Screening and validation of atherosclerosis PAN-apoptotic immune-related genes based on single-cell sequencing

Front Immunol. 2024 Apr 26:15:1297298. doi: 10.3389/fimmu.2024.1297298. eCollection 2024.

Abstract

Background: Carotid atherosclerosis (CAS) is a complication of atherosclerosis (AS). PAN-optosome is an inflammatory programmed cell death pathway event regulated by the PAN-optosome complex. CAS's PAN-optosome-related genes (PORGs) have yet to be studied. Hence, screening the PAN-optosome-related diagnostic genes for treating CAS was vital.

Methods: We introduced transcriptome data to screen out differentially expressed genes (DEGs) in CAS. Subsequently, WGCNA analysis was utilized to mine module genes about PANoptosis score. We performed differential expression analysis (CAS samples vs. standard samples) to obtain CAS-related differentially expressed genes at the single-cell level. Venn diagram was executed to identify PAN-optosome-related differential genes (POR-DEGs) associated with CAS. Further, LASSO regression and RF algorithm were implemented to were executed to build a diagnostic model. We additionally performed immune infiltration and gene set enrichment analysis (GSEA) based on diagnostic genes. We verified the accuracy of the model genes by single-cell nuclear sequencing and RT-qPCR validation of clinical samples, as well as in vitro cellular experiments.

Results: We identified 785 DEGs associated with CAS. Then, 4296 module genes about PANoptosis score were obtained. We obtained the 7365 and 1631 CAS-related DEGs at the single-cell level, respectively. 67 POR-DEGs were retained Venn diagram. Subsequently, 4 PAN-optosome-related diagnostic genes (CNTN4, FILIP1, PHGDH, and TFPI2) were identified via machine learning. Cellular function tests on four genes showed that these genes have essential roles in maintaining arterial cell viability and resisting cellular senescence.

Conclusion: We obtained four PANoptosis-related diagnostic genes (CNTN4, FILIP1, PHGDH, and TFPI2) associated with CAS, laying a theoretical foundation for treating CAS.

Keywords: PAN-apoptosome related genes; bioinformatics; carotid atherosclerosis; diagnostic genes; single-cell sequencing.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Apoptosis / genetics
  • Atherosclerosis* / genetics
  • Atherosclerosis* / immunology
  • Female
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Humans
  • Male
  • Single-Cell Analysis* / methods
  • Transcriptome

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the Natural Science Foundation of Shandong Province (ZR2020MH139).