Burden of rare pathogenic variants suggests disrupted cytoskeletal organisation in the pathogenesis of pulmonary fibrosis

Abstract

BackgroundRare genetic variants contribute to pulmonary fibrosis (PF) risk and outcome, with known variants highlighting the importance of impaired telomere maintenance and surfactant biology. However, much of the disrupted genetic architecture of PF remains unexplained. This study aimed to identify genes with rare pathogenic coding variants that represented a burden at the exon level associated with the pathogenesis of PF. MethodsPF case cohorts included the PROFILE study of incident idiopathic pulmonary fibrosis (IPF) and PF-classified participants from the Genomics England 100K (GE100KGP) study. Whole genome sequencing data were used to test the burden of rare protein altering variants (PAVs; CADD score >20) defined by minor allele frequency <0.1% in the summary level gnomAD reference database (v3.1.2). A summary exon-level pathogenicity score was derived by standardising PAV predictions from functional annotation tools (AlphaMissense, REVEL, ClinPred, CADD, PolyPhen-2, SIFT) averaged across exons. SKAT-O based kernel regression associated exon-level pathogenicity features with disease progression and survival. Single cell lung transcriptomic datasets were harmonised to evaluate expression patterns and gene ontology characterised enriched molecular functions. ResultsAcross 507 PROFILE cases and 451 GE100KGP cases, each compared against 76,156 reference participants, 77 genes showed overlapping significant rare PAV burden, comprising 206 concordant PAVs. Of these, 15 genes had exons with pathogenicity scores that were associated with worse clinical outcomes in IPF, including FAT4 exon-10 and DNAH7 exon-43. Dysregulated gene expression of COL6A3 and FAT4 was observed in IPF lung fibroblasts, while DNAH7, DNAH12 and PCM1 showed high expression in IPF epithelial cells. The top enriched molecular functions were related to cytoskeletal motor activity. ConclusionsRare PAV burden highlighted that pathogenicity within specific exons was associated with PF risk and worse clinical outcomes, identifying genes with dysregulated expression in disease lung cells. The genetic architecture implicates disrupted cytoskeletal organisation in the pathogenesis of PF.