Sex difference in mRNA expressions of lungs post bleomycin-induced acute lung injury

We performed mRNA sequencing to comprehensively and unbiasedly examine the transcriptional landscape of lung tissue in female and male rats following bleomycin acute lung injury (ALI). Comparative analysis of bleomycin-induced ALI transcriptional responses demonstrated marked sex differences in both magnitude and directionality. Males exhibited significantly greater transcriptional perturbation with 2,393 differentially expressed genes (DEGs) (1,602 upregulated, 791 downregulated) versus 1,533 DEGs in females (1,129 upregulated, 404 downregulated) (|log2FC| ≥ 1, FDR < 0.05). Direct comparison of bleomycin-treated animals identified 826 DEGs (307 female-enriched, 519 male-enriched). Baseline sex differences were minimal, with only 262 DEGs between sham-treated animals (51 female-enriched, 211 male-enriched), indicating that observed transcriptional divergence primarily reflects sex-specific injury responses rather than constitutive sexual dimorphism. Gene Ontology (GO) analysis of these 826 DEGs began to define this polarity. The biological processes with the most divergent expression patterns included proteolysis (GO:0006508) and immune response (GO:0006955). Cellular components included both membrane and extracellular space (GO:0016020, GO:0005615), and molecular functions included protein binding (GO:0005515). KEGG pathway analysis further highlighted the contrast. Direct comparison between females and males revealed divergent pathways, including: cytokine-cytokine receptor interaction (ko04060), complement and coagulation cascades (ko04610), and ECM-receptor interaction (ko04512). A more granular analysis of the DEGs comprising these divergent functional categories and pathways identified male lungs selectively upregulating chemokines (Cxcl10, Cxcl11, Ccl17), complement/coagulation factors, (F7, Plg, C1qa), and components of the acute-phase protease inhibitor system (Timp1, Serpina3a, Tmprss9), whereas females induced BMP signaling genes (Bmpr2, Smad9, Bmp6) and an integrin scaffolding proteins (Itga1/2/9/11, Itgb3, Flrt3) . Notable findings from within-sex analyses showed females with enriched GO and KEGG themes related to extracellular matrix organization and cell-cycle progression, while males were more focused on immune pathways, specifically cytokine induction and viral response modules. A complete list of all DEGs across comparisons is provided in the supplementary materials.