Integrated NEK7-inflammasome and platelet transcriptomic signature generates mechanistic hypotheses in heart failure

Background The relationship between NEK7-NLRP3 inflammasome activation and elevated platelet activity in the progression of heart failure (HF) is not well understood. Additionally, a comprehensive gene network linking these processes to cardiac fibrosis has not been established. Our study aimed to explore the transcriptomic associations between NEK7-inflammasome, platelet activation and cardiac fibrosis in heart failure (HF), and to generate pathogenic hypotheses. Methods We integrated bulk RNA-Seq (GSE116250, GSE57338) and scRNA-Seq (GSE183852) data from human HF samples. Through differential expression analysis, WGCNA, and machine learning techniques (LASSO and SVM-RFE), we identified key genes. A candidate diagnostic nomogram was subsequently developed and internally validated. We also conducted functional enrichment and immune infiltration analyses, and molecular docking studies. Key findings were explored in an angiotensin II-induced murine HF model using quantitative PCR. Results We identified a novel four-gene signature, TIMP2 , COL16A1 , MDK , and ISLR , that shows co-expression patterns with NEK7 and platelet‑activation‑related gene sets. These genes were significantly upregulated in human HF tissues and showed similar expression trends in murine hearts, although ISLR exhibited a non-significant increase. A preliminary discrimination model based on these genes showed preliminary discriminatory efficacy in the training cohort (AUC = 0.993), however, this model requires further validation in prospective, multi-center cohorts before any clinical application can be considered. Functional enrichment analysis indicated their synergistic involvement in the TGF-β signaling pathway. Immune profiling underscored a correlation with CD56dim natural killer cell infiltration, identifying fibroblasts as the primary expressors of these genes. Pseudotime trajectory analysis illustrated dynamic expression patterns during fibroblast activation, and potential therapeutic compounds, such as β-Heparin and WZ4002, were predicted via molecular docking. Conclusion This study introduces a novel fibro-inflammatory gene module linked to NEK7-mediated inflammation, platelet activation, and TGF-β signaling in HF. These findings generate integrated mechanistic hypotheses for HF pathogenesis and provide a foundation for subsequent diagnostic and mechanistic explorations.