1
|
Su W, Tian Y, Wei Y, Hao F, Ji J. Key genes and immune infiltration in chronic spontaneous urticaria: a study of bioinformatics and systems biology. Front Immunol 2023; 14:1279139. [PMID: 38045687 PMCID: PMC10693338 DOI: 10.3389/fimmu.2023.1279139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Background Chronic spontaneous urticaria (CSU) is defined by the spontaneous occurrence of wheals and/or angioedema for >6 weeks. The pathogenesis involves skin mast cells, but the complex causes of their activation remain to be characterized in detail. Objectives To explore disease-driving genes and biological pathways in CSU. Methods Two microarray data sets, e.g., GSE57178 and GSE72540, with mRNA information of skin from CSU patients, were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics pipeline including identification of differentially expressed genes (DEGs), functional enrichment analysis, protein-protein interaction (PPI) network analysis, co-expression and drug prediction analysis, and immune and stromal cells deconvolution analyses were applied to identify hub genes and key drivers of CSU pathogenesis. Results In total, we identified 92 up-regulated and 7 down-regulated genes in CSU lesions. These were significantly enriched in CSU-related pathways such as TNF, NF-κB, and JAK-STAT signaling. Based on PPI network modeling, four genes, i.e., IL-6, TLR-4, ICAM-1, and PTGS-2, were computationally identified as key pathogenic players in CSU. Immune infiltration analyses indicated that dendritic cells, Th2 cells, mast cells, megakaryocyte-erythroid progenitor, preadipocytes, and M1 macrophages were increased in lesional CSU skin. Conclusion Our results offer new insights on the pathogenesis of CSU and suggest that TNF, NF-κB, JAK-STAT, IL-6, TLR-4, ICAM-1, and PTGS-2 may be candidate targets for novel CSU treatments.
Collapse
Affiliation(s)
- Wenxing Su
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Dermatology and Plastic Surgery Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Tian
- Department of Dermatology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yuqian Wei
- Department of Dermatology, Nantong Third People’s Hospital, Nantong, China
| | - Fei Hao
- Dermatology and Plastic Surgery Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiang Ji
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
2
|
Zhang L, Qiu L, Wu J, Qi Y, Gao X, He C, Qi R, Wang H, Yao X, Zhu H, Li Y, Hao S, Lu Q, Long H, Lian S, Zhu W, Zhang H, Lai W, Su X, Lu R, Guo Z, Li J, Li M, Liu Q, Wang H, He L, Nong X, Li F, Li Y, Yao C, Xu J, Tang H, Wang D, Li Z, Yu H, Xiao S, An J, Pu X, Yu S, Zhang J, Chen X, Wang H, Huang W, Chen H, Xiao T. GWAS of Chronic Spontaneous Urticaria Reveals Genetic Overlap with Autoimmune Diseases, Not Atopic Diseases. J Invest Dermatol 2023; 143:67-77.e15. [PMID: 35933036 DOI: 10.1016/j.jid.2022.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/03/2022] [Accepted: 07/09/2022] [Indexed: 02/08/2023]
Abstract
Although chronic spontaneous urticaria (CSU) is a common disease, GWASs of CSU are lacking. We aimed to identify susceptibility SNPs by performing a GWAS in Chinese Han adults with CSU. The discovery cohort included 430 CSU cases and 482 healthy controls. The GWAS findings were validated in 800 CSU cases and 900 healthy controls. Genetic, functional enrichment, and bioinformatic analyses of genome-wide significant SNPs were performed to assess the association between CSU and autoimmunity or atopy. Five genome-wide significant SNPs were identified: rs434124/LILRA3, rs61986182/IGHG1/2, rs73075571/TDGF1, rs9378141/HLA-G, and rs3789612/PTPN22. The first four SNPs were in linkage disequilibrium with autoimmune-related diseases‒associated SNPs and were cis-expression quantitative trait loci in immune cells. The five SNPs-annotated genes were significantly enriched in immune processes. Higher polygenic risk scores and allele frequencies of rs3789612∗T, rs9378141∗C, and rs73075571∗G were significantly associated with autoimmune-related CSU phenotypes, including positive antithyroglobulin IgG, positive anti-FcεRIα IgG, total IgE <40 IU/ml, and positive antithyroid peroxidase IgG but not with atopic or allergic sensitized CSU phenotypes. This GWAS of CSU identifies five risk loci and reveals that CSU shares genetic overlap with autoimmune diseases and that genetic factors predisposing to CSU mainly manifest through associations with autoimmune traits.
Collapse
Affiliation(s)
- Liming Zhang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Li Qiu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Jian Wu
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Yumeng Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xinghua Gao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Chundi He
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ruiqun Qi
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Hexiao Wang
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Hong Zhu
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yuzhen Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Siyu Hao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hai Long
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shi Lian
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Zhu
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Haiping Zhang
- Department of Dermatology, Xuan Wu Hospital Capital Medical Univerisity, Beijing, China
| | - Wei Lai
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiangyang Su
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Rongbiao Lu
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zaipei Guo
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Jingyi Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, China
| | - Quanzhong Liu
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huiping Wang
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiang Nong
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fuqiu Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Yang Li
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Chunli Yao
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Hui Tang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Duoqin Wang
- Department of Dermatology, Huashan Hospital, Fudan Univeristy, Shanghai, China
| | - Zhenlu Li
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Huiqian Yu
- Department of Dermatology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shengxiang Xiao
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Jingang An
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xiongming Pu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Shirong Yu
- Department of Dermatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Key Laboratory of Dermatology Research (XJYS1707), Xinjiang, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Xue Chen
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Haifeng Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC), Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Hongduo Chen
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China
| | - Ting Xiao
- Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, China.
| |
Collapse
|
3
|
Prosty C, Gabrielli S, Ben-Shoshan M, Le M, Giménez-Arnau AM, Litvinov IV, Lefrançois P, Netchiporouk E. In silico Identification of Immune Cell-Types and Pathways Involved in Chronic Spontaneous Urticaria. Front Med (Lausanne) 2022; 9:926753. [PMID: 35872776 PMCID: PMC9302568 DOI: 10.3389/fmed.2022.926753] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/13/2022] [Indexed: 12/20/2022] Open
Abstract
Background The immunopathogenesis of chronic spontaneous urticaria (CSU) is poorly understood, but recent research suggests that patients can be divided into autoallergic and autoimmune subtypes. Given that not all patients can be controlled with current treatment regimens, including anti-IgE monoclonal antibodies, a better understanding of the immune pathways involved in CSU may enable the repurposing of monoclonal antibodies used for other dermatologic diseases (e.g., Th2 and Th17 inhibitors). Therefore, we investigated the implicated immune cells and pathways by reanalyzing publicly available transcriptomic data. Methods Microarray data of CSU and healthy control (HC) skin and blood were obtained from the Gene Expression Omnibus (GSE72542, GSE57178). Differentially expressed genes were defined as a false discovery rate <0.05 and a |log2 fold change| ≥1. Pathway analyses were conducted using ToppGene and KEGG. Cell-type enrichment was determined by CIBERSORT and xCell and was correlated with clinical characteristics. Results Th2 (IL-4/13 signaling) and Th17-related (IL-17/23 signaling) pathways were upregulated in lesional compared to non-lesional and HC samples. In non-lesional versus lesional samples, CIBERSORT analysis revealed increased regulatory T-cells (Treg) and resting mast cells. xCell analysis established that Th1 and Th2 scores were not significantly different between lesional and HC samples. However, Th2 scores in both lesional and non-lesional samples correlated positively with disease severity. Few differentially expressed genes and pathways were identified between CSU and HC blood samples. Conclusion Our results support the involvement of Th2 and Th17-related genes and pathways in CSU. Th2 scores associate with disease severity, which indicates the clinical relevance of these findings. Increased resting mast cell and Treg scores in non-lesional samples may suggest local suppression of wheal formation. Moreover, disease activity seemed to be restricted to the skin as there were limited findings from blood. Larger studies using next-generation sequencing will be helpful to confirm these results.
Collapse
Affiliation(s)
- Connor Prosty
- Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sofianne Gabrielli
- Division of Allergy, Immunology and Dermatology, Montreal Children's Hospital, Montreal, QC, Canada
| | - Moshe Ben-Shoshan
- Division of Allergy, Immunology and Dermatology, Montreal Children's Hospital, Montreal, QC, Canada
| | - Michelle Le
- Division of Dermatology, McGill University, Montreal, QC, Canada
| | - Ana M Giménez-Arnau
- Department of Dermatology, Hospital del Mar, Institut Mar d'Investigacions Mediques (IMIM), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Ivan V Litvinov
- Division of Dermatology, McGill University, Montreal, QC, Canada.,Division of Dermatology, University of Ottawa, Ottawa, ON, Canada
| | | | | |
Collapse
|