Identification of key cell subpopulations and associated biomarkers for mouse dry eye disease based on the Scissor-CIBERSORTx algorithm integration strategy.

Dry eye disease (DED) is characterized by tear film instability and chronic inflammation, with the cornea serving as a key target site vulnerable to inflammatory damage. This study integrated single-cell and bulk transcriptomics combined with Scissor and CIBERSORTx algorithms to screen corneal key cell populations and biomarkers in murine DED. Corneal wing cells were identified as core disease-associated cells, among which interferon-response wing cells (IFN-response-wing) were the pivotal pathogenic subtype. Three IFN-response-wing signature biomarkers Upk3b, Dusp1 and Ly6e were screened, enriched in immune pathways including antigen processing and presentation, primary immunodeficiency, and cytokine receptor interaction. We constructed a chemical-induced DED mouse model for multi-layered validation via immunofluorescence, Real-time polymerase chain reaction (RT-qPCR) and Western blot. Immunofluorescence revealed tissue-specific protein patterns: DED corneal epithelium exhibited elevated IRF1, Dusp1 and Ly6e protein yet reduced Upk3b, with Ly6e co-localized with IRF1-positive cells. However, RT-qPCR and Western blot of whole corneal tissue demonstrated significant upregulation of Upk3b, Dusp1 and Ly6e at both mRNA and total protein levels. Collectively, IFN-response-wing drives DED pathogenesis, and Upk3b, Dusp1, Ly6e act as tissue-specific DED biomarkers with inconsistent trends between epithelial localized protein and global corneal molecular abundance, providing novel mechanistic clues for DED diagnosis and targeted therapy.