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Li Y, Zeng T, Huang P, Tan W, Feng Y, Xia X, Feng Z, Shen C, Fan H, Zhu C, Yin W, Qian L, Ren C, Yue M. Investigating the role of killer cell immunoglobulin-like receptors and human leukocyte antigen genetic variants in hepatitis C virus infection. J Med Virol 2024; 96:e29776. [PMID: 38953430 DOI: 10.1002/jmv.29776] [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: 04/17/2024] [Revised: 05/30/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
The genetic diversity of killer cell immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) genes influences the host's immune response to viral pathogens. This study aims to explore the impact of five single nucleotide polymorphisms (SNPs) in KIR3DL2 and HLA-A genes on hepatitis C virus (HCV) infection. A total of 2251 individuals were included in the case-control study. SNPs including KIR3DL2 rs11672983, rs3745902, rs1654644, and HLA-A rs3869062, rs12202296 were genotyped. By controlling various confounding factors using a modified logistic regression model, as well as incorporating stratified analysis, joint effects analysis, and multidimensional bioinformatics analysis, we analyzed the relationship between SNPs and HCV infection. The logistic regression analysis showed a correlation between KIR3DL2 rs11672983 AA, KIR3DL2 rs3745902 TT, and increased HCV susceptibility (p < 0.01). Stratified analysis indicated that KIR3DL2 rs1654644 and HLA-A rs3869062 also heightened HCV susceptibility in certain subgroups. A linear trend of rising HCV infection rates was observed when combining KIR3DL2 rs11672983 AA and KIR3DL2 rs3745902 TT (ptrend = 0.007). Bioinformatics analysis suggested these SNPs' regulatory potential and their role in altering messenger RNA secondary structure, implying their functional relevance in HCV susceptibility. Our findings indicate that KIR3DL2 rs11672983 AA and KIR3DL2 rs3745902 TT are significantly associated with increased susceptibility to HCV infection.
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Affiliation(s)
- Yuwen Li
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tian Zeng
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Weilong Tan
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Yunnan Provincial Key Laboratory of Public Health and Biosafety, Kunming Medical University, Kunming, China
| | - Zepei Feng
- Department of Occupational Disease Control, Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Chao Shen
- Department of Immunization Program, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Haozhi Fan
- Department of Information, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanlong Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Tropical Diseases, the Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Wen Yin
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liqin Qian
- Department of Epidemiology, School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Chengrui Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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2
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Hu Y, Sun Y, Li T, Han W, Wang P. Identification of rat Vstm1 with conservative anti-inflammatory effect between rat and human homologs. Genomics 2024; 116:110774. [PMID: 38163574 DOI: 10.1016/j.ygeno.2023.110774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/17/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Human VSTM1 (also known as SIRL1) is an inhibitory immune checkpoint receptor involved in leukocyte activation. Identification of the homologous genes in other species, such as mice and rats, will undoubtedly contribute to functional studies and clinical applications. Here, we successfully cloned the Vstm1 gene in rats, as supported by high-throughput sequencing data. However, Vstm1 is degenerated to a pseudogene in the mouse genome. Rat Vstm1 mRNA contains a complete open reading frame (ORF) of 630 nucleotides encoding 209 amino acids. Rat Vstm1 is highly expressed in bone marrow, especially in granulocytes. The expression levels of Vstm1 gradually increase with the development of granulocytes in bone marrow but are downregulated in response to inflammatory stimuli. Rat VSTM1 does not have an immunoreceptor tyrosine-based inhibitory motif (ITIM), however, it shows a conservative function of inflammatory inhibition with human VSTM1, and both are anti-correlated with many inflammatory cytokines, such as IL-1α and TNF-α. In bone marrow-derived macrophages (BMDMs), either rat or human VSTM1 suppressed the secretion of inflammatory cytokines in response to LPS stimulation. Further analysis in lung cancer microenvironment revealed that VSTM1 is mainly expressed in myeloid cells, anti-correlated with inflammatory cytokines and associated with tumor development and metastasis.
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Affiliation(s)
- Yuzhe Hu
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Yingzhe Sun
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Ting Li
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Wenling Han
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China.
| | - Pingzhang Wang
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China.
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Wang P, Zhuang W, Zheng Z, Zhang L, Zhang X, Chen Q. Dissecting T-cell heterogeneity in esophageal squamous cell carcinoma reveals the potential role of LAIR2 in antitumor immunity. Clin Exp Immunol 2023; 214:36-49. [PMID: 37422711 PMCID: PMC10711353 DOI: 10.1093/cei/uxad073] [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: 09/11/2022] [Revised: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), one of the most commonly diagnosed and lethal malignant diseases, has a complex tumor ecosystem. An obvious requirement for T-cell-mediated tumor control is the infiltration of tumor-reactive T cells into the tumor. Here, we obtained detailed T-cell compositions in both ESCC tumors and matched peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We demonstrated that T cells in tumors and PBMCs had different compositions and functional states. ESCC tumors were rich in Treg and exhausted T cells but poor in cytotoxic and naïve T cells compared with PBMCs. The exhausted T cells showed higher exhausted signature in tumors than in PBMCs, while the cytotoxic T cells exhibited higher cytotoxic signature in PBMCs than in tumors. Our data indicated an immunosuppressive status and a defect at the level of T-cell priming in the tumor microenvironment. Leukocyte-associated Ig-like receptor-2 (LAIR2), a soluble collagen receptor that prevents the binding of human leukocyte-associated Ig-like receptor-1 (LAIR1) to collagens, was predominantly expressed in proliferating CD8+ T and Treg cells in tumors but in cytotoxic cells in PBMCs. LAIR2 could inhibit tumor metastasis, invasion, and collagen deposition via suppressing transforming growth factor-β signaling. These findings revealed differential T-cell populations in tumors and PBMCs and provided convincing evidence that LAIR2 acted as a tumor suppressor.
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Affiliation(s)
- Ping Wang
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Weitao Zhuang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Zhuojun Zheng
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Liyun Zhang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xu Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Qingyun Chen
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
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Identification of Key Genes Related to the Obesity Patients with Osteoarthritis Based on Weighted Gene Coexpression Network Analysis (WGCNA). COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8953807. [PMID: 35860189 PMCID: PMC9293492 DOI: 10.1155/2022/8953807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 11/18/2022]
Abstract
Background. Increasing evidence has suggested that obesity affects the occurrence and progression of osteoarthritis (OA). However, the underlying molecular mechanism that obesity affects the course of OA is not fully understood and remains to be studied. Methods. The gene expression profiles of the GSE117999 and GSE98460 datasets were derived from the Gene Expression Omnibus (GEO) database. Firstly, we explored the correlation between obesity and OA using chi-square test. Next, weighted gene coexpression network analysis (WGCNA) was executed to identify obesity patients with OA- (obesity OA-) related genes in the GSE117999 dataset by “WGCNA” package. Moreover, differential expression analysis was performed to select the hub genes by “limma” package. Furthermore, ingenuity pathway analysis (IPA) and functional enrichment analysis (“clusterProfiler” package) were conducted to investigate the functions of genes. Finally, the regulatory networks of hub genes and protein-protein interaction (PPI) network were created by the Cytoscape 3.5.1 software and STRING. Results. A total of 15 differentially expressed obesity OA-related genes, including 9 lncRNAs and 6 protein coding genes, were detected by overlapping 66 differentially expressed genes (DEGs) between normal BMI samples and obesity OA samples and 451 obesity OA-related genes. Moreover, CCR10, LENG8, QRFPR, UHRF1BP1, and HLA-DRB4 were identified as hub genes. IPA results indicated that the hub genes were noticeably enriched in antimicrobial response, inflammatory response, and humoral immune response. PPI network showed that CCR10 interacted more with other proteins. Gene set enrichment analysis (GSEA) indicated that the hub genes were related to protein translation, cancer, chromatin modification, antigen processing, and presentation. Conclusion. Our results further demonstrated the role of obesity in OA and might provide new targets for the treatment of obesity OA.
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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6
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Kneiber D, Kowalski EH, Amber KT. The Immunogenetics of Autoimmune Blistering Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:173-212. [DOI: 10.1007/978-3-030-92616-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Papara C, Zillikens D, Sadik CD, Baican A. MicroRNAs in pemphigus and pemphigoid diseases. Autoimmun Rev 2021; 20:102852. [PMID: 33971341 DOI: 10.1016/j.autrev.2021.102852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
Autoimmune blistering diseases are a heterogenous group of dermatological disorders characterized by blisters and erosions of the skin and/or mucous membranes induced by autoantibodies against structural proteins of the desmosome or the dermal-epidermal adhesion complex including the hemidesmosome. They consist of the two major disease groups, pemphigus and pemphigoid diseases (PPDs). The diagnosis is based on clinical findings, histopathology, direct immunofluorescence, and detection of circulating autoantibodies. The pathogenesis is not fully elucidated, prognostic factors are lacking, and to date, there is no cure for PPDs. MicroRNAs (miRNAs) represent small, non-coding RNAs that play a pivotal role in the posttranscriptional regulation of gene expression. Their dysfunction was highlighted to play a significant role in the pathogenesis of various diseases. Even though a link between miRNAs and autoimmune blistering diseases had been suggested, the research of their involvement in the pathogenesis of PPDs is still in its infancy. miRNAs hold promise for uncovering new layers in the pathogenesis of PPDs, in order to improve diagnosis and also to develop potential therapeutic options. In the current article, we provide an overview regarding current knowledge of miRNAs in terms of complex pathogenesis of PPDs, and, also, their potential role as biomarkers, predictive factors and therapeutic targets.
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Affiliation(s)
- Cristian Papara
- Department of Dermatology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Detlef Zillikens
- Department of Dermatology, Allergy, and Venereology, University of Lübeck, Lübeck, Germany; Center for Research on Inflammation of the Skin (CRIS), University of Lübeck, Lübeck, Germany.
| | - Christian D Sadik
- Department of Dermatology, Allergy, and Venereology, University of Lübeck, Lübeck, Germany; Center for Research on Inflammation of the Skin (CRIS), University of Lübeck, Lübeck, Germany
| | - Adrian Baican
- Department of Dermatology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Chen Z, Yu M, Yan J, Guo L, Zhang B, Liu S, Lei J, Zhang W, Zhou B, Gao J, Yang Z, Li X, Zhou J, Fan J, Ye Q, Li H, Xu Y, Xiao Y. PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology. Front Immunol 2021; 12:647209. [PMID: 33841428 PMCID: PMC8024580 DOI: 10.3389/fimmu.2021.647209] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Background Cholangiocarcinoma was a highly malignant liver cancer with poor prognosis, and immune infiltration status was considered an important factor in response to immunotherapy. In this investigation, we tried to locate immune infiltration related genes of cholangiocarcinoma through combination of bulk-sequencing and single-cell sequencing technology. Methods Single sample gene set enrichment analysis was used to annotate immune infiltration status in datasets of TCGA CHOL, GSE32225, and GSE26566. Differentially expressed genes between high- and low-infiltrated groups in TCGA dataset were yielded and further compressed in other two datasets through backward stepwise regression in R environment. Single-cell sequencing data of GSE138709 was loaded by Seurat software and was used to examined the expression of infiltration-related gene set. Pathway changes in malignant cell populations were analyzed through scTPA web tool. Results There were 43 genes differentially expressed between high- and low-immune infiltrated patients, and after further compression, PNOC and LAIR2 were significantly correlated with high immune infiltration status in cholangiocarcinoma. Through analysis of single-cell sequencing data, PNOC was mainly expressed by infiltrated B cells in tumor microenvironment, while LAIR2 was expressed by Treg cells and partial GZMB+ CD8 T cells, which were survival related and increased in tumor tissues. High B cell infiltration levels were related to better overall survival. Also, malignant cell populations demonstrated functionally different roles in tumor progression. Conclusion PNOC and LAIR2 were biomarkers for immune infiltration evaluation in cholangiocarcinoma. PNOC, expressed by B cells, could predict better survival of patients, while LAIR2 was a potential marker for exhaustive T cell populations, correlating with worse survival of patients.
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MESH Headings
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Bile Duct Neoplasms/genetics
- Bile Duct Neoplasms/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cholangiocarcinoma/genetics
- Cholangiocarcinoma/metabolism
- Databases, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Prognosis
- Protein Precursors/genetics
- Protein Precursors/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Opioid/genetics
- Receptors, Opioid/metabolism
- Sequence Analysis, DNA/methods
- Single-Cell Analysis/methods
- Survival Analysis
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
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Affiliation(s)
- Zheng Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Mincheng Yu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Jiuliang Yan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Lei Guo
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Bo Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Shuang Liu
- Neurosurgery Department of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Lei
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Wentao Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Binghai Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jie Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Zhangfu Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Xiaoqiang Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Qinghai Ye
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Hui Li
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Yongfeng Xu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Yongsheng Xiao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
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9
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Salviano-Silva A, Farias TDJ, Bumiller-Bini V, Castro MDS, Lobo-Alves SC, Busch H, Pföhler C, Worm M, Goebeler M, van Beek N, Franke A, Wittig M, Zillikens D, de Almeida RC, Hundt JE, Boldt ABW, Ibrahim S, Augusto DG, Petzl-Erler ML, Schmidt E, Malheiros D. Genetic variability of immune-related lncRNAs: polymorphisms in LINC-PINT and LY86-AS1 are associated with pemphigus foliaceus susceptibility. Exp Dermatol 2021; 30:831-840. [PMID: 33394553 DOI: 10.1111/exd.14275] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Pemphigus foliaceus (PF) is an autoimmune blistering disease of the skin, clinically characterized by erosions and, histopathologically, by acantholysis. PF is endemic in the Brazilian Central-Western region. Numerous single nucleotide polymorphisms (SNPs) have been shown to affect the susceptibility for PF, including SNPs at long non-coding RNA (lncRNA) genes, which are known to participate in many physiological and pathogenic processes, such as autoimmunity. Here, we investigated whether the genetic variation of immune-related lncRNA genes affects the risk for endemic and sporadic forms of PF. We analysed 692 novel SNPs for PF from 135 immune-related lncRNA genes in 227 endemic PF patients and 194 controls. The SNPs were genotyped by Illumina microarray and analysed by applying logistic regression at additive model, with correction for sex and population structure. Six associated SNPs were also evaluated in an independent German cohort of 76 sporadic PF patients and 150 controls. Further, we measured the expression levels of two associated lncRNA genes (LINC-PINT and LY86-AS1) by quantitative PCR, stratified by genotypes, in peripheral blood mononuclear cells of healthy subjects. We found 27 SNPs in 11 lncRNA genes associated with endemic PF (p < .05 without overlapping with protein-coding genes). Among them, the LINC-PINT SNP rs10228040*A (OR = 1.47, p = .012) was also associated with increased susceptibility for sporadic PF (OR = 2.28, p = .002). Moreover, the A+ carriers of LY86-AS1*rs12192707 mark lowest LY86-AS1 RNA levels, which might be associated with a decreasing autoimmune response. Our results suggest a critical role of lncRNA variants in immunopathogenesis of both PF endemic and sporadic forms.
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Affiliation(s)
- Amanda Salviano-Silva
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | | | - Valéria Bumiller-Bini
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Mariana de Sousa Castro
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Sara Cristina Lobo-Alves
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Claudia Pföhler
- Department of Dermatology, Saarland University Medical Center, Homburg, Germany
| | - Margitta Worm
- Division of Allergy and Immunology, Department of Dermatology, Venerology and Allergy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Nina van Beek
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | | | | | | | - Saleh Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Danillo Gardenal Augusto
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Enno Schmidt
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Danielle Malheiros
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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10
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Calonga‐Solís V, Amorim LM, Farias TDJ, Petzl‐Erler ML, Malheiros D, Augusto DG. Variation in genes implicated in B-cell development and antibody production affects susceptibility to pemphigus. Immunology 2021; 162:58-67. [PMID: 32926429 PMCID: PMC7730027 DOI: 10.1111/imm.13259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 12/12/2022] Open
Abstract
Pemphigus foliaceus (PF) is an autoimmune blistering skin disease characterized by the presence of pathogenic autoantibodies against desmoglein 1, a component of intercellular desmosome junctions. PF occurs sporadically across the globe and is endemic in some Brazilian regions. Because PF is a B-cell-mediated disease, we aimed to study the impact of variants within genes encoding molecules involved in the different steps of B-cell development and antibody production on the susceptibility of endemic PF. We analysed 3,336 single nucleotide polymorphisms (SNPs) from 167 candidate genes genotyped with Illumina microarray in a cohort of 227 PF patients and 193 controls. After quality control and exclusion of non-informative and redundant SNPs, 607 variants in 149 genes remained in the logistic regression analysis, in which sex and ancestry were included as covariates. Our results revealed 10 SNPs within or nearby 11 genes that were associated with susceptibility to endemic PF (OR >1.56; p < 0.005): rs6657275*G (TGFB2); rs1818545*A (RAG1/RAG2/IFTAP);rs10781530*A (PAXX), rs10870140*G and rs10781522*A (TRAF2); rs535068*A (TNFRSF1B); rs324011*A (STAT6);rs6432018*C (YWHAQ); rs17149161*C (YWHAG); and rs2070729*C (IRF1). Interestingly, these SNPs have been previously associated with differential gene expression, mostly in peripheral blood, in publicly available databases. For the first time, we show that polymorphisms in genes involved in B-cell development and antibody production confer differential susceptibility to endemic PF, and therefore are candidates for possible functional studies to understand immunoglobulin gene rearrangement and its impact on diseases.
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Affiliation(s)
- Verónica Calonga‐Solís
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Leonardo M. Amorim
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Ticiana D. J. Farias
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Maria Luiza Petzl‐Erler
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Danielle Malheiros
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
| | - Danillo G. Augusto
- Programa de Pós‐Graduação em GenéticaDepartamento de GenéticaUniversidade Federal do ParanáCuritibaBrasil
- Department of NeurologyUniversity of California San FranciscoSan FranciscoCAUSA
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Petzl-Erler ML. Beyond the HLA polymorphism: A complex pattern of genetic susceptibility to pemphigus. Genet Mol Biol 2020; 43:e20190369. [PMID: 32639508 PMCID: PMC7341728 DOI: 10.1590/1678-4685-gmb-2019-0369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pemphigus is a group of autoimmune bullous skin diseases that result in
significant morbidity. As for other multifactorial autoimmune disorders,
environmental factors may trigger the disease in genetically susceptible
individuals. The goals of this review are to summarize the state of knowledge
about the genetic variation that may affect the susceptibility and pathogenesis
of pemphigus vulgaris and pemphigus foliaceus – both the endemic and the
sporadic forms –, to compare and discuss the possible meaning of the
associations reported, and to propose recommendations for new research
initiatives. Understanding how genetic variants translate into pathogenic
mechanisms and phenotypes remains a mystery for most of the polymorphisms that
contribute to disease susceptibility. However, genetic studies provide a strong
foundation for further developments in this field by generating testable
hypotheses. Currently, results still have limited influence on disease
prevention and prognosis, drug development, and clinical practice, although the
perspectives for future applications for the benefit of patients are
encouraging. Recommendations for the continued advancement of our understanding
as to the impact of genetic variation on pemphigus include these partially
overlapping goals: (1) Querying the functional effect of genetic variants on the
regulation of gene expression through their impact on the nucleotide sequence of
cis regulatory DNA elements such as promoters and enhancers, the splicing of
RNA, the structure of regulatory RNAs and proteins, binding of these regulatory
molecules to regulatory DNA elements, and alteration of epigenetic marks; (2)
identifying key cell types and cell states that are implicated in pemphigus
pathogenesis and explore their functional genomes; (3) integrating structural
and functional genomics data; (4) performing disease-progression longitudinal
studies to disclose the causal relationships between genetic and epigenetic
variation and intermediate disease phenotypes; (5) understanding the influence
of genetic and epigenetic variation in the response to treatment and the
severity of the disease; (6) exploring gene-gene and genotype-environment
interactions; (7) developing improved pemphigus-prone and non-prone animal
models that are appropriate for research about the mechanisms that link
genotypes to pemphigus. Achieving these goals will demand larger samples of
patients and controls and multisite collaborations.
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Affiliation(s)
- Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Yu K, Davidson CE, Burshtyn DN. LILRB1 Intron 1 Has a Polymorphic Regulatory Region That Enhances Transcription in NK Cells and Recruits YY1. THE JOURNAL OF IMMUNOLOGY 2020; 204:3030-3041. [PMID: 32321755 DOI: 10.4049/jimmunol.2000164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022]
Abstract
LILRB1 is a highly polymorphic receptor expressed by subsets of innate and adaptive immune cells associated with viral and autoimmune diseases and targeted by pathogens for immune evasion. LILRB1 expression on human NK cells is variegated, and the frequency of LILRB1+ cells differs among people. However, little is known about the processes and factors mediating LILRB1 transcription in NK cells. LILRB1 gene expression in lymphoid and myeloid cells arises from two distinct promoters that are separated by the first exon and intron. In this study, we identified a polymorphic 3-kb region within LILRB1 intron 1 that is epigenetically marked as an active enhancer in human lymphoid cells and not monocytes. This region possesses multiple YY1 sites, and complexes of the promoter/enhancer combination were isolated using anti-YY1 in chromatin immunoprecipitation-loop. CRISPR-mediated deletion of the 3-kb region lowers LILRB1 expression in human NKL cells. Together, these results indicate the enhancer in intron 1 binds YY1 and suggest YY1 provides a scaffold function enabling enhancer function in regulating LILRB1 gene transcription in human NK cells.
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Affiliation(s)
- Kang Yu
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Chelsea E Davidson
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
| | - Deborah N Burshtyn
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada; .,Alberta Transplant Institute, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; and.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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