Comprehensive analysis of cuproptosis-related genes in immune infiltration in ischemic stroke

Xuehui Fan; Hongping Chen; Fangchao Jiang; Chen Xu; Yingju Wang; Haining Wang; Meng Li; Wan Wei; Jihe Song; Di Zhong; Guozhong Li

doi:10.3389/fneur.2022.1077178

Comprehensive analysis of cuproptosis-related genes in immune infiltration in ischemic stroke

Front Neurol. 2023 Feb 2:13:1077178. doi: 10.3389/fneur.2022.1077178. eCollection 2022.

Authors

Xuehui Fan¹, Hongping Chen¹, Fangchao Jiang¹, Chen Xu¹, Yingju Wang¹, Haining Wang¹, Meng Li¹, Wan Wei¹, Jihe Song¹, Di Zhong¹, Guozhong Li¹

Affiliation

¹ Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.

Abstract

Background: Immune infiltration plays an important role in the course of ischemic stroke (IS) progression. Cuproptosis is a newly discovered form of programmed cell death. To date, no studies on the mechanisms by which cuproptosis-related genes regulate immune infiltration in IS have been reported.

Methods: IS-related microarray datasets were retrieved from the Gene Expression Omnibus (GEO) database and standardized. Immune infiltration was extracted and quantified based on the processed gene expression matrix. The differences between the IS group and the normal group as well as the correlation between the infiltrating immune cells and their functions were analyzed. The cuproptosis-related DEGs most related to immunity were screened out, and the risk model was constructed. Finally, Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and drug target were performed using the Enrichr website database. miRNAs were predicted using FunRich software. Finally, cuproptosis-related differentially expressed genes (DEGs) in IS samples were typed, and Gene Set Variation Analysis (GSVA) was used to analyze the differences in biological functions among the different types.

Results: Seven Cuproptosis-related DEGs were obtained by merging the GSE16561 and GSE37587 datasets. Correlation analysis of the immune cells showed that NLRP3, NFE2L2, ATP7A, LIPT1, GLS, and MTF1 were significantly correlated with immune cells. Subsequently, these six genes were included in the risk study, and the risk prediction model was constructed to calculate the total score to analyze the risk probability of the IS group. KEGG analysis showed that the genes were mainly enriched in the following two pathways: D-glutamine and D-glutamate metabolism; and lipids and atherosclerosis. Drug target prediction found that DMBA CTD 00007046 and Lithocholate TTD 00009000 were predicted to have potential therapeutic effects of candidate molecules. GSVA showed that the TGF-β signaling pathway and autophagy regulation pathways were upregulated in the subgroup with high expression of cuproptosis-related DEGs.

Conclusions: NLRP3, NFE2L2, ATP7A, LIPT1, GLS and MTF1 may serve as predictors of cuproptosis and play an important role in the pathogenesis of immune infiltration in IS.

Keywords: cuproptosis; immune infiltration; ischemic stroke; predictors; risk model construction.

Grants and funding

This work was supported by the Heilongjiang Province Key R&D Program (Grant No. GA21C005) and the National Natural Science Foundation of China (No. 81873746).