Pathway-Centric Transcriptomic Profiling of Middle Ear Cholesteatoma Identifies Selective Dysregulation of the IL-6/JAK-STAT/MAPK and MMP9/ZEB1 Pathways

<title>Abstract</title> <p> <bold>Background</bold> : Cholesteatoma is a destructive lesion of the middle ear characterized by hyperproliferative keratinocytes and chronic bone erosion. Although histologically benign, its aggressive behaviour causes severe otologic complications. The precise molecular mechanisms dividing active drivers from unaltered regulators within key pathogenic pathways remain poorly defined. <bold>Methods</bold> : Public transcriptomic data from the GSE42256 dataset were analyzed to compare human cholesteatoma tissue against normal middle ear mucosa. Differential gene expression analysis was performed using linear modeling (R limma) in R/Bioconductor. P-values were adjusted using the Benjamini-Hochberg procedure, with significance set at adjusted p &lt; 0.05 and |log ₂ FC| &gt; 0.5. Targeted analysis was mapped onto TNF-α, IL-6, S100, and invasive signaling cascades. <bold>Results</bold> : Specific transcriptomic profiles revealed highly selective, non-generalized pathway dysregulations. Within the S100 family, S100A7, S100A8, S100A9, and S100A12 were significantly upregulated, driving leukocyte recruitment. The TNF-α cascade exhibited a highly constrained pattern in CASP8, FADD, and TNFRSF1B genes, triggering localised remodelling. The IL-6 axis demonstrated a comprehensive and coordinated upregulation of its intracellular downstream machinery, specifically concentrated in the JAK1, STAT3, MAPK3, GRB2, SHC1, ELK1, and MAP2K1 genes, fueling continuous proliferation. Finally, tissue invasion was characterized by the marked upregulation of matrix metalloproteinases (MMP2/MMP9) and the transcription factor ZEB1, orchestrating extracellular matrix degradation. <bold>Conclusions</bold> : Cholesteatoma pathogenesis is driven by targeted intracellular relays rather than a generalised transcriptional surge. Pinpointing the extensive dysregulation of the IL-6/JAK-STAT/MAPK and MMP9/ZEB1 pathways isolates precise molecular checkpoints, providing novel therapeutic opportunities to halt keratinocyte hyperproliferation and osteolytic bone destruction. </p>