Monocyte Subset Predict Clinical Outcomes in Fibrotic Hypersensitivity Pneumonitis

RationaleHypersensitivity pneumonitis (HP) is an immunologically mediated form of lung disease resulting from inhalational exposure to various antigens. While there is growing understanding of the immune cells involved in HP, the relationship between clinical outcomes and circulating cell types in HP is not well established. MethodsSingle-cell RNA sequencing was performed on peripheral blood mononuclear cells (PBMCs) from 40 patients with fibrotic hypersensitivity pneumonitis (fHP) in a clinical trial of pirfenidone (NCT02958917). After quality control, we compared data from 33 fHP patients with 36 sex-matched healthy controls (GSE196735). Using Seurat v5, we harmonized the data, formed clusters, and reduced dimensionality through UMAP. Cell type identities were assigned based on a published reference (GSE271789), with clusters annotated for predominant cell type(s) present in at least 30% of the cells. We compared cell type proportions between fHP and HC using the chi-squared test and performed differential expression analysis with DESeq2 on pseudobulk counts, adjusting for sex. Genes significantly upregulated in fHP versus HC at an FDR-adjusted p-value of 0.01 were used to create a multivariate predictive signature for clinical outcomes in fHP participants. Performance was assessed through leave-one-out cross-validation for prediction accuracy. ResultsCompared to HC, fHP has an increased proportion of non-classical CD16+ monocytes (4.2% fHP vs. 1.5% HC), C14+ monocytes with a myeloid-derived dendritic phenotype (2.1% fHP vs. 0.1% HC), platelets (1.0% fHP vs. 0.3% HC), plasmacytoid dendritic cells (0.5% fHP vs. 0.1% HC) and predominantly classical CD14+ monocytes (29.5% fHP vs. 3.4% HC, adjusted-p<0.001). In patients with fHP, cell clusters were associated with the presence of baseline chest CT honeycombing, increased extent of CT lung fibrosis, and worse progression-free survival. CD14+ monocytes consistently demonstrated a high prediction accuracy (>0.90) for these clinical metrics. ConclusionsPeripheral monocyte clusters may be valuable prognostic markers, potentially helping identify at-risk fHP patients.