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Kerns S, Owen KA, Schwalbe D, Grammer AC, Lipsky PE. Examination of the shared genetic architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel lupus risk loci. Hum Genet 2024; 143:703-719. [PMID: 38609570 DOI: 10.1007/s00439-024-02672-3] [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: 10/05/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease with heterogeneous manifestations, including neurological and psychiatric symptoms. Genetic association studies in SLE have been hampered by insufficient sample size and limited power compared to many other diseases. Multiple Sclerosis (MS) is a chronic relapsing autoimmune disease of the central nervous system (CNS) that also manifests neurological and immunological features. Here, we identify a method of leveraging large-scale genome wide association studies (GWAS) in MS to identify novel genetic risk loci in SLE. Statistical genetic comparison methods including linkage disequilibrium score regression (LDSC) and cross-phenotype association analysis (CPASSOC) to identify genetic overlap in disease pathophysiology, traditional 2-sample and novel PPI-based mendelian randomization to identify causal associations and Bayesian colocalization were applied to association studies conducted in MS to facilitate discovery in the smaller, more limited datasets available for SLE. Pathway analysis using SNP-to-gene mapping identified biological networks composed of molecular pathways with causal implications for CNS disease in SLE specifically, as well as pathways likely causal of both pathologies, providing key insights for therapeutic selection.
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Affiliation(s)
- Sophia Kerns
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA.
- The RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Dana Schwalbe
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
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2
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Qin T, Liu M, Lv Y, Zheng A, Wang L, Wu Y, Kasianenko O, Wei X, Teng Z, Xia X, Hu J. Comprehensive Analysis of lncRNA and mRNA Expression Profile of Macrophage RAW264.7 Stimulated by Antimicrobial Peptide BSN-37. Protein Pept Lett 2023; 30:783-793. [PMID: 37587823 DOI: 10.2174/0929866530666230816110009] [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: 03/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND BSN-37, a novel antimicrobial peptide (AMP) containing 37 amino acid residues isolated from the bovine spleen, has not only antibacterial activity but also immunomodulatory activity. Recent evidence shows that long non-coding RNAs (lncRNAs) play an important role in regulating the activation and function of immune cells. The purpose of this experiment was to investigate the lncRNA and mRNA expression profile of mouse macrophages RAW264.7 stimulated by bovine antimicrobial peptide BSN-37. METHODS The whole gene expression microarray was used to detect the differentially expressed lncRNA and mRNA between antimicrobial peptide BSN-37 activated RAW264.7 cells and normal RAW264.7 cells. KEGG pathway analysis and GO function annotation analysis of differentially expressed lncRNAs and mRNA were carried out. Eight kinds of lncRNAs and nine kinds of mRNA with large differences were selected for qRT-PCR verification, respectively. RESULTS In the current study, we found that 1294 lncRNAs and 260 mRNAs were differentially expressed between antibacterial peptide BSN-37 treatment and control groups. Among them, Bcl2l12, Rab44, C1s, Cd101 and other genes were associated with immune responses and were all significantly up-regulated. Mest and Prkcz are related to cell growth, and other genes are related to glucose metabolism and lipid metabolism. In addition, some immune-related terms were also found in the GO and KEGG analyses. At the same time, real-time quantitative PCR was used to verify selected lncRNA and mRNA with differential expression. The results of qRT-PCR verification were consistent with the sequencing results, indicating that our data were reliable. CONCLUSION This study provides the lncRNA and mRNA expression profiles of RAW264.7 macrophages stimulated by antimicrobial peptide BSN-37 and helps to provide a reference value for subsequent studies on lncRNA regulation of antimicrobial peptide BSN-37 immune function.
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Affiliation(s)
- Ting Qin
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Mingcheng Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Faculty of Veterinary Medicine, Sumy National Agrarian University, Sumy, Ukraine
| | - Yanhe Lv
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Airong Zheng
- Forage and Feed Station of Henan Province, Zhengzhou, China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Yundi Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Oksana Kasianenko
- Faculty of Veterinary Medicine, Sumy National Agrarian University, Sumy, Ukraine
| | - Xiaobing Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhanwei Teng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojing Xia
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
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A functional microRNA binding site variant in IL-23R gene in systemic lupus erythematosus and rheumatoid arthritis: is there any correlation? Mol Biol Rep 2022; 49:11821-11828. [DOI: 10.1007/s11033-022-07922-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022]
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Feng R, Lu M, Yang Y, Luo P, Liu L, Xu K, Xu P. Genome- and transcriptome-wide association studies show that pulmonary embolism is associated with bone-forming proteins. Expert Rev Hematol 2022; 15:951-958. [PMID: 35848930 DOI: 10.1080/17474086.2022.2103534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Pulmonary embolism (PE) is a leading cause of death in stroke patients and a severe health burden worldwide. There is a pressing need to understand the mechanisms by which it occurs and to identify at-risk patients efficiently and accurately. OBJECTIVES The aim of this paper was to analyze the genetic correlation between PE and human plasma proteins through genome-wide association study (GWAS) with transcriptome-wide association study (TWAS), in combination with mRNA expression profiling at three levels: DNA, RNA, and protein. METHODS First, based on data from GWAS in European populations, we performed a linkage disequilibrium score regression (LDSC) analysis of plasma proteins and PE in 3,283 individuals and additionally analyzed the genetic association between PE and fracture. Then, we performed a TWAS on PE GWAS data using skeletal muscle and blood for gene expression references. Finally, we validated the genetic correlation between PE and human plasma proteins by co-matching the genes encoding the identified proteins and those identified using TWAS with the differentially expressed genes obtained from mRNA expression profiling of PE (Figure1). RESULTS We identified five plasma proteins associated with PE, including hydroxycarboxylic acid receptor 2, defensin 118, and bone morphogenetic protein (BMP) 7, as well as a relationship between PE and fracture. Comparison of genes encoding these proteins with genes obtained from TWAS and then with differentially expressed genes obtained from PE mRNA expression profiling revealed that PE was highly correlated with the BMP family of genes.
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Affiliation(s)
- Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yanni Yang
- Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Pan Luo
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Lin Liu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi, 710054, China
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Tseng CC, Lin YZ, Lin CH, Hwang DY, Li RN, Tsai WC, Ou TT, Wu CC, Lin YC, Sung WY, Chen KY, Chang SJ, Yen JH. Genetic and epigenetic alterations of cyclic AMP response element modulator in rheumatoid arthritis. Eur J Clin Invest 2022; 52:e13715. [PMID: 34783021 DOI: 10.1111/eci.13715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/07/2022]
Abstract
BACKGROUND Genetic and epigenetic factors are strongly associated with the autoimmune disease rheumatoid arthritis (RA). Cyclic AMP response element modulator (CREM), a gene related to immune system regulation, has been implicated in various immune-mediated inflammatory processes, although it remains unknown whether CREM is involved in RA. METHODS This study enrolled 278 RA patients and 262 controls. Three variants [rs12765063, rs17499247, rs1213386] were identified through linkage disequilibrium and expression quantitative trait locus analysis, and CREM transcript abundance was determined by quantitative real-time polymerase chain reaction. The identified variants were genotyped using the TaqMan Allelic Discrimination assay, and CREM promoter methylation was assessed by bisulphite sequencing. Differences between groups and correlations between variables were assessed with Student's t-tests and Pearson's correlation coefficients. Associations between phenotypes and genotypes were evaluated with logistic regression. RESULTS Rheumatoid arthritis patients exhibited increased CREM expression (p < .0001), which was decreased by methotrexate (p = .0223) and biologics (p = .0001), but could not be attributed to CREM variants. Interestingly, rs17499247 displayed a significant association with serositis (p = .0377), and rs1213386 increased the risk of lymphadenopathy (p = .0398). Furthermore, seven CpG sites showed decreased methylation in RA (p = .0477~ p < .0001). CONCLUSIONS Collectively, our results indicate that CREM hypomethylation and CREM upregulation occur in RA and that CREM variants are involved in the development of serositis and lymphadenopathy in RA. This study highlights the novel roles of CREM in RA pathophysiology.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yuan-Zhao Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Hui Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Chan Tsai
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Tsan-Teng Ou
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Cheng-Chin Wu
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yu-Chih Lin
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Medical Humanities and Education, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Yu Sung
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Kuan-Yu Chen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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Chung CW, Hsiao TH, Huang CJ, Chen YJ, Chen HH, Lin CH, Chou SC, Chen TS, Chung YF, Yang HI, Chen YM. Machine learning approaches for the genomic prediction of rheumatoid arthritis and systemic lupus erythematosus. BioData Min 2021; 14:52. [PMID: 34895289 PMCID: PMC8666017 DOI: 10.1186/s13040-021-00284-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) and systemic lupus erythematous (SLE) are autoimmune rheumatic diseases that share a complex genetic background and common clinical features. This study's purpose was to construct machine learning (ML) models for the genomic prediction of RA and SLE. METHODS A total of 2,094 patients with RA and 2,190 patients with SLE were enrolled from the Taichung Veterans General Hospital cohort of the Taiwan Precision Medicine Initiative. Genome-wide single nucleotide polymorphism (SNP) data were obtained using Taiwan Biobank version 2 array. The ML methods used were logistic regression (LR), random forest (RF), support vector machine (SVM), gradient tree boosting (GTB), and extreme gradient boosting (XGB). SHapley Additive exPlanation (SHAP) values were calculated to clarify the contribution of each SNPs. Human leukocyte antigen (HLA) imputation was performed using the HLA Genotype Imputation with Attribute Bagging package. RESULTS Compared with LR (area under the curve [AUC] = 0.8247), the RF approach (AUC = 0.9844), SVM (AUC = 0.9828), GTB (AUC = 0.9932), and XGB (AUC = 0.9919) exhibited significantly better prediction performance. The top 20 genes by feature importance and SHAP values included HLA class II alleles. We found that imputed HLA-DQA1*05:01, DQB1*0201 and DRB1*0301 were associated with SLE; HLA-DQA1*03:03, DQB1*0401, DRB1*0405 were more frequently observed in patients with RA. CONCLUSIONS We established ML methods for genomic prediction of RA and SLE. Genetic variations at HLA-DQA1, HLA-DQB1, and HLA-DRB1 were crucial for differentiating RA from SLE. Future studies are required to verify our results and explore their mechanistic explanation.
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Affiliation(s)
- Chih-Wei Chung
- Department of Information Management, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chih-Jen Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yen-Ju Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Division of Allergy, Immunology and Rheumatology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsin-Hua Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Division of Allergy, Immunology and Rheumatology, Taichung Veterans General Hospital, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine & Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Seng-Cho Chou
- Department of Information Management, National Taiwan University, Taipei, Taiwan
| | - Tzer-Shyong Chen
- Department of Information Management, Tunghai University, Taichung, Taiwan
| | - Yu-Fang Chung
- Department of Electrical Engineering, Tunghai University, Taichung, Taiwan
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Ming Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.
- Division of Allergy, Immunology and Rheumatology, Taichung Veterans General Hospital, Taichung, Taiwan.
- Rong Hsing Research Center for Translational Medicine & Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- College of Medicine, National Chung Hsing University, 40227, Taichung City, Taiwan.
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Ishigaki K. Beyond GWAS: from simple associations to functional insights. Semin Immunopathol 2021; 44:3-14. [PMID: 34605948 DOI: 10.1007/s00281-021-00894-5] [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: 06/30/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
Each human, when born, has slightly different DNA sequences, which make each of us unique. The variations in DNA sequences are called genetic variants. The primary aim of genome-wide association study (GWAS) is to detect associations between genetic variants and human phenotypes. Since GWAS focuses on germ-line variants, there is no reverse causation. Therefore, GWAS is one of the few tools that can assess the causality of human diseases. In the past 10 years, many large-scale GWAS have been conducted. Although the primary outputs of GWAS are just a series of statistics, its downstream analyses provided many insights beyond simple associations: the causal mechanisms for autoimmune diseases and shared etiology between diseases. Moreover, GWAS downstream analyses generated scores potentially helpful in predicting clinical outcomes of each patient. This review focuses on GWAS for autoimmune diseases and introduces significant achievements of its downstream analyses. We also provide future directions that potentially overcome current limitations. We restrict our discussion to common autoimmune diseases (e.g., rheumatoid arthritis) since rare Mendelian diseases possess distinct genetic etiologies and are not tested by GWAS.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
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