Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases

Zhao, A. Y.; Unterman, A.; Abu Hussein, N.; Sharma, P.; Flint, J.; Yan, X.; Adams, T. S.; Justet, A.; Sumida, T. S.; Zhao, J.; Schupp, J. C.; Raredon, M. S. B.; Ahangari, F. C.; Zhang, Y.; Buendia-Roldan, I.; Adegunsoye, A.; Sperling, A. I.; Prasse, A.; Ryu, C.; Herzog, E.; Selman, M.; Pardo, A.; Kaminski, N.

doi:10.1101/2023.09.20.558301

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bioRxiv · 10.1101/2023.09.20.558301

Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases

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Abstract

Rationale and ObjectivesThe extent and commonality of peripheral blood immune aberrations in fibrotic interstitial lung diseases are not well characterized. In this study, we aimed to identify common and distinct immune aberrations in patients with idiopathic pulmonary fibrosis (IPF) and fibrotic hypersensitivity pneumonitis (FHP) using cutting-edge single-cell profiling technologies. MethodsSingle-cell RNA sequencing was performed on patients and healthy controls peripheral blood and bronchoalveolar lavage samples using 10X Genomics 5 gene expression and V(D)J profiling. Cell type composition, transcriptional profiles, cellular trajectories and signaling, and T and B cell receptor repertoires were studied. The standard Seurat R pipeline was followed for cell type composition and differential gene expression analyses. Transcription factor activity was imputed using the DoRothEA-VIPER algorithm. Pseudotime analyses were conducted using Monocle3, while RNA velocity analyses were performed with Velocyto, scVelo, and CellRank. Cell-cell connectomics were assessed using the Connectome R package. V(D)J analyses were conducted using CellRanger and Immcantation frameworks. Across all analyses, disease group differences were assessed using the Wilcoxon rank-sum test. Measurements and Main Results327,990 cells from 83 samples were profiled. Overall, changes in monocytes were common to IPF and FHP, whereas lymphocytes exhibited disease-specific aberrations. Both diseases displayed enrichment of CCL3hi/CCL4hi CD14+ monocytes (p<2.2e-16) and S100Ahi CD14+ monocytes (p<2.2e-16) versus controls. Trajectory and RNA velocity analysis suggested that pro-fibrotic macrophages observed in BAL originated from peripheral blood monocytes. Lymphocytes exhibited disease-specific aberrations, with CD8+ GZMKhi T cells and activated B cells primarily enriched in FHP patients. V(D)J analyses revealed unique T and B cell receptor complementarity-determining region 3 (CDR3) amino acid compositions (p<0.05) in FHP and significant IgA enrichment in IPF (p<5.2e-7). ConclusionsWe identified common and disease-specific immune mechanisms in IPF and FHP; S100Ahi monocytes and SPP1hi macrophages are common to IPF and FHP, whereas GMZKhi T lymphocytes and T and B cell receptor repertoires were unique in FHP. Our findings open novel strategies for the diagnosis and treatment of IPF and FHP.

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Zhao, A. Y., Unterman, A., Abu Hussein, N., Sharma, P., Flint, J., Yan, X., Adams, T. S., Justet, A., Sumida, T. S., Zhao, J., Schupp, J. C., Raredon, M. S. B., Ahangari, F. C., Zhang, Y., Buendia-Roldan, I., Adegunsoye, A., Sperling, A. I., Prasse, A., Ryu, C., Herzog, E., Selman, M., Pardo, A., Kaminski, N.. 2023-09-22. Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases. https://doi.org/10.1101/2023.09.20.558301

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