Emergence of inflammatory fibroblasts with aging in Hermansky-Pudlak syndrome associated pulmonary fibrosis

The longitudinal cellular interactions that drive pulmonary fibrosis are not well understood. To investigate the disease underpinnings associated with fibrosis onset and progression, we generated a scRNAseq atlas of lungs from young and aged mouse models of multiple subtypes of Hermansky-Pudlak syndrome (HPS), a collection of rare autosomal recessive diseases associated with albinism, platelet dysfunction, and pulmonary fibrosis. We identified an age-dependent increase in SAA3+ inflammatory lung fibroblasts in HPS mice, including in double-mutant HPS1-2 mice which develop spontaneous fibrosis. HPS1 fibroblasts showed increased expression of IL-1R1, whereas alveolar type II epithelial cells from HPS2 mice induced the inflammatory gene signature in co-cultured fibroblasts. scRNAseq of lung tissue from three HPS1 patients similarly showed the presence of inflammatory fibroblasts and increased IL1R1 expression on fibroblasts. These data posit complex interactions between dysfunctional epithelial cells, inflammatory fibroblasts, and recruited immune cells, suggesting potential opportunities for mitigation of the fibrotic cascade. 

This record contains gzipped anndata h5ad (hdf5) files corresponding to the human scRNA-seq data analyzed during this study. One file (`adata_processed_data_generated_in_study_zenodo.h5ad`) contains only data derived from new samples processed in this study. Another file (`adata_processed_combined_zenodo.h5ad`) contains the aforementioned data from new samples, as well as data from previously published studies that are publicly available (Guo et. al., 2023, Tsukui et.al., 2022, Habermann et. al., 2020). Raw gene expression counts, as well as normalized counts, are provided as values in the `layers` attribute of the anndata object. Cell annotations and projection coordinates are similarly provided in the `obs` and `obsm` attributes of the object, respectively. The AnnData and Scanpy python libraries are required to load and re-process these data.