biostudies-literatureUnknownVannan ANHLBI NIH HHSNHGRI NIH HHSThe human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characteribioRxiv : the preprint server for biology2023.12.15.571954https://www.ebi.ac.uk/biostudies/studies/S-EPMC10760144biostudies-literatureImage-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis.PMC10760144R01 HG011886R01 HL126176K08 HL143051R01 HL168556T32 HL094296P01 HL092870R01 HL158906R01 HL145372Ware LBBlackwell TSWilliams ALSerezani APKropski JANichols DSNegretti NMMcCall ASMcCarthy DJVannan AWalia RShim HCalvi CLGokey JJMee EDHirsh STaylor CJSucre JMShaver CMHirsh JPolosukhin VVBacchetta MJBanovich NELyu RfalseImage-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis.The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characteri2023-01-01T00:00:00Z2023 Dec2026-04-07T16:18:48.813Z2026-04-07T15:15:07.976ZS-EPMC107601443816831710.1101/2023.12.15.571954