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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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2
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Wang T, Ren Y, Yin X, Sun Y. Editorial: Genetics of inflammatory and immune diseases. Front Genet 2024; 14:1355794. [PMID: 38259613 PMCID: PMC10801178 DOI: 10.3389/fgene.2023.1355794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Affiliation(s)
- Tianyu Wang
- Hospital for Skin Diseases, Shandong First Medical University, Jinan, Shandong, China
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yunqing Ren
- Department of Dermatology, Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xianyong Yin
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States
| | - Yonghu Sun
- Hospital for Skin Diseases, Shandong First Medical University, Jinan, Shandong, China
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
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Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
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Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
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rs9459874 and rs1012656 in CCR6/FGFR1OP confer susceptibility to primary biliary cholangitis. J Autoimmun 2021; 126:102775. [PMID: 34864633 DOI: 10.1016/j.jaut.2021.102775] [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: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022]
Abstract
Primary biliary cholangitis (PBC) is a chronic cholestatic autoimmune liver disease that appears to be strongly influenced by genetic factors. Recently, an international meta-analysis of genome-wide association studies (GWAS) identified CC-Motif Chemokine Receptor-6 (CCR6) and FGFR1 Oncogene-Partner (FGFR1OP) as PBC-susceptibility genes. However, the lead single nucleotide polymorphisms (SNPs) of CCR6/FGFR1OP showed low linkage disequilibrium with each other in East Asian and European populations. Additionally, the primary functional variants and the molecular mechanisms responsible for PBC-susceptibility remain unclear. Here, among the PBC-susceptibility SNPs identified by high-density association mapping in our previous meta-GWAS (Patients: n = 10,516; healthy controls: n = 20,772) within the CCR6/FGFR1OP locus, rs9459874 and rs1012656 were identified as primary functional variants. These functional variants accounted for the effects of GWAS-identified lead SNPs in CCR6/FGFR1OP. Additionally, the roles of rs9459874 and rs1012656 in regulating FGFR1OP transcription and CCR6 translation, respectively, were supported by expression quantitative trait loci (eQTL) analysis and gene editing technology using the CRISPR/Cas9 system. Immunohistochemistry showed higher expression of CCR6 protein in the livers of patients with PBC than in those of a non-diseased control. In conclusion, we identified primary functional variants in CCR6/FGFR1OP and revealed the molecular mechanisms by which these variants confer PBC-susceptibility in an eQTL-dependent or -independent manner. The approach in this study is applicable for the elucidation of the pathogenesis of other autoimmune disorders in which CCR6/FGFR1OP is known as a susceptibility locus, as well as PBC.
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Jia X, Yamamura T, Gbadegesin R, McNulty MT, Song K, Nagano C, Hitomi Y, Lee D, Aiba Y, Khor SS, Ueno K, Kawai Y, Nagasaki M, Noiri E, Horinouchi T, Kaito H, Hamada R, Okamoto T, Kamei K, Kaku Y, Fujimaru R, Tanaka R, Shima Y, Baek J, Kang HG, Ha IS, Han KH, Yang EM, Abeyagunawardena A, Lane B, Chryst-Stangl M, Esezobor C, Solarin A, Dossier C, Deschênes G, Vivarelli M, Debiec H, Ishikura K, Matsuo M, Nozu K, Ronco P, Cheong HI, Sampson MG, Tokunaga K, Iijima K. Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome. Kidney Int 2020; 98:1308-1322. [PMID: 32554042 DOI: 10.1016/j.kint.2020.05.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/23/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
To understand the genetics of steroid-sensitive nephrotic syndrome (SSNS), we conducted a genome-wide association study in 987 childhood SSNS patients and 3,206 healthy controls with Japanese ancestry. Beyond known associations in the HLA-DR/DQ region, common variants in NPHS1-KIRREL2 (rs56117924, P=4.94E-20, odds ratio (OR) =1.90) and TNFSF15 (rs6478109, P=2.54E-8, OR=0.72) regions achieved genome-wide significance and were replicated in Korean, South Asian and African populations. Trans-ethnic meta-analyses including Japanese, Korean, South Asian, African, European, Hispanic and Maghrebian populations confirmed the significant associations of variants in NPHS1-KIRREL2 (Pmeta=6.71E-28, OR=1.88) and TNFSF15 (Pmeta=5.40E-11, OR=1.33) loci. Analysis of the NPHS1 risk alleles with glomerular NPHS1 mRNA expression from the same person revealed allele specific expression with significantly lower expression of the transcript derived from the risk haplotype (Wilcox test p=9.3E-4). Because rare pathogenic variants in NPHS1 cause congenital nephrotic syndrome of the Finnish type (CNSF), the present study provides further evidence that variation along the allele frequency spectrum in the same gene can cause or contribute to both a rare monogenic disease (CNSF) and a more complex, polygenic disease (SSNS).
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Affiliation(s)
- Xiaoyuan Jia
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rasheed Gbadegesin
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Michelle T McNulty
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA
| | - Kyuyong Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Dongwon Lee
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuko Ueno
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eisei Noiri
- Department of Hemodialysis and Apheresis, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshitsugu Kaku
- Department of Nephrology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Rika Fujimaru
- Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | | | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Jeju, Korea
| | - Eun Mi Yang
- Department of Pediatrics, Chonnam National University Children's Hospital, Gwangju, Korea
| | | | - Asiri Abeyagunawardena
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Brandon Lane
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Megan Chryst-Stangl
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher Esezobor
- Department of Paediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Adaobi Solarin
- Department of Pediatrics, Lagos State University Teaching Hospital, Ikeja, Nigeria
| | | | - Claire Dossier
- Department of Paediatric Nephrology, Public Assistance Hospital of Paris, Robert-Debré Hospital, Paris, France
| | - Georges Deschênes
- Center of Research on Inflammation, Institut National de la Santé et de la Recherche Médicale UMR 1149, University Sorbonne-Paris, Paris, France
| | | | - Marina Vivarelli
- Division of Nephrology and Dialysis, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Hanna Debiec
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan; KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Pierre Ronco
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Matthew G Sampson
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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Mi Z, Liu H, Zhang F. Advances in the Immunology and Genetics of Leprosy. Front Immunol 2020; 11:567. [PMID: 32373110 PMCID: PMC7176874 DOI: 10.3389/fimmu.2020.00567] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/12/2020] [Indexed: 12/21/2022] Open
Abstract
Leprosy, a disease caused by the intracellular parasite Mycobacterium leprae or Mycobacterium lepromatosis, has affected humans for more than 4,000 years and is a stigmatized disease even now. Since clinical manifestations of leprosy patients present as an immune-related spectrum, leprosy is regarded as an ideal model for studying the interaction between host immune response and infection; in fact, the landscape of leprosy immune responses has been extensively investigated. Meanwhile, leprosy is to some extent a genetic disease because the genetic factors of hosts have long been considered major contributors to this disease. Many immune-related genes have been discovered to be associated with leprosy. However, immunological and genetic findings have rarely been studied and discussed together, and as a result, the effects of gene variants on leprosy immune responses and the molecular mechanisms of leprosy pathogenesis are largely unknown. In this context, we summarized advances in both the immunology and genetics of leprosy and discussed the perspective of the combination of immunological and genetic approaches in studying the molecular mechanism of leprosy pathogenesis. In our opinion, the integrating of immunological and genetic approaches in the future may be promising to elucidate the molecular mechanism of leprosy onset and how leprosy develops into different types of leprosy.
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Affiliation(s)
- Zihao Mi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
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Zhang M, Liu S, Xu J, Lv S, Fan Y, Zhang Y, Zhang Y, Wu Y, Su Y, Yu H, Song S, He J, Li H. TNFSF15 Polymorphisms are Associated with Graves’ Disease and Graves’ Ophthalmopathy in a Han Chinese Population. Curr Eye Res 2019; 45:888-895. [PMID: 31869260 DOI: 10.1080/02713683.2019.1705494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Meiqin Zhang
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Shichun Liu
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Ji Xu
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Sha Lv
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Yujie Fan
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Yao Zhang
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Yongye Zhang
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Yufei Wu
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Yang Su
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Hongsong Yu
- Department of Immunology, Zunyi Medical University, Guizhou, China
| | - Shengfang Song
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Jianhua He
- Department of Nuclear Medicine, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
| | - Hua Li
- Department of Ophthalmology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
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8
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Xu WD, Fu L, Liu XY, Wang JM, Yuan ZC, Su LC, Huang AF. Association between TL1A gene polymorphisms and systemic lupus erythematosus in a Chinese Han population. J Cell Physiol 2019; 234:22543-22553. [PMID: 31081141 DOI: 10.1002/jcp.28818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 01/28/2023]
Abstract
Our previous studies showed elevated tumor necrosis factor-like ligand 1 aberrance (TL1A) expression in systemic lupus erythematosus (SLE). However, TL1A polymorphisms with SLE susceptibility remain to be elucidated. In addition, we made meta-analysis to evaluate the relationship of TL1A polymorphisms and autoimmune diseases owing to inconsistent results. The present research was carried out by 404 SLE, 150 primary Sjogren's syndrome (pSS) patients, and 574 healthy individuals. Three TL1A polymorphisms (rs3810936, rs6478109, rs7848647) were genotyped using TaqMan genotyping assay. Then, the meta-analysis was performed by collecting the present case-control study and previously published research. Results showed that genotypes of rs3810936, rs7848647 were different between SLE patients and healthy controls, whereas no significant association was observed in the three polymorphisms and pSS patients. Genotypes distribution of rs6478109, rs7848647 were strongly related to lupus nephritis within SLE (p = 0.004, p = 0.011), respectively. Moreover, combined meta-analysis consisted of ten comparative research involving 4,305 patients and 5,600 controls. An association between autoimmune diseases and rs6478109 polymorphism was found. Our findings indicate that gene polymorphisms (rs3810936, rs7848647) of TL1A might correlate with lupus.
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Affiliation(s)
- Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Lu Fu
- Laboratory Animal Center, Southwest Medical University, Luzhou, China
| | - Xiao-Yan Liu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Jia-Min Wang
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Zhi-Chao Yuan
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Lin-Chong Su
- Department of Rheumatology and Immunology, Hubei Minzu University, Enshi, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, China
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9
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Valatas V, Kolios G, Bamias G. TL1A (TNFSF15) and DR3 (TNFRSF25): A Co-stimulatory System of Cytokines With Diverse Functions in Gut Mucosal Immunity. Front Immunol 2019; 10:583. [PMID: 30972074 PMCID: PMC6445966 DOI: 10.3389/fimmu.2019.00583] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
TL1A and its functional receptor DR3 are members of the TNF/TNFR superfamilies of proteins. Binding of APC-derived TL1A to lymphocytic DR3 provides co-stimulatory signals for activated lymphocytes. DR3 signaling affects the proliferative activity of and cytokine production by effector lymphocytes, but also critically influences the development and suppressive function of regulatory T-cells. DR3 was also found to be highly expressed by innate lymphoid cells (ILCS), which respond to stimulation by TL1A. Several recent studies with transgenic and knockout mice as well as neutralizing or agonistic antibodies for these two proteins, have clearly shown that TL1A/DR3 are important mediators of several chronic immunological disorders, including Inflammatory Bowel Disease (IBD). TL1A and DR3 are abundantly localized at inflamed intestinal areas of patients with IBD and mice with experimental ileitis or colitis and actively participate in the immunological pathways that underlie mucosal homeostasis and intestinal inflammation. DR3 signaling has demonstrated a dichotomous role in mucosal immunity. On the one hand, during acute mucosal injury it exerts protective functions by ameliorating the severity of acute inflammatory responses and facilitating tissue repair. On the other hand, it critically participates in the pro-inflammatory pathways that underlie chronic inflammatory responses, such as those that take place in IBD. These effects are mediated through modulation of the relative mucosal abundance and function of Th1, Th2, Th17, Th9, and Treg lymphocytes, but also of all types of ILCs. Recently, an important role was demonstrated for TL1A/DR3 as potential mediators of intestinal fibrosis that is associated with the presence of gut inflammation. These accumulating data have raised the possibility that TL1A/DR3 pathways may represent a valid therapeutic target for chronic immunological diseases. Nevertheless, applicability of such a therapeutic approach will greatly rely on the net result of TL1A/DR3 manipulation on the various cell populations that will be affected by this approach.
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Affiliation(s)
- Vassilis Valatas
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Giorgos Bamias
- GI-unit, National & Kapodistrian University of Athens, Third Department of Internal Medicine, Sotiria Hospital, Athens, Greece
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Distinct Expression Patterns of Two Tumor Necrosis Factor Superfamily Member 15 Gene Isoforms in Human Colon Cancer. Dig Dis Sci 2019; 64:1857-1867. [PMID: 30788683 PMCID: PMC6584785 DOI: 10.1007/s10620-019-05507-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 01/29/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Tumor necrosis factor superfamily member 15 (TNFSF15) gene is involved in development of several cancers. It encodes two proteins: tumor necrosis factor ligand-related molecule 1A (TL1A) and vascular endothelial growth inhibitor 192 (VEGI-192). The main receptor for TL1A is death receptor 3 (DR3). AIMS We investigated expression of TL1A, VEGI-192, and DR3 transcripts in different stages of colon cancer and compared them with survival of patients. We also aimed to reveal possible effects of microsatellite instability (MSI) and selected TNFSF15 single-nucleotide polymorphisms (SNPs) on expression of this gene. METHODS Forty-five healthy individuals and 95 colon cancer patients were included in the study. Expression of VEGI-192, TL1A, and DR3 was measured by quantitative PCR. SNP and MSI analyses were performed on DNA isolated from normal or cancer tissue. RESULTS Expression of VEGI-192 and TL1A was elevated in colon cancer, although the level of VEGI-192 decreased, while the level of TL1A increased with the progression of cancer. Patients with low expression of TL1A and/or high expression of VEGI-192 in tumor-transformed tissue showed longer survival. DR3 expression was decreased in the cancer, but it did not change with the tumor progression. Alleles T of rs6478108 and G of rs6478109 SNPs were associated with elevated expression of the TNFSF15 gene. There was no relation between the MSI status and TNFSF15 expression levels. CONCLUSIONS Expression of the TNFSF15 gene isoforms was associated with the progression of colon cancer. Levels of TL1A and VEGI-192 transcripts can be considered as independent prognostic factors for colon cancer.
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Hitomi Y, Nakatani K, Kojima K, Nishida N, Kawai Y, Kawashima M, Aiba Y, Nagasaki M, Nakamura M, Tokunaga K. NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. Cell Mol Gastroenterol Hepatol 2018; 7:515-532. [PMID: 30528300 PMCID: PMC6396435 DOI: 10.1016/j.jcmgh.2018.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Primary biliary cholangitis (PBC) is a chronic and cholestatic liver disease that eventually leads to cirrhosis and hepatic failure. We recently identified several susceptibility genes included NFKB1 and MANBA for PBC in the Japanese population by genome-wide association study. However, the primary functional variants in the NFKB1/MANBA region and the molecular mechanism for conferring disease susceptibility to PBC have not yet been clarified. METHODS We performed high-density association mapping based on a single-nucleotide polymorphism (SNP) imputation analysis, using data from a whole-genome sequence reference panel of 1070 Japanese individuals and the previous genome-wide association study (1389 PBC patients, 1508 healthy controls). Among SNPs (P < 5.0 × 10-7) in the NFKB1/MANBA region, putative primary functional variants and the molecular mechanism for conferring disease susceptibility to PBC were identified by in silico/in vitro functional analysis. RESULTS Among the SNPs in the NFKB1/MANBA region, rs17032850 and rs227361, which changed the binding of transcription factors lymphoid enhancer-binding factor 1 (LEF-1) and retinoid X receptor α (RXRα), respectively, were identified as putative primary functional variants that regulate gene expression. In addition, expression-quantitative trait locus data and gene editing using a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system supported the potential role of rs17032850 and rs227361 in regulating NFKB1 and MANBA expression, respectively. CONCLUSIONS We identified independent putative primary functional variants in NFKB1/MANBA and showed the distinct molecular mechanism by which each putative primary functional variant conferred susceptibility to PBC. Our approach was useful to dissect the pathogenesis not only of PBC, but also other digestive diseases in which NFKB1/MANBA has been reported as a susceptibility locus.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Correspondence Address correspondence to: Yuki Hitomi, PhD, Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. fax: (81) 3-5802-8619.
| | - Ken Nakatani
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Japan Science and Technology Agency, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Minoru Nakamura
- Headquarters of Primary Biliary Cholangitis (PBC) Research in National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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Richard AC, Peters JE, Savinykh N, Lee JC, Hawley ET, Meylan F, Siegel RM, Lyons PA, Smith KGC. Reduced monocyte and macrophage TNFSF15/TL1A expression is associated with susceptibility to inflammatory bowel disease. PLoS Genet 2018; 14:e1007458. [PMID: 30199539 PMCID: PMC6130856 DOI: 10.1371/journal.pgen.1007458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 06/01/2018] [Indexed: 12/15/2022] Open
Abstract
Chronic inflammation in inflammatory bowel disease (IBD) results from a breakdown of intestinal immune homeostasis and compromise of the intestinal barrier. Genome-wide association studies have identified over 200 genetic loci associated with risk for IBD, but the functional mechanisms of most of these genetic variants remain unknown. Polymorphisms at the TNFSF15 locus, which encodes the TNF superfamily cytokine commonly known as TL1A, are associated with susceptibility to IBD in multiple ethnic groups. In a wide variety of murine models of inflammation including models of IBD, TNFSF15 promotes immunopathology by signaling through its receptor DR3. Such evidence has led to the hypothesis that expression of this lymphocyte costimulatory cytokine increases risk for IBD. In contrast, here we show that the IBD-risk haplotype at TNFSF15 is associated with decreased expression of the gene by peripheral blood monocytes in both healthy volunteers and IBD patients. This association persists under various stimulation conditions at both the RNA and protein levels and is maintained after macrophage differentiation. Utilizing a "recall-by-genotype" bioresource for allele-specific expression measurements in a functional fine-mapping assay, we localize the polymorphism controlling TNFSF15 expression to the regulatory region upstream of the gene. Through a T cell costimulation assay, we demonstrate that genetically regulated TNFSF15 has functional relevance. These findings indicate that genetically enhanced expression of TNFSF15 in specific cell types may confer protection against the development of IBD.
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Affiliation(s)
- Arianne C. Richard
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States of America
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James E. Peters
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Natalia Savinykh
- NIHR Cambridge BRC Cell Phenotyping Hub, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - James C. Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eric T. Hawley
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Françoise Meylan
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Richard M. Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Paul A. Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kenneth G. C. Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
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