Bioinformatics analyses of gene expression profile to identify pathogenic mechanisms for COVID-19 infection and cutaneous lupus erythematosus

Zhenyu Gao; Xinchao Zhai; Guoqing Yan; Yao Tian; Xia Huang; Qingchao Wu; Lin Yuan; Linchong Su

doi:10.3389/fimmu.2023.1268912

Bioinformatics analyses of gene expression profile to identify pathogenic mechanisms for COVID-19 infection and cutaneous lupus erythematosus

Front Immunol. 2023 Oct 31:14:1268912. doi: 10.3389/fimmu.2023.1268912. eCollection 2023.

Authors

Zhenyu Gao^#^{1

2}, Xinchao Zhai^#^{1

2}, Guoqing Yan^{1

2}, Yao Tian^{1

2}, Xia Huang^{1

2}, Qingchao Wu^{1

2}, Lin Yuan¹, Linchong Su^{1

2}

Affiliations

¹ Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China.
² Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China.

^# Contributed equally.

Abstract

Objective: The global mortality rates have surged due to the ongoing coronavirus disease 2019 (COVID-19), leading to a worldwide catastrophe. Increasing incidents of patients suffering from cutaneous lupus erythematosus (CLE) exacerbations after either contracting COVID-19 or getting immunized against it, have been observed in recent research. However, the precise intricacies that prompt this unexpected complication are yet to be fully elucidated. This investigation seeks to probe into the molecular events inciting this adverse outcome.

Method: Gene expression patterns from the Gene Expression Omnibus (GEO) database, specifically GSE171110 and GSE109248, were extracted. We then discovered common differentially expressed genes (DEGs) in both COVID-19 and CLE. This led to the creation of functional annotations, formation of a protein-protein interaction (PPI) network, and identification of key genes. Furthermore, regulatory networks relating to these shared DEGs and significant genes were constructed.

Result: We identified 214 overlapping DEGs in both COVID-19 and CLE datasets. The following functional enrichment analysis of these DEGs highlighted a significant enrichment in pathways related to virus response and infectious disease in both conditions. Next, a PPI network was constructed using bioinformatics tools, resulting in the identification of 5 hub genes. Finally, essential regulatory networks including transcription factor-gene and miRNA-gene interactions were determined.

Conclusion: Our findings demonstrate shared pathogenesis between COVID-19 and CLE, offering potential insights for future mechanistic investigations. And the identification of common pathways and key genes in these conditions may provide novel avenues for research.

Keywords: COVID-19; cutaneous lupus erythematosus; differentially expressed genes; pathogenic mechanisms; regulatory network.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / genetics
Computational Biology
Humans
Lupus Erythematosus, Cutaneous* / genetics
MicroRNAs*
Transcriptome

Substances

MicroRNAs

Associated data

GEO/GSE109248
GEO/GSE171110

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Natural Science Foundation of Hubei Province of China, Grant No: 2014CFC1123.