Exploring the potential common denominator pathogenesis of system lupus erythematosus with COVID-19 based on comprehensive bioinformatics analysis

Huiqiong Zeng; Yu Zhuang; Xiaojuan Li; Zhihua Yin; Xia Huang; Haiyan Peng

doi:10.3389/fimmu.2023.1179664

Exploring the potential common denominator pathogenesis of system lupus erythematosus with COVID-19 based on comprehensive bioinformatics analysis

Front Immunol. 2023 Jun 22:14:1179664. doi: 10.3389/fimmu.2023.1179664. eCollection 2023.

Authors

Huiqiong Zeng¹, Yu Zhuang², Xiaojuan Li³, Zhihua Yin¹, Xia Huang⁴, Haiyan Peng¹

Affiliations

¹ Department of Rheumatology, Shenzhen Futian Hospital for Rheumatic Diseases, Futian District, Shenzhen, Guangdong, China.
² Department of Rheumatology and Immunology, Huizhou Central People's Hospital, Huizhou, Guangdong, China.
³ Department of Public Health, Shenzhen Hospital of Southern Medical University, Shenzhen, China.
⁴ Department of Xi Yuan Community Health Service Center, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China.

Abstract

Objective: Evidences show that there may be a link between SLE and COVID-19. The purpose of this study is to screen out the diagnostic biomarkers of systemic lupus erythematosus (SLE) with COVID-19 and explore the possible related mechanisms by the bioinformatics approach.

Methods: SLE and COVID-19 datasets were extracted separately from the NCBI Gene Expression Omnibus (GEO) database. The limma package in R was used to obtain the differential genes (DEGs). The protein interaction network information (PPI) and core functional modules were constructed in the STRING database using Cytoscape software. The hub genes were identified by the Cytohubba plugin, and TF-gene together with TF-miRNA regulatory networks were constructed via utilizing the Networkanalyst platform. Subsequently, we generated subject operating characteristic curves (ROC) to verify the diagnostic capabilities of these hub genes to predict the risk of SLE with COVID-19 infection. Finally, a single-sample gene set enrichment (ssGSEA) algorithm was used to analyze immune cell infiltration.

Results: A total of 6 common hub genes (CDC6, PLCG1, KIF15, LCK, CDC25C, and RASGRP1) were identified with high diagnostic validity. These gene functional enrichments were mainly involved in cell cycle, and inflammation-related pathways. Compared to the healthy controls, abnormal infiltration of immune cells was found in SLE and COVID-19, and the proportion of immune cells linked to the 6 hub genes.

Conclusion: Our research logically identified 6 candidate hub genes that could predict SLE complicated with COVID-19. This work provides a foothold for further study of potential pathogenesis in SLE and COVID-19.

Keywords: COVID-19; bioinformatics; diagnostic biomarkers; immune cells infiltration; system lupus erythematosus.

Publication types

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

MeSH terms

COVID-19* / genetics
Cell Cycle
Computational Biology
Genes, cdc
Humans
Kinesins
Lupus Erythematosus, Systemic* / genetics

Substances

KIF15 protein, human
Kinesins

Grants and funding

This work was financially supported in part by research grants from the Sanming Project of Medicine in Shenzhen(SZSM201602087), Shenzhen Science and Technology Project (JCYJ20180302145033769), Futian Healthcare Research Project (FTWS 2021062). Futian Healthcare Research Project (FTWS2021006).