Fibroblast exhibit TB-specific phenotypes. (A) Fibroblast (n = 1,627) subclustering reveals five subclusters (left), also colored by patient ID (middle) and disease condition (right). (B) Heatmap of subtype top 10 DE genes in each of the fibroblast subcluster. Columns (cells) are annotated by fibroblast subclusters and sample source disease status. (C) Comparing annotation against literature stromal annotation from Travaglini et al. (2020). Left: Original fibroblast UMAP as seen in A colored by mapped cell types in Travaglini et al. (2020). Right: Barplot showing distributions of mapped cell type in each original subcluster. ASM, airway smooth muscle; VSM, vascular smooth muscle; MyoF, myofibroblast; FibM, fibromyocyte; AdvF, adventitial fibroblast; AlvF, alveolar fibroblast; LipF, lipofibroblast; Peri, pericyte; Meso, mesothelial. (D) Reference mapping to the HLCA. Query (all cells in this study, n = 19,632) vs. reference cells (n = 584,944) on integrated UMAP with transferred label from HLCA to query cells. (E) Query (all fibroblasts in this study that was mapped to fibroblast/myofibroblast in label transfer, n = 1,601) and reference lung fibroblast cells (n = 17,500) from HLCA colored by annotation (either “Fibroblast” or “Myofibroblast”) and TB conditions. (F) GSEA on DE genes between TB fibroblasts and TB-negative fibroblasts on HLCA-integrated data.