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Song X, Ru M, Steinsnyder Z, Tkachuk K, Kopp RP, Sullivan J, Gümüş ZH, Offit K, Joseph V, Klein RJ. SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiol Biomarkers Prev 2022; 31:1466-1472. [PMID: 35511739 PMCID: PMC9250608 DOI: 10.1158/1055-9965.epi-22-0053] [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: 01/14/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown. METHODS These variants were genotyped in a cohort of 1,298 patients. Samples were linked with age, PSA level, Gleason score, cancer stage at surgery, and times from surgery to biochemical recurrence to death from prostate cancer. SNPs rs2702185 and rs73055188 were tested for association with prostate cancer-specific survival time using a multivariate Cox proportional hazard model. SNP rs2702185 was further tested for association with time to biochemical recurrence and time from biochemical recurrence to death with a multi-state model. RESULTS SNP rs2702185 at SMG7 was associated with prostate cancer-specific survival time, specifically the time from biochemical recurrence to prostate cancer death (HR, 2.5; 95% confidence interval, 1.4-4.5; P = 0.0014). Nine variants were in linkage disequilibrium (LD) with rs2702185; one, rs10737246, was found to be most likely to be functional based on LD patterns and overlap with open chromatin. Patterns of open chromatin and correlation with gene expression suggest that this SNP may affect expression of SMG7 in T cells. CONCLUSIONS The SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional. IMPACT These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.
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Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Meng Ru
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Ryan P. Kopp
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239 USA
| | - John Sullivan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zeynep H. Gümüş
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Robert J. Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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3
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Owen KA, Grammer AC, Lipsky PE. Deconvoluting the heterogeneity of SLE: The contribution of ancestry. J Allergy Clin Immunol 2021; 149:12-23. [PMID: 34857396 DOI: 10.1016/j.jaci.2021.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Systemic lupus erythematosus (SLE) is a multiorgan autoimmune disorder with a prominent genetic component. Evidence has shown that individuals of non-European ancestry experience the disease more severely, exhibiting an increased incidence of cardiovascular disease, renal involvement, and tissue damage compared with European ancestry populations. Furthermore, there seems to be variability in the response of individuals within different ancestral groups to standard medications, including cyclophosphamide, mycophenolate, rituximab, and belimumab. Although the widespread application of candidate gene, Immunochip, and genome-wide association studies has contributed to our understanding of the link between genetic variation (typically single nucleotide polymorphisms) and SLE, despite decades of research it is still unclear why ancestry remains a key determinant of poorer outcome in non-European-ancestry patients with SLE. Here, we will discuss the impact of ancestry on SLE disease burden in patients from diverse backgrounds and highlight how research efforts using novel bioinformatic and pathway-based approaches have begun to disentangle the complex genetic architecture linking ancestry to SLE susceptibility. Finally, we will illustrate how genomic and gene expression analyses can be combined to help identify novel molecular pathways and drug candidates that might uniquely impact SLE among different ancestral populations.
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4
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Suzuki A, Guerrini MM, Yamamoto K. Functional genomics of autoimmune diseases. Ann Rheum Dis 2021; 80:689-697. [PMID: 33408079 DOI: 10.1136/annrheumdis-2019-216794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022]
Abstract
For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.
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Affiliation(s)
- Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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5
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Kwon YC, Chun S, Kim K, Mak A. Update on the Genetics of Systemic Lupus Erythematosus: Genome-Wide Association Studies and Beyond. Cells 2019; 8:cells8101180. [PMID: 31575058 PMCID: PMC6829439 DOI: 10.3390/cells8101180] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of complex etiology that primarily affects women of childbearing age. The development of SLE is attributed to the breach of immunological tolerance and the interaction between SLE-susceptibility genes and various environmental factors, resulting in the production of pathogenic autoantibodies. Working in concert with the innate and adaptive arms of the immune system, lupus-related autoantibodies mediate immune-complex deposition in various tissues and organs, leading to acute and chronic inflammation and consequent end-organ damage. Over the past two decades or so, the impact of genetic susceptibility on the development of SLE has been well demonstrated in a number of large-scale genetic association studies which have uncovered a large fraction of genetic heritability of SLE by recognizing about a hundred SLE-susceptibility loci. Integration of genetic variant data with various omics data such as transcriptomic and epigenomic data potentially provides a unique opportunity to further understand the roles of SLE risk variants in regulating the molecular phenotypes by various disease-relevant cell types and in shaping the immune systems with high inter-individual variances in disease susceptibility. In this review, the catalogue of SLE susceptibility loci will be updated, and biological signatures implicated by the SLE-risk variants will be critically discussed. It is optimistically hoped that identification of SLE risk variants will enable the prognostic and therapeutic biomarker armamentarium of SLE to be strengthened, a major leap towards precision medicine in the management of the condition.
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Affiliation(s)
- Young-Chang Kwon
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222–1 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea;
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| | - Anselm Mak
- Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
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6
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Fike AJ, Elcheva I, Rahman ZSM. The Post-GWAS Era: How to Validate the Contribution of Gene Variants in Lupus. Curr Rheumatol Rep 2019; 21:3. [DOI: 10.1007/s11926-019-0801-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Chen YC, Chiu WC, Su FM, Chen JF. Generalized estimating equation model to compare drug effects on synovitis of the dominant wrist in severe rheumatoid arthritis between tocilizumab versus adalimumab versus abatacept using high-resolution ultrasound. Int J Rheum Dis 2018; 21:1695-1700. [DOI: 10.1111/1756-185x.13188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying-Chou Chen
- Department of Rheumatology; Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Taiwan
| | - Wen-Chan Chiu
- Department of Rheumatology; Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Taiwan
| | - Fu-Mei Su
- Department of Rheumatology; Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Taiwan
| | - Jia-Feng Chen
- Department of Rheumatology; Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Taiwan
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8
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Higgins SP, Tang Y, Higgins CE, Mian B, Zhang W, Czekay RP, Samarakoon R, Conti DJ, Higgins PJ. TGF-β1/p53 signaling in renal fibrogenesis. Cell Signal 2017; 43:1-10. [PMID: 29191563 DOI: 10.1016/j.cellsig.2017.11.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Fibrotic disorders of the renal, pulmonary, cardiac, and hepatic systems are associated with significant morbidity and mortality. Effective therapies to prevent or curtail the advancement to organ failure, however, remain a major clinical challenge. Chronic kidney disease, in particular, constitutes an increasing medical burden affecting >15% of the US population. Regardless of etiology (diabetes, hypertension, ischemia, acute injury, urologic obstruction), persistently elevated TGF-β1 levels are causatively linked to the activation of profibrotic signaling networks and disease progression. TGF-β1 is the principal driver of renal fibrogenesis, a dynamic pathophysiologic process that involves tubular cell injury/apoptosis, infiltration of inflammatory cells, interstitial fibroblast activation and excess extracellular matrix synthesis/deposition leading to impaired kidney function and, eventually, to chronic and end-stage disease. TGF-β1 activates the ALK5 type I receptor (which phosphorylates SMAD2/3) as well as non-canonical (e.g., src kinase, EGFR, JAK/STAT, p53) pathways that collectively drive the fibrotic genomic program. Such multiplexed signal integration has pathophysiological consequences. Indeed, TGF-β1 stimulates the activation and assembly of p53-SMAD3 complexes required for transcription of the renal fibrotic genes plasminogen activator inhibitor-1, connective tissue growth factor and TGF-β1. Tubular-specific ablation of p53 in mice or pifithrin-α-mediated inactivation of p53 prevents epithelial G2/M arrest, reduces the secretion of fibrotic effectors and attenuates the transition from acute to chronic renal injury, further supporting the involvement of p53 in disease progression. This review focuses on the pathophysiology of TGF-β1-initiated renal fibrogenesis and the role of p53 as a regulator of profibrotic gene expression.
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Affiliation(s)
- Stephen P Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Yi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Craig E Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Badar Mian
- Department of Surgery, Albany Medical College, Albany, NY 12208, United States; The Urological Institute of Northeastern New York, Albany Medical College, Albany, NY 12208, United States.
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Ralf-Peter Czekay
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - David J Conti
- Department of Surgery, Albany Medical College, Albany, NY 12208, United States; Division of Transplantation Surgery, Albany Medical College, Albany, NY 12208, United States.
| | - Paul J Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States; Department of Surgery, Albany Medical College, Albany, NY 12208, United States; The Urological Institute of Northeastern New York, Albany Medical College, Albany, NY 12208, United States.
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9
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Kim JJ, Yun SW, Yu JJ, Yoon KL, Lee KY, Kil HR, Kim GB, Han MK, Song MS, Lee HD, Ha KS, Sohn S, Johnson TA, Takahashi A, Kubo M, Tsunoda T, Ito K, Onouchi Y, Hong YM, Jang GY, Lee JK. A genome-wide association analysis identifies NMNAT2 and HCP5 as susceptibility loci for Kawasaki disease. J Hum Genet 2017; 62:1023-1029. [PMID: 28855716 DOI: 10.1038/jhg.2017.87] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/11/2017] [Accepted: 07/31/2017] [Indexed: 02/07/2023]
Abstract
Kawasaki disease (KD), a systemic vasculitis of infants and children, manifests as fever and mucocutaneous inflammation. Although its etiology is largely unknown, the epidemiological data suggest that genetic factors are important in KD susceptibility. To identify genetic variants influencing KD susceptibility, we performed a genome-wide association study (GWAS) and replication study using a total of 915 children with KD and 4553 controls in the Korean population. Six single-nucleotide polymorphisms (SNPs) in three loci were associated significantly with KD susceptibility (P<1.0 × 10-5), including the previously reported BLK locus (rs6993775, odds ratio (OR)=1.52, P=2.52 × 10-11). The other two loci were newly identified: NMNAT2 on chromosome 1q25.3 (rs2078087, OR=1.33, P=1.15 × 10-6) and the human leukocyte antigen (HLA) region on chromosome 6p21.3 (HLA-C, HLA-B, MICA and HCP5) (rs9380242, rs9378199, rs9266669 and rs6938467; OR=1.33-1.51, P=8.93 × 10-6 to 5.24 × 10-8). Additionally, SNP rs17280682 in NLRP14 was associated significantly with KD with a family history (18 cases vs 4553 controls, OR=6.76, P=5.46 × 10-6). These results provide new insights into the pathogenesis and pathophysiology of KD.
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Affiliation(s)
- Jae-Jung Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Sin Weon Yun
- Department of Pediatrics, Chung-Ang University Hospital, Seoul, Korea
| | - Jeong Jin Yu
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Kyung Lim Yoon
- Department of Pediatrics, Kyung Hee University Hospital at Gangdong, Seoul, Korea
| | - Kyung-Yil Lee
- Department of Pediatrics, The Catholic University of Korea, Daejeon St Mary's Hospital, Daejeon, Korea
| | - Hong-Ryang Kil
- Department of Pediatrics, Chungnam National University Hospital, Daejeon, Korea
| | - Gi Beom Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Myung-Ki Han
- Department of Pediatrics, University of Ulsan, Gangneung Asan Hospital, Gangneung, Korea
| | - Min Seob Song
- Department of Pediatrics, Inje University Paik Hospital, Busan, Korea
| | - Hyoung Doo Lee
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Kee Soo Ha
- Department of Pediatrics, Korea University Hospital, Seoul, Korea
| | - Sejung Sohn
- Department of Pediatrics, Ewha Womans University Hospital, Seoul, Korea
| | - Todd A Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Omics Informatics, Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshihiro Onouchi
- Laboratory for Cardiovascular diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Young Mi Hong
- Department of Pediatrics, Ewha Womans University Hospital, Seoul, Korea
| | - Gi Young Jang
- Department of Pediatrics, Korea University Hospital, Seoul, Korea
| | - Jong-Keuk Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
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10
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Abstract
PURPOSE OF REVIEW To describe the recent studies on the genetics of systemic lupus erythematosus (SLE) and Sjögren's syndrome. RECENT FINDINGS We overview the most recent findings on the genetic susceptibility of the diseases and provide information on their genetic similarities and differences. SUMMARY SLE and Sjögren's syndrome are two closely related systemic autoimmune diseases that share multiple clinical and molecular aspects, including a significant number of susceptibility genes. Several genome-wide association studies were recently published in different populations that provide a better picture of their molecular mechanisms. It is becoming clear that their genetic architecture is quite well established, but more information is required on expression quantitative trait loci, epigenetic genome-wide analyses, gene × gene interactions and the role of rare variants.
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11
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Teruel M, Alarcón-Riquelme ME. The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned. J Autoimmun 2016; 74:161-175. [PMID: 27522116 DOI: 10.1016/j.jaut.2016.08.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Abstract
The genome-wide association study is a free-hypothesis approach based on screening of thousands or even millions of genetic variants distributed throughout the whole human genome in relation to a phenotype. The relevant role of the genome-wide association studies in the last decade is undisputed because it has permitted to elucidate multiple risk genetic factors associated with the susceptibility to several human complex diseases. Regarding systemic lupus erythematosus (SLE) this approach has allowed to identify more than 60 risk loci for SLE susceptibility across populations to date, increasing our understanding on the pathogenesis of this disease. We present the latest findings in the genetic of SLE across populations using genome-wide approaches. These studies revealed that most of the genetic risk is shared across borders and ethnicities. Finally, we focus on describing the most important risk loci for SLE attempting to cover the genetic findings in relation to functional polymorphisms, such as missense single nucleotide polymorphisms (SNPs) or regulatory variants involved in the development of the disease. The functional studies try to identify the causality of some GWAS-associated variants, many of which fall in non-coding regions of the genome, suggesting a regulatory role. Many loci show an environmental interaction, another aspect revealed by the studies of epigenetic modifications and those associated with genetic variants. Finally, new-generation sequencing technologies can open other paths in the research on SLE genetics, the role of rare variants and the detailed identification of causal regulatory variation. The clinical relevance of the genetic factors will be shown when we are able to use them or in combination with other molecular measurements to re-classify a heterogeneous disease such as SLE.
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Affiliation(s)
- Maria Teruel
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain.
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research, GENYO, Pfizer/University of Granada/Andalusian Government, PTS, Granada, 18016, Spain; Institute of Environmental Medicine, Karolinska Institute, Stockholm, 171 67, Sweden.
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12
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Abstract
The genes associated with Sjögren syndrome (SS) can be assigned to the NF-kB pathway, the IFN signaling pathway, lymphocyte signaling, and antigen presentation. The frequencies of risk variants show they are common with modest genetic effects. The strongest genetic association outside the human leukocyte antigen region is in IRF5, a gene relevant in the IFN signaling pathway and for B cell differentiation. Although no association has been found with the NF-kB gene itself, associations in TNFAIP3 and TNIP1 (both genome-wide significant), VCAM1 and IRAK1BP (both suggestive), point to genetic explanations for dysregulation of the NF-kB pathway in SS.
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Affiliation(s)
- Tove Ragna Reksten
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, The Laboratory Building, Haukeland University Hospital, Jonas Lies vei 87, N-5021 Bergen, Norway
| | - Christopher J Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, MBSB 451, Oklahoma City, OK 73104, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, MBSB 451, Oklahoma City, OK 73104, USA.
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