Online Supplement: Peripheral Blood Monocyte Clusters Predict Radiographic Severity and Progression in Fibrotic Hypersensitivity Pneumonitis

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Online Supplement

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Single-cell RNA sequencing (scRNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from 33 adult patients with fibrotic hypersensitivity pneumonitis (fHP) enrolled in a prospective 52-week pirfenidone clinical trial (ClinicalTrials.gov: NCT02958917). Baseline blood samples were collected prior to treatment initiation. Thirty-six sex-matched healthy controls were obtained from a publicly available dataset (GEO: GSE196735, pools 1–3). Single-cell libraries were prepared using the 10x Genomics Chromium platform and sequenced on an Illumina sequencer. Standard scRNA-seq processing (including quality control, normalization, integration, clustering, and cell type annotation via label transfer from a published fHP PBMC reference GEO: GSE271789) was performed in R using Seurat, DESeq2, glmnet, and mdatools. Clinical outcomes (progression-free survival events) and HRCT fibrosis extent (quantified by data-driven texture analysis) were modeled using elastic net regularization and partial least-squares discriminant analysis. Full methodological details, including all software versions, parameters, quality control thresholds, and analytical workflows, are provided in the Online Supplement deposited alongside this dataset.

Institutions

• National Jewish Health

  Colorado, Denver

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