Abstract Rationale To identify critical mechanisms driving early disease progression and develop better biomarkers of pre-clinical progression in Familial Pulmonary Fibrosis (FPF), we investigated transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) that correlate with radiographic changes interstitial lung abnormalities (ILA) and progression towards clinical disease. Methods We processed over 1.5 million PBMCs to identify shifts in peripheral immune cells between non-diseased control samples (n = 7), ‘at-risk’ unaffected subjects in FPF kindreds from our ongoing longitudinal cohort study categorized by lung HRCT appearance at the time of blood draw (no ILA; n = 76, early/mild ILA; n = 74, and extensive ILA; n = 6), and subjects with IPF (n = 41). Cell populations were annotated using canonical markers, and cell-type abundance and proportion was assessed using tool propeller (cell proportion analysis with Fisher’s Exact Test). Differential gene (DG) expression was performed with scVI v1.1.2 and gene set enrichment analysis (GSEA) was conducted with GSEApy tool using preranked analysis with MSigDB Hallmark pathways (FDR0.1 cutoff). Results Leiden clustering identified 29 distinct clusters, visualized by UMAP, which were annotated into 14 major PBMC cell types. Among all PBMC clusters, the proportion of classical monocytes progressively increased across the proposed disease progression categories (non-diseased control 13.2% ± 3.7%; No ILA 22.0% ± 1.25%; mild ILA 21.6% ± 1.4%; extensive ILA 23.3% ± 6.1%; and IPF 25.1% ± 2.3%). Non-classical monocyte proportions also increased along this trajectory (control 2.3% ± 0.7%; no ILA 3.5% ± 0.3%; mild ILA 3.4% ± 0.3; extensive ILA 5.4% ± 2.1%; and IPF 4.1% ± 0.5%). In contrast, total lymphocytes progressively decreased along this trajectory (non-diseased 80.9 ± 7.8%, No ILA 70.2 ± 1.82%, mild ILA 70.9 ± 2.2%Extensive ILA 67.1 ± 10.1%, IPF 65.9 ± 3.6%). Based on similarities between the extensive ILA and IPF groups, we combined these into an ‘advanced disease’ group. In this ‘advanced disease group’, we found 225 up-/105 down-regulated DGs in classical monocytes compared to unaffected subjects (controls) and 41 up-/304 down-regulated DGs compared to the early ILA group. In both classical and non-classical monocytes, type I interferon-α response pathway genes were enriched in ‘advanced disease’ compared to other groups, while TNF-alpha/NF-kB, hypoxia, and p53 pathways were downregulated in the ‘advanced disease’ group. Conclusions Our findings establish a framework for developing predictive biomarkers and investigating circulating immune cell contributions to early pulmonary fibrotic processes in the lungs. This abstract is funded by: P01HL172729
Ciavattone et al. (Fri,) studied this question.