Screening of Genes Associated with Immune Infiltration of Discoid Lupus Erythematosus Based on Weighted Gene Co-expression Network Analysis

Yuru Han; Shuang Liu; Shuo Shi; Yongyong Shu; Changlian Lu; Xuefeng Gu

doi:10.1007/s10528-023-10603-6

Screening of Genes Associated with Immune Infiltration of Discoid Lupus Erythematosus Based on Weighted Gene Co-expression Network Analysis

Biochem Genet. 2024 Mar 7. doi: 10.1007/s10528-023-10603-6. Online ahead of print.

Authors

Yuru Han^#^{1

2}, Shuang Liu^#^{1

2}, Shuo Shi³, Yongyong Shu², Changlian Lu^{4

5}, Xuefeng Gu^{6

7}

Affiliations

¹ Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Rd. Pudong New District, Shanghai, 201318, China.
² School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
³ China COMAC Shanghai Aircraft Design and Research Institute, Shanghai, China.
⁴ Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Rd. Pudong New District, Shanghai, 201318, China. lvcl@sumhs.edu.cn.
⁵ School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China. lvcl@sumhs.edu.cn.
⁶ Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Rd. Pudong New District, Shanghai, 201318, China. guxf@sumhs.edu.cn.
⁷ School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China. guxf@sumhs.edu.cn.

^# Contributed equally.

PMID: 38451400
DOI: 10.1007/s10528-023-10603-6

Abstract

Discoid lupus erythematosus (DLE) is a disorder of the immune system commonly seen in women of childbearing age. The pathophysiology and aetiology are still poorly understood, and no cure is presently available. Therefore, there is an urgent need to explore the underlying molecular mechanisms, as well as search for new therapeutic targets. Gene expression data from skin biopsies samples of DLE patients and healthy controls were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between DLE and healthy control samples were identified by differential expression analysis. Samples were analysed using CIBERSORT to examine the proportion of immune infiltration. Weighted gene co-expression network analysis was used to screen for the module most relevant to immune infiltration. Candidate genes were uploaded to the TRRUST database to obtain the potential transcription factors regulating these genes. Protein-protein interaction (PPI) analysis was performed to obtain the hub genes most associated with immune infiltration among the candidate genes. A total of 273 DEGs were identified between the DLE and healthy control samples. The results of immunoinfiltration analysis showed that the abundances of resting memory CD4 T cells, activated memory CD4 T cells and M1 macrophages were significantly higher, while those of resting infiltration of plasma cells, regulatory T cells and dendritic cells were lower in DLE samples than in healthy control samples. Correlation analysis showed that ISG15, TRIM22, XAF1, IFIT2, OAS2, OAS3, OAS1, IFI44, IFI6, BST2, IFIT1 and MX2 were negatively correlated with the abundances of plasma cells, T-cell regulatory cells and resting dendritic cells and positively correlated with activated memory CD4 T cells and M1 macrophages. Our study shows that these hub genes may regulate DLE via immune-related pathways mediated by the infiltration of these immune cells.

Keywords: CIBERSORT; Discoid lupus erythematosus; Immune infiltration; Weighted gene co-expression network analysis.