Comprehensive analysis of genes associated with necroptosis and pyroptosis in intestinal ischemia-reperfusion injury

Shuang Bao, YanBo Sun, YiChen Hu, XueFen Lei, YuanPei Zhao and WeiMing Li

PLOS ONE, 2025, vol. 20, issue 12, 1-22

Abstract: Background: Intestinal ischemia–reperfusion (II/R) injury is a severe clinical condition in which regulated cell death programs—including pyroptosis and necroptosis—have emerged as key drivers of tissue damage and inflammation. We sought to delineate cell-death–related molecular signatures and candidate therapeutic targets in II/R injury. Methods: We obtained transcriptome datasets from Gene Expression Omnibus (GEO) databases for mice (GSE96733, GSE232246) and humans (GSE37013). We cross-referenced genes associated with necroptosis and pyroptosis with differentially expressed genes to identify death-related features. Hub genes were identified through the topological structure of protein interaction networks and validated using an internal validation set, an independent validation set, WGCNA, and qRT-PCR. These genes were also associated with immune cell infiltration. Drug–gene interactions were predicted using DGIdb and verified through molecular docking. Results: We identified 1,027 differentially expressed genes (DEGs) in the training set and derived 7 cell death-related differentially expressed genes (DCDEGs) by intersecting gene sets associated with necroptosis and pyroptosis. PPI-based prioritization identified four hub genes—Il1β, Ripk3, Sting1 (Tmem173), and Tnfaip3—suggesting cross-regulatory interactions between inflammation and cell death in ischemia-reperfusion pathology. These hub genes were validated using WGCNA analysis and an internal validation set. Immune infiltration analysis indicated significant correlations between hub genes and multiple immune compartments. A predictive model showed good discrimination in the discovery data, and 54 candidate drugs targeting the hub genes were retrieved. qRT-PCR confirmed dysregulation of three hub genes. Conclusion: Il1β, Ripk3, Sting1, and Tnaip3 were identified as hub genes associated with necroptosis and pyroptosis in intestinal ischemia-reperfusion (II/R) injury. This study provides a reproducible framework and identifies testable targets for translational exploration.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0338420

DOI: 10.1371/journal.pone.0338420

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