Shared and Disease-Preferential Matrisome Programs in Fibrosing Interstitial Lung Disease: Evidence from Cross-Cohort and Within-Cohort Analysis

Abstract

Idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), and systemic sclerosis-associated interstitial lung disease (SSc-ILD) share the same structural outcome: extracellular matrix (ECM) deposition. Whether this shared endpoint reflects shared or distinct molecular programs remains unresolved. Differential expression results from four GEO datasets representing IPF, HP, non-IPF ILD, and SSc-ILD were intersected with the 1027-gene human matrisome masterlist and classified by threshold-defined disease preference. All four diseases shared a 21-gene upregulated matrisome core, and the matrisome fraction rose with cross-disease sharing, from 4.3% of single-disease upregulated genes to 45.7% of genes upregulated in all four (significant Cochran–Armitage trend), and the enrichment persisted when any single cohort was removed. Apparent disease preference was largely attributable to unequal statistical power: of 29 genes measurable in all four datasets, 24 showed a concordant sub-threshold effect in at least one comparator disease. Category composition of the threshold-defined signatures did not differ significantly between diseases, and the exploratory pathway panel is reported within diseases only, because significance scales with cohort size. In a within-cohort comparison of IPF with chronic HP in GSE150910, with platform, cohort, and control population held constant, matrisome genes were over-represented among the 2732 genes separating the two diseases, and 205 matrisome genes distinguished them. Fibrosing ILDs share a cross-cohort ECM core, and the apparent disease preference of the remaining signatures largely reflects differences in statistical power between cohorts. Disease-preferential matrisome expression is nonetheless detectable when disease and study are not confounded, so the limitation lies in threshold-based cross-study intersection rather than in the matrisome compartment itself.