Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis

Niklas J. Lang, Janine Gote-Schniering, Diana Porras-Gonzalez, Lin Yang, Laurens J. De Sadeleer, R. Christoph Jentzsch, Vladimir A. Shitov, Shuhong Zhou, Meshal Ansari, Ahmed Agami, Christoph H. Mayr, Baharak Hooshiar Kashani, Yuexin Chen, Lukas Heumos, Jeanine C. Pestoni, Eszter Sarolta Molnar, Emiel Geeraerts, Vincent Anquetil, Laurent Saniere, Melanie WögrathMichael Gerckens, Mareike Lehmann, Ali Önder Yildirim, Rudolf Hatz, Nikolaus Kneidinger, Jürgen Behr, Wim A. Wuyts, Mircea Gabriel Stoleriu, Malte D. Luecken, Fabian J. Theis, Gerald Burgstaller, Herbert B. Schiller

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. 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–staged 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–specific 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.

Original languageEnglish
Article numbereadh0908
JournalScience Translational Medicine
Volume15
Issue number725
DOIs
StatePublished - 2023

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