The transcriptome of CD14 + CD163 − HLA-DR low monocytes predicts mortality in idiopathic pulmonary fibrosis

Background The association between immune-cell-specific transcriptomic profiles and mortality in idiopathic pulmonary fibrosis (IPF) is unknown. Methods We profiled peripheral blood mononuclear cells by single-cell RNA sequencing (scRNA-seq) and investigated which immune-cell-specific transcriptomic profile predicted IPF outcomes consistently. Prognostic accuracy was investigated in peripheral blood mononuclear cells (PBMCs), bronchoalveolar lavage (BAL) and lung tissue. Findings were validated by flow cytometry, analysis of independent scRNA-seq datasets and cellular deconvolution. We investigated the function of this transcriptomic profile and its cellular source in lung tissue (overall sample size, n=1054; IPF, n=555; other, n=499). Connectivity map analysis and LASSO regression were used to identify drug candidates and a subset of genes with prognostic potential, respectively. Results A 230-gene up-score (Pittsburgh PBMC cohort) from CD14 + CD163 − HLA-DR low monocytes predicted mortality in the Chicago PBMC cohort (HR 6.58, 95% CI 2.15–20.13; p=0.001), in BAL pooled analysis (HR 2.20, 95% CI 1.44–3.37; p=0.0003), and negatively correlated with forced vital capacity in lung tissues (ρ= −0.2, p=0.02). Proportions of CD14 + CD163 − HLA-DR low monocytes were higher in progressive versus stable IPF (12.59%, 95% CI 9.66–16.23%, versus 7.61%, 95% CI 6.68–10.21%; p=0.014). High-risk patients with IPF had decreased expression of T-cell co-stimulatory genes (Pittsburgh and Chicago, p<0.01). CD14 + HLA-DR low monocytes had higher expression of profibrotic, proangiogenic and chemotactic factors compared to CD14 + HLA-DR hi monocytes (p<0.05). The 230-gene up-score correlated with the secreted phosphoprotein 1 (SPP1) + fibrosis-associated macrophages gene-score in lung tissues (ρ=0.19, p<2.2e −16 ). Connectivity map analysis identified drug categories to reverse the 230-gene signature. A subset of six genes retained predictive performance (pooled PBMC cohorts HR 4.79, 95% CI 2.58–8.92; p<0.0001). Conclusions The transcriptome of CD14 + CD163 − HLA-DR low monocytes is associated with increased mortality in patients with IPF. Its reversal should be investigated as a precision-based therapy in IPF.