading to delay in definitive treatment are common. Monitoring treatment remains problematic due to the paucity of sensitive biomarkers. Current treatment regimens rely heavily on corticosteroids, even though corticosteroids are well known to cause organ damage. Treatment of refractory disease manifestations such as nephritis, recalcitrant cutaneous lesions and neurological involvement require new approaches with greater efficacy. Cognitive dysfunction is common in SLE patients, but early recognition and adequate treatment are yet to be established. Premature accelerated atherosclerosis remains a leading cause of morbidity and mortality. Fatigue is one of the most disabling symptoms, and contributes to the poor quality of life in patients with SLE. Ongoing research in SLE faces many challenges, including enrollment of homogeneous patient populations, use of reliable outcome measures and a standard control arm. The current review will highlight some of the outstanding unmet challenges in the management of this complex disease.
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Affiliation(s)
- Aisha Lateef
- Division of Rheumatology, University Medicine Cluster, National University Health System, 1E Kent Ridge Road, Singapore 119074, Singapore
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Gene-gene and gene-sex epistatic interactions of MiR146a, IRF5, IKZF1, ETS1 and IL21 in systemic lupus erythematosus. PLoS One 2012; 7:e51090. [PMID: 23236436 PMCID: PMC3517573 DOI: 10.1371/journal.pone.0051090] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/29/2012] [Indexed: 11/21/2022] Open
Abstract
Several confirmed genetic susceptibility loci involved in the interferon signaling and Th17/B cell response for SLE in Chinese Han populations have been described. Available data also indicate that sex-specific genetic differences contribute to SLE susceptibility. The aim of this study was to test for gene–gene/gene-sex epistasis (interactions) in these known lupus susceptibility loci. Six single-nucleotide polymorphisms (SNPs) in MiR146a, IRF5, IKZF1, ETS1 and IL21 were genotyped by Sequenom MassArray system. A total of 1,825 subjects (858 SLE patients and 967 controls) were included in the final analysis. Epistasis was tested by additive model, multiplicative model and multifactor dimensionality reduction (MDR) method. Additive interaction analysis revealed interactions between IRF5 and IKZF1 (OR 2.26, 95% CI 1.48–3.44 [P = 1.21×104]). A similar tendency was also observed between IL21 and ETS1 by parametric methods. In addition, multiple high dimensional gene-gene or gene-sex interactions (three-and four-way) were identified by MDR analysis. Our study identified novel gene–gene/gene-sex interactions in lupus. Furthermore, these findings highlight sex, interferon pathway, and Th17/B cells as important contributors to the pathogenesis of SLE.
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Rose AM, Bell LCK. Epistasis and immunity: the role of genetic interactions in autoimmune diseases. Immunology 2012; 137:131-8. [PMID: 22804709 DOI: 10.1111/j.1365-2567.2012.03623.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Autoimmune disorders are a complex and varied group of diseases that are caused by breakdown of self-tolerance. The aetiology of autoimmunity is multi-factorial, with both environmental triggers and genetically determined risk factors. In recent years, it has been increasingly recognized that genetic risk factors do not act in isolation, but rather the combination of individual additive effects, gene-gene interactions and gene-environment interactions determine overall risk of autoimmunity. The importance of gene-gene interactions, or epistasis, has been recently brought into focus, with research demonstrating that many autoimmune diseases, including rheumatic arthritis, autoimmune glomerulonephritis, systemic lupus erythematosus and multiple sclerosis, are influenced by epistatic interactions. This review sets out to examine the basic mechanisms of epistasis, how epistasis influences the immune system and the role of epistasis in two major autoimmune conditions, systemic lupus erythematosus and multiple sclerosis.
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK.
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Louvain de Souza T, de Souza Campos Fernandes RC, Medina-Acosta E. HIV-1 control in battlegrounds: important host genetic variations for HIV-1 mother-to-child transmission and progression to clinical pediatric AIDS. Future Virol 2012. [DOI: 10.2217/fvl.12.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 mother-to-child transmission (MTCT) is the passing of maternal HIV-1 to the offspring during pregnancy, labor and delivery, and/or breastfeeding. HIV-1 MTCT and the evolution to pediatric AIDS are multifactorial, dynamic and variable phenotypic conditions. Both genetic and nongenetic variables can influence susceptibility to HIV-1 MTCT or the rate of progression to clinical pediatric AIDS. In this review, we summarize the current state of knowledge about the roles of genetic variations seen in host immune response genes, and those that have been independently associated, mostly through population genetics of candidate genes, with interindividual susceptibility to HIV-1 MTCT, and progression to pediatric AIDS. We examine common and rare host genetic variations at coding and noncoding polymorphisms, whether functional or not, in agonists and antagonists of the immune response, which have been implicated in HIV-1 control in battlegrounds of cell entry, replication and evolution to AIDS. Further, we point to over 380 single-nucleotide polymorphisms, mostly within the HLA super region, recently identified in unbiased genome-wide association studies of HIV replication and evolution in adults, still unexplored in the context of HIV-1 MTCT, and which are likely to also influence susceptibility to pediatric HIV-1/AIDS.
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Affiliation(s)
- Thais Louvain de Souza
- Molecular Identification & Diagnosis Unit, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Regina Célia de Souza Campos Fernandes
- Municipal Program for the Surveillance of Sexually Transmitted Diseases & Acquired Immunodeficiency Syndrome of Campos dos Goytacazes, Brazil
- Faculty of Medicine of Campos, Campos dos Goytacazes, Brazil
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Sawalha AH, Wang L, Nadig A, Somers EC, McCune WJ, Hughes T, Merrill JT, Scofield RH, Strickland FM, Richardson B. Sex-specific differences in the relationship between genetic susceptibility, T cell DNA demethylation and lupus flare severity. J Autoimmun 2012; 38:J216-22. [PMID: 22305513 PMCID: PMC3313010 DOI: 10.1016/j.jaut.2011.11.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 11/19/2011] [Accepted: 11/22/2011] [Indexed: 12/21/2022]
Abstract
Lupus is less common in men than women, and the reason is incompletely understood. Current evidence indicates that lupus flares when genetically predisposed individuals encounter environmental agents that trigger the disease, and that the environmental contribution is mediated at least in part by T cell DNA demethylation. We hypothesized that lupus disease activity is directly related to total genetic risk and inversely related to T cell DNA methylation levels in each patient. Since women are predisposed to lupus in part because of their second X chromosome, we also hypothesized that men would require a greater genetic risk, a greater degree of autosomal T cell DNA demethylation, or both, to achieve a lupus flare equal in severity to women. Genetic risk was determined by genotyping men and women with lupus across 32 confirmed lupus susceptibility loci. The methylation status of two autosomal genes known to demethylate in T cells in proportion to disease activity, KIR2DL4 (KIR) and PRF1, was measured by bisulfite sequencing. Lupus disease activity was determined by the SLEDAI. Interactions between genetic score, T cell DNA demethylation, and the SLEDAI score were compared between the men and women by regression analysis. Combining the degree of DNA demethylation with the genetic risk score for each patient demonstrated that the (genetic risk)/(DNA methylation) ratio increased directly with disease activity in both men and women with lupus. Importantly, men required a greater (genetic risk)/(DNA methylation) ratio to achieve a SLEDAI score equivalent to women (P = 0.010 for KIR and P = 0.0054 for PRF1). This difference was not explained by a difference in the genetic risk or T cell DNA demethylation alone, suggesting a genetic-epigenetic interaction. These results suggest that genetic risk and T cell DNA demethylation interact in lupus patients to influence the severity of lupus flares, and that men require a higher genetic risk and/or greater degree of T cell DNA demethylation to achieve a lupus flare equal in severity to women.
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Affiliation(s)
- Amr H Sawalha
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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45
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Hughes T, Adler A, Merrill JT, Kelly JA, Kaufman KM, Williams A, Langefeld CD, Gilkeson GS, Sanchez E, Martin J, Boackle SA, Stevens AM, Alarcón GS, Niewold TB, Brown EE, Kimberly RP, Edberg JC, Ramsey-Goldman R, Petri M, Reveille JD, Criswell LA, Vilá LM, Jacob CO, Gaffney PM, Moser KL, Vyse TJ, Alarcón-Riquelme ME, James JA, Tsao BP, Scofield RH, Harley JB, Richardson BC, Sawalha AH. Analysis of autosomal genes reveals gene-sex interactions and higher total genetic risk in men with systemic lupus erythematosus. Ann Rheum Dis 2012; 71:694-9. [PMID: 22110124 PMCID: PMC3324666 DOI: 10.1136/annrheumdis-2011-200385] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a sexually dimorphic autoimmune disease which is more common in women, but affected men often experience a more severe disease. The genetic basis of sexual dimorphism in SLE is not clearly defined. A study was undertaken to examine sex-specific genetic effects among SLE susceptibility loci. METHODS A total of 18 autosomal genetic susceptibility loci for SLE were genotyped in a large set of patients with SLE and controls of European descent, consisting of 5932 female and 1495 male samples. Sex-specific genetic association analyses were performed. The sex-gene interaction was further validated using parametric and non-parametric methods. Aggregate differences in sex-specific genetic risk were examined by calculating a cumulative genetic risk score for SLE in each individual and comparing the average genetic risk between male and female patients. RESULTS A significantly higher cumulative genetic risk for SLE was observed in men than in women. (P=4.52x10-8) A significant sex-gene interaction was seen primarily in the human leucocyte antigen (HLA) region but also in IRF5, whereby men with SLE possess a significantly higher frequency of risk alleles than women. The genetic effect observed in KIAA1542 is specific to women with SLE and does not seem to have a role in men. CONCLUSIONS The data indicate that men require a higher cumulative genetic load than women to develop SLE. These observations suggest that sex bias in autoimmunity could be influenced by autosomal genetic susceptibility loci.
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Affiliation(s)
- Travis Hughes
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Adam Adler
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Joan T Merrill
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Clinical Pharmacology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kenneth M Kaufman
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - Adrienne Williams
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Winston-Salem, North Carolina, USA
| | - Gary S Gilkeson
- Department of Medicine, Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Elena Sanchez
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Susan A Boackle
- Division of Rheumatology, School of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Anne M Stevens
- Department of Pediatrics, Division of Rheumatology, University of Washington, Seattle, Washington, USA
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, Washington, USA
| | | | - Timothy B Niewold
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Elizabeth E Brown
- Department of Medicine, University of Alabama, Birmingham, Alabama, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama, Birmingham, Alabama, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama, Birmingham, Alabama, USA
| | | | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Reveille
- Department of Medicine, University of Texas-Houston Health Science Center, Houston, Texas, USA
| | - Lindsey A Criswell
- Rosalind Russell Medical Research Center for Arthritis, University of California, San Francisco, San Francisco, California, USA
| | - Luis M Vilá
- Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, California, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy L Moser
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Timothy J Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, Infection and Inflammatory Disease, King’s College London, Guy’s Hospital, London, UK
| | - Marta E Alarcón-Riquelme
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Center for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucia, Granada, Spain
| | | | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Betty P Tsao
- Department of Medicine, Division of Rheumatology, University of California, Los Angeles, Los Angeles, California, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - John B Harley
- Rheumatology Division and Autoimmune Genomics Center, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Bruce C Richardson
- Division of Rheumatology, University of Michigan, Ann Arbor, Michigan, USA
- US Department of Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Amr H Sawalha
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, USA
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