Integrative single-cell and bulk RNA-seq analyses identify CD4+ T-cell subpopulation infiltration and biomarkers of regulatory T cells involved in mediating the progression of atherosclerotic plaque
Authors: Zhang Yifeng , Lu Shuxian , Qiu Liang , Qin Manman , Shan Dan , Xie Lianhua , Yi Yao , Yu Jun 
Published: January 2025

Background

Atherosclerosis (AS) is a chronic inflammatory disease with a significant contributor to mortality worldwide. Regulatory T cells (Tregs) are atheroprotective. However, the potential pathways and genes associated with atherosclerotic plaque progression in Tregs remain largely unknown. Therefore, this study aimed to identify critical target genes and pathways of Tregs associated with the progression of AS.

Methods

The gene expression data and single cell RNA-seq data of AS were downloaded from the Gene Expression Omnibus (GEO) database. Initially, we quantified CD4+ T cell proportions in non-plaque and plaque tissues using cell infiltration by estimation of RNA sequences (CIBERSORT) analysis, identifying pivotal transcription factors regulating the number of Tregs in atherosclerotic plaque. Subsequently, we identified significantly differential expressed genes of Tregs during the progression of atherosclerotic plaque and investigated the key pathways and transcription factors for these differentially expressed genes using gene ontology (GO) analysis and transcription factor enrichment analysis (TFEA), respectively. We also employed high dimensional weighted gene co-expression network analysis (hdWGCNA) and cell-cell communication analysis to elucidate the modules and cascade reaction of Tregs in the progression of AS. The key genes diagnostic potential was assessed via receiver operating characteristic (ROC) curve analysis. Finally, the target genes were validated in AS model using Ldlr−/− mice.

Results

We found that the proportion of Tregs significantly decreased, and Th2 cells showed a significant increase in atherosclerotic plaque compared to that in non-plaque arterial tissues. The five transcription factors (TEFC, IRF8, ZNF267, KLF2, and JUNB), identified as key targets associated with the function and the number of Tregs driving the progression of AS, primarily regulate immune response, ubiquitination, cytokine production, and T-cell differentiation pathways. ZNF267 may mainly involve in regulating ubiquitination, TGF-beta, and MAPK pathways of Tregs to regulate the function and the number of Tregs during the progress of AS. Interestingly, we found that IRF8 and ZNF267 as potential biomarkers were upregulated in circulating CD4+ T cells in patients with atherosclerotic coronary artery disease. Moreover, we also found that the changes of the function and the number of Tregs could modulate endothelial cell and smooth muscle cell functions to counteract AS through ligand–receptor pairs such as the MIF signaling pathway. Finally, we validated that two of the five transcription factors were also upregulated in mice atherosclerotic plaque through AS model using Ldlr−/− mice.

Conclusion

Our results indicate that the transcription factors TEFC, IRF8, ZNF267, KLF2, and JUNB in Tregs could be potential targets for the clinical management of AS.