Exploratory proteomic analysis of idiopathic pulmonary fibrosis and fibrotic hypersensitivity pneumonitis using data-independent acquisition

Idiopathic pulmonary fibrosis (IPF) and fibrotic hypersensitivity pneumonitis (fHP) are two distinct interstitial lung diseases often showing similar clinical features, making differentiation challenging. Precise diagnosis is essential because treatment strategies for these conditions differ. We employed a data-independent acquisition mass spectrometry-based proteomics approach to identify potential diagnostic biomarkers and gain insights into the pathogenic mechanisms of IPF and fHP. We analyzed formalin-fixed, paraffin-embedded lung tissue samples from patients with IPF ( n = 5), fHP ( n = 10), and controls ( n = 7). A total of 7,939 proteins were identified, with both IPF and fHP groups exhibiting distinct protein expression profiles compared with the control group. In gene enrichment analysis, proteins upregulated in IPF compared with fHP were predominantly associated with cilium-related functions and were exclusively expressed in MUC5AC + or ciliated epithelial cells. The upregulation of cilium-related proteins in IPF was further validated using publicly available single-cell RNA sequencing data. We identified key biological processes, pathways, and upstream regulators specific to each disease. In IPF, protein glycosylation and fatty acid metabolism were prominently upregulated, whereas immune system signaling pathways were enriched in fHP. Upstream analysis implicated SENP2, FER, and EFS as potential regulators in IPF and MAP3K8, SENP2, TEC, and FER as potential regulators in fHP. Our study provides novel insights into the molecular mechanisms underlying IPF and fHP and highlights potential diagnostic biomarkers. This study lays the groundwork for future validation and functional studies aimed at improving diagnosis and treatment of these devastating lung diseases.