Spatial transcriptomic characterization of pathologic niches in IPF

• DOI: 10.1126/sciadv.adl5473
• Publication Date: 2024-08-09T18:01:16Z
• Authors: Christoph H. Mayr; Diana Santacruz; Sebastian Jarosch; Marina Bleck; John Dalton; Angela McNabola; Charlotte Lempp; Lavinia Neubert; Berenice Rath; Jan C. Kamp; Danny Jonigk; Mark Kühnel; Holger Schlüter; Alexander Klimowicz; Jonas Doerr; Alec Dick; Fidel Ramirez; Matthew J. Thomas
• Keywords: 0301 basic medicine; 0303 health sciences; Macrophages; Gene Expression Profiling; Humans; Biomedicine and Life Sciences; Single-Cell Analysis; Transcriptome; Myofibroblasts; Lung; Idiopathic Pulmonary Fibrosis

Despite advancements in antifibrotic therapy, idiopathic pulmonary fibrosis (IPF) remains a medical condition with unmet needs. Single-cell RNA sequencing (scRNA-seq) has enhanced our understanding of IPF but lacks the cellular tissue context and gene expression localization that spatial transcriptomics provides. To bridge this gap, we profiled control patient lung using transcriptomics, integrating data an scRNA-seq atlas. We identified three disease-associated niches unique compositions localizations. These include fibrotic niche, consisting myofibroblasts aberrant basaloid cells, located around airways adjacent to airway macrophage niche lumen, containing SPP1