Single-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis

• Published in: American journal of respiratory and critical care medicine Vol. 210; no. 10; pp. 1252 - 1266
• Main Authors: Zhao, Amy Y., Unterman, Avraham, Abu Hussein, Nebal S., Sharma, Prapti, Nikola, Fadi, Flint, Jasper, Yan, Xiting, Adams, Taylor S., Justet, Aurelien, Sumida, Tomokazu S., Zhao, Jiayi, Schupp, Jonas C., Raredon, Micha Sam B., Ahangari, Farida, Deluliis, Giuseppe, Zhang, Yingze, Buendia-Roldan, Ivette, Adegunsoye, Ayodeji, Sperling, Anne I., Prasse, Antje, Ryu, Changwan, Herzog, Erica, Selman, Moises, Pardo, Annie, Kaminski, Naftali
• Format: Journal Article
• Language: English
• Published: United States American Thoracic Society 15.11.2024
• Subjects: Adult; Aged; Alveolitis, Extrinsic Allergic - immunology; Biomarkers; Bronchoalveolar Lavage Fluid - cytology; Bronchoalveolar Lavage Fluid - immunology; Case-Control Studies; Cells; Female; Humans; Idiopathic Pulmonary Fibrosis - genetics; Idiopathic Pulmonary Fibrosis - immunology; Immune system; Leukocytes, Mononuclear - immunology; Male; Medical research; Medical treatment; Mexico; Middle Aged; Monocytes - immunology; Original; Pulmonary fibrosis; Ribonucleic acid; RNA; Single-Cell Analysis - methods; Mexico; single-cell RNA sequencing; idiopathic pulmonary fibrosis; usual interstitial pneumonia; interstitial lung disease; fibrotic hypersensitivity pneumonitis
• ISSN: 1073-449X; 1535-4970; 1535-4970
• DOI: 10.1164/rccm.202401-0078OC

Fibrotic hypersensitivity pneumonitis (FHP) is a debilitating interstitial lung disease driven by incompletely understood immune mechanisms. To elucidate immune aberrations in FHP in single-cell resolution. 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). 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-  = 2.5 × 10 ) and is enriched in CCL3 /CCL4 and S100A classical monocytes (adjusted-  < 2.2 × 10 ). Trajectory analyses demonstrate that S100A classical monocytes differentiate into SPP1 lung macrophages associated with fibrosis. Compared with both control subjects and IPF, cells from patients with FHP are significantly enriched in GZM cytotoxic T cells. These cells exhibit TF activities indicative of TGFβ and TNFα and NFκB pathways. These results are publicly available at http://ildimmunecellatlas.com. Single-cell transcriptomics of patients with FHP uncovered novel immune perturbations, including previously undescribed increases in GZM cytotoxic CD4  and CD8  T cells-reflecting this disease's unique inflammatory T cell-driven nature-as well as increased S100A and CCL3 /CCL4 classical monocytes also observed in IPF. Both cell populations may guide the development of new biomarkers and therapeutic interventions.