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We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT\u2013staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type\u2013specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.<\/jats:p>","DOI":"10.1126\/scitranslmed.adh0908","type":"journal-article","created":{"date-parts":[[2023,12,6]],"date-time":"2023-12-06T13:59:15Z","timestamp":1701871155000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":97,"title":["Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis"],"prefix":"10.1126","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7452-8292","authenticated-orcid":true,"given":"Niklas J.","family":"Lang","sequence":"first","affiliation":[{"name":"Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive\/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7869-4936","authenticated-orcid":true,"given":"Janine","family":"Gote-Schniering","sequence":"additional","affiliation":[{"name":"Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive\/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany."},{"name":"Department of Rheumatology and Immunology, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland."},{"name":"Lung Precision Medicine Program, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2858-7921","authenticated-orcid":true,"given":"Diana","family":"Porras-Gonzalez","sequence":"additional","affiliation":[{"name":"Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive\/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0469-9288","authenticated-orcid":true,"given":"Lin","family":"Yang","sequence":"additional","affiliation":[{"name":"Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive\/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1237-7369","authenticated-orcid":true,"given":"Laurens J.","family":"De Sadeleer","sequence":"additional","affiliation":[{"name":"Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive\/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany."},{"name":"Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5537-3087","authenticated-orcid":true,"given":"R. 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