Single-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis
Amy Zhao, Avraham Unterman, Nebal Abu Hussein, Prapti Sharma, Fadi Nikola, Jasper Flint, Xiting Yan, Taylor Adams, A. Justet, Tomokazu S. Sumida, Jiayi Zhao, Jonas C. Schupp, Micha Sam Brickman Raredon, Farida Ahangari, G. Deluliis, Yingze Zhang, Ivette Buendía-Roldán, Ayodeji Adegunsoye, Anne I. Sperling, Antje Prasse, Changwan Ryu, Erica L. Herzog, Moisés Selman, Annie Pardo, Naftali Kaminski
Abstract
Abstract Rationale Fibrotic hypersensitivity pneumonitis (FHP) is a debilitating interstitial lung disease driven by incompletely understood immune mechanisms. Objectives To elucidate immune aberrations in FHP in single-cell resolution. Methods Single-cell 5′ RNA sequencing was conducted on peripheral blood mononuclear cells and BAL cells obtained from 45 patients with FHP, 63 patients with idiopathic pulmonary fibrosis (IPF), 4 patients with nonfibrotic hypersensitivity pneumonitis, and 36 healthy control subjects in the United States and Mexico. Analyses included differential gene expression (Seurat), TF (transcription factor) activity imputation (DoRothEA-VIPER), and trajectory analyses (Monocle3 and Velocyto-scVelo-CellRank). Measurements and Main Results Overall, 501,534 peripheral blood mononuclear cells from 110 patients and control subjects and 88,336 BAL cells from 19 patients were profiled. Compared with control samples, FHP has elevated classical monocytes (adjusted-P = 2.5 × 10−3) and is enriched in CCL3hi/CCL4hiand S100Ahiclassical monocytes (adjusted-P < 2.2 × 10−16). Trajectory analyses demonstrate that S100Ahiclassical monocytes differentiate into SPP1hilung macrophages associated with fibrosis. Compared with both control subjects and IPF, cells from patients with FHP are significantly enriched in GZMhicytotoxic T cells. These cells exhibit TF activities indicative of TGFβ and TNFα and NFκB pathways. These results are publicly available at http://ildimmunecellatlas.com. Conclusions Single-cell transcriptomics of patients with FHP uncovered novel immune perturbations, including previously undescribed increases in GZMhicytotoxic CD4+ and CD8+ T cells—reflecting this disease’s unique inflammatory T cell–driven nature—as well as increased S100Ahiand CCL3hi/CCL4hiclassical monocytes also observed in IPF. Both cell populations may guide the development of new biomarkers and therapeutic interventions.