Integrated RNA sequencing reanalysis reveals reproducible matrix-immune signatures in idiopathic pulmonary fibrosis

Abstract

In idiopathic pulmonary fibrosis (IPF), the lung is remodeled through coordinated epithelial, stromal, and immune-associated programs, but individual transcriptomic cohorts are often too small to separate shared disease signals from demographic and study-level variation. To increase statistical power while preserving study-aware interpretation, we integrated raw bulk lung RNA sequencing (RNA-seq) data from five well-annotated studies and analyzed 223 samples in a common framework that modeled sex, age, library layout and repeated sampling. IPF showed a broad and reproducible expression shift, with 2,443 genes meeting the differential-expression threshold of false discovery rate (FDR) < 0.05 and absolute log2 fold change at least 1. The dominant program combined extracellular matrix remodeling, stromal and epithelial activation, complement and B-cell-related pathways, cilium-associated processes, and relative depletion of oxidative phosphorylation and proteasome pathways. Sex-stratified analyses recovered a shared fibrotic core with smaller sex-skewed components, whereas age-related disease effects were weaker and centered on immune activation. A leave-one-study-out elastic-net analysis using fixed disease-gene panels classified IPF across held-out studies, supporting cross-study portability of the core signature. This integrated reanalysis strengthens evidence for a stable matrix-immune IPF program and reinforces the view that core disease-associated transcriptional programs are reproducible across heterogeneous cohorts.