EID1-EP300 axis dysregulation in airway fibroproliferation: a single-cell transcriptomic analysis with implications for tracheostomy-associated granulation

Abstract

Abstract Background Tracheostomy is a common life-saving procedure, yet recurrent granulation tissue formation at the tracheostomy site remains a challenging clinical problem with unclear mechanisms. Current endoscopic resection offers only temporary relief, and the molecular drivers of persistent fibroproliferation are poorly understood. Methods We performed single-cell RNA sequencing analysis on 74,139 cells from human airway tissues to investigate the role of the ROBO2-EID1-EP300 epigenetic regulatory axis in tracheal fibrogenesis. Differential expression, correlation, and Gene Ontology enrichment analyses were conducted to characterize this pathway in fibrotic versus normal airway mesenchymal cells. Results Airway mesenchymal cells from fibrotic specimens showed consistent EID1 downregulation (FC = 0.73) and EP300 upregulation (FC = 1.64), with robust statistical support ( p < 0.001 for both comparisons). ROBO2, an upstream regulator, was also upregulated (FC = 1.52, p = 4.96 × 10 -10 ). EID1 and EP300 showed significant positive correlation ( ρ = 0.232, p < 2.2 × 10 -16 ), suggesting a compensatory feedback mechanism. GO enrichment implicated TGF-β signaling, mesenchymal development, and morphogenetic pathways. Conclusions EID1 downregulation with compensatory EP300 upregulation represents a novel epigenetic mechanism driving recurrent airway granulation after tracheostomy. This axis provides potential therapeutic targets and explains why inflammation-driven fibroproliferation persists despite mechanical resection. These findings provide a molecular basis for developing EP300-targeted therapies for tracheostomy granulation, a common complication with no current targeted treatment.