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Yuan Y, You Y, Wen Y, Liu J, Li H, Zhang Y, Wu N, Liu S, Zhang S, Chen J, Ai J, Zhang W, Zhang Y. Identification of novel genetic loci GAL3ST4 and CHGB involved in susceptibility to leprosy. Sci Rep 2017; 7:16352. [PMID: 29180661 PMCID: PMC5703986 DOI: 10.1038/s41598-017-16422-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/30/2017] [Indexed: 01/26/2023] Open
Abstract
Leprosy has long been thought to have a strong genetic component, and so far, only positional cloning and genomewide association studies have been used to study the genetic susceptibility to leprosy,while whole exome sequencing (WES) approach has not yet been applied. In this study, we used WES approach on four leprosy patients and four healthy control relatives from two leprosy families. We found three new susceptible loci of leprosy, one in GAL3ST4 and two in CHGB. We went on to validate the findings of WES using 151 leprosy cases and 226 healthy controls by Sanger sequencing. Stratified by gender, GAL3ST4 was found to be the susceptible gene only for the female population, and CHGB48 and CHGB23 were susceptibile to leprosy for the male population, respectively). Moreover, the gene expression levels of the three susceptible loci were measured by real-time PCR after the stimulation by M. leprae antigens in the PBMC (peripheral blood mononuclear cells) of 69 healthy people. The results showed that the female subjects with high frequent genotype in GAL3ST4 had a fivefold elevated expression. We suggest the polymorphisms in GAL3ST4 in different population are associated with increased risk of leprosy.
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Affiliation(s)
- Youhua Yuan
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Clinical laboratory, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yuangang You
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
| | - Yan Wen
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jian Liu
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Huanying Li
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yumeng Zhang
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nan Wu
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuang Liu
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanshan Zhang
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingwen Ai
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Zhang
- Key Laboratory of Medical Virology, Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China. .,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.
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Li GD, Wang D, Zhang DF, Xiang Q, Feng JQ, Li XA, Li YY, Yao YG. Fine mapping of the GWAS loci identifies SLC35D1 and IL23R as potential risk genes for leprosy. J Dermatol Sci 2016; 84:322-329. [PMID: 27712858 DOI: 10.1016/j.jdermsci.2016.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND Previous genome-wide association study (GWAS) identified two new leprosy associated loci (1p31.3 [rs3762318] and 6q24.3 [rs2275606]). However, there were insufficient validations in independent populations. OBJECTIVE To validate the association and to map the potentially causal variants/genes underlying the association between the confirmed GWAS hit and leprosy. METHODS We genotyped 10 variants in the regions encompassing the two loci in 1110 Han Chinese subjects with and without leprosy, followed by expression quantitative trait loci (eQTL), mRNA expression profiling, and network analysis. We further sequenced the exon region of four genes that were located in the confirmed GWAS hit region in 80 leprosy patients and 99 individuals without leprosy. RESULTS We validated the positive association of rs3762318 with multibacillary leprosy (P=7.5×10-4), whereas the association of rs2275606 could not be validated. eQTL analysis showed that both the GWAS locus rs3762318 and one surrounding positively associated SNP rs2144658 (P=1.8×10-3) significantly affected the mRNA expression of a nearby gene SLC35D1, which might be involved in metabolism. Moreover, SLC35D1 was differentially expressed in skin tissues of leprosy patients, and the differential expression pattern was consistent among leprosy subtypes. Rare damaging missense variants in IL23R were significantly enriched in leprosy patients. CONCLUSION Our results supported the positive association between the GWAS reported rs3762318 and leprosy, and SLC35D1 and IL23R might be the causal genes.
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Affiliation(s)
- Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Qun Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Jia-Qi Feng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Xiao-An Li
- Yuxi City Center for Disease Control and Prevention, Yuxi, Yunnan 653100, China
| | - Yu-Ye Li
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
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Silva GAV, Ramasawmy R, Boechat AL, Morais AC, Carvalho BKS, Sousa KBA, Souza VC, Cunha MGS, Barletta-Naveca RH, Santos MP, Naveca FG. Association of TNF -1031 C/C as a potential protection marker for leprosy development in Amazonas state patients, Brazil. Hum Immunol 2015; 76:137-41. [PMID: 25636570 DOI: 10.1016/j.humimm.2015.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 12/26/2014] [Accepted: 01/14/2015] [Indexed: 12/30/2022]
Abstract
Polymorphisms present in the TNF promoter region has shown to influence the gene transcription. Leprosy displays different clinical manifestations according to the immune responses of the individual infected with Mycobacterium leprae. In this study, we evaluated the single nucleotide polymorphisms (SNPs) -238 G/A (rs361525), -308 G/A (rs1800629), -857 C/T (rs1799724), -863 A/C (rs1800630) and -1031 T/C (rs1799964) in the promoter region of the TNF to see whether these SNPs influence host-susceptibility to leprosy and the different clinical manifestation. Nucleotide sequencing was performed with DNA samples from 108 leprosy patients and 253 control subjects. An association between -1031 C/C genotype and protection from leprosy was observed when leprosy patients were compared to controls (OR 0.11; 95% CI=0.01-0.82; p=0.012). The -857 C/T genotype may be associated with susceptibility to leprosy (OR=1.81; 95% CI=1.09-3.00; p=0.028). Similar genotype and allele frequencies for the SNPs -308 G/A and -238 G/A were observed between leprosy patients and control subjects. Altogether, TNF polymorphisms in the promoter region may be predictive of leprosy outcome.
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Affiliation(s)
- G A V Silva
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil.
| | - R Ramasawmy
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Amazonas, Brazil; Faculdade de Medicina, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - A L Boechat
- Laboratório de Imunologia, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - A C Morais
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil
| | - B K S Carvalho
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil
| | - K B A Sousa
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil
| | - V C Souza
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil
| | - M G S Cunha
- Fundação de Dermatologia e Venereologia Alfredo da Matta, Manaus, Amazonas, Brazil
| | - R H Barletta-Naveca
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - M P Santos
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - F G Naveca
- Instituto Leônidas e Maria Deane, FIOCRUZ Amazônia, Manaus, Amazonas, Brazil
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