Transcriptomic sequencing reveals key programmed cell death gene signatures in middle ear cholesteatoma

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Abstract Background Programmed cell death (PCD) plays a crucial role in various diseases. However, the mechanisms of PCD in middle ear cholesteatoma (MEC) is not fully understood. Methods In this study, the transcriptome files of MEC and control samples were sequenced. Differentially enriched PCD patterns were detected by the ssGSEA algorithm. WGCNA was performed to identify gene modules associated with MEC. The overlapped genes among differentially expressed genes (DEGs) between MEC and controls, genes related to differentially enriched PCDs and WGCNA modular genes were defined as PCD candidate genes. Subsequently, the PCD candidate genes were subjected to LASSO and Boruta analyses to identify key PCD signatures in MEC. Furthermore, the potential molecular mechanisms of PCD signatures in regulating MEC were analyzed via the CIBERSORT and GSEA algorithms. Results Nine PCD patterns, including pyroptosis, entotic cell death, disulfidptosis, lysosome-dependent cell death, apoptosis, necroptosis, alkaliptosis, netotic cell death, and parthanatos showed differential enrichment. By LASSO and Boruta algorithms, BID, CASP1, FZD9, INHBA, and STXBP2, were selected as key PCD signatures. Quantitative PCR (qPCR) results showed that CASP1 and STXBP2 were significantly upregulated in the MEC group, while BID and INHBA exhibited an upward trend, further validating our findings. We observed altered infiltration levels of macrophage M0, M1, and M2 in MEC patients, all of which were strongly correlated with key PCD signatures. Conclusion We identified 9 PCD patterns involved in MEC and screened 5 key PCD genes (BID, CASP1, FZD9, INHBA, and STXBP2) associated with macrophage infiltration in MEC.

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