Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
Pepe-Mooney, Brian J.; Dill, Michael T.; Alemany, Anna; Ordovas-Montanes, Jose; Matsushita, Yuki; Rao, Anuradha; Sen, Anushna; Miyazaki, Makoto; Anakk, Sayeepriyadarshini; Dawson, Paul A.; Ono, Noriaki; Shalek, Alex K.; van Oudenaarden, Alexander; Camargo, Fernando D.
(2019) Cell Stem Cell, volume 25, issue 1, pp. 23 - 38.e8
(Article)
Abstract
The liver can substantially regenerate after injury, with both main epithelial cell types, hepatocytes and biliary epithelial cells (BECs), playing important roles in parenchymal regeneration. Beyond metabolic functions, BECs exhibit substantial plasticity and in some contexts can drive hepatic repopulation. Here, we performed single-cell RNA sequencing to examine BEC and
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hepatocyte heterogeneity during homeostasis and after injury. Instead of evidence for a transcriptionally defined progenitor-like BEC cell, we found significant homeostatic BEC heterogeneity that reflects fluctuating activation of a YAP-dependent program. This transcriptional signature defines a dynamic cellular state during homeostasis and is highly responsive to injury. YAP signaling is induced by physiological bile acids (BAs), required for BEC survival in response to BA exposure, and is necessary for hepatocyte reprogramming into biliary progenitors upon injury. Together, these findings uncover molecular heterogeneity within the ductal epithelium and reveal YAP as a protective rheostat and regenerative regulator in the mammalian liver. The transcriptional landscape of the epithelium in healthy and regenerating murine livers was investigated, revealing a dynamically fluctuating and heterogeneous YAP transcriptional program. Further analysis uncovered YAP signaling dualism: it is essential in biliary epithelial cells for homeostatic maintenance and in hepatocytes for the regenerative response to injury.
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Keywords: bile acids, biliary epithelial cells, cellular plasticity, cholangiocytes, hepatocytes, liver biology, liver progenitor cells, regeneration, single-cell RNA sequencing, YAP signaling, Molecular Medicine, Genetics, Cell Biology
ISSN: 1934-5909
Publisher: Cell Press
Note: Funding Information: The authors are grateful to Ronald Mathieu and Mahnaz Paktinat for assistance with FACS and Luigi Terracciano for his assistance in evaluation of histopathology. The authors thank Charles Murtaugh for Hes1CreER mice and the members of the Camargo laboratory for helpful discussion. This work was supported by a National Science Foundation Predoctoral Award and NIH grant F31 DK107049-01A1 (B.J.P.-M.); Swiss National Science Foundation fellowships P2BSP3_161941 and P300PB_171568 and the Eugen and Elisabeth Schellenberg-Stiftung (M.T.D.); European Research Council Advanced grant ERC-AdG 742225-IntScOmics; Nederlandse Organisatie voor Wetenschappelijk Onderzoek TOP award NWO-CW 714.016.001; and the Foundation for Fundamental Research on Matter, financially supported by the NWO (FOM-14NOISE01) (A.v.O.). A.K.S. was supported by the Searle Scholars Program, the Beckman Young Investigator Program, the Alfred P. Sloan Foundation, the NIH (grants 1DP2GM119419, 2U19AI089992, 1U54CA217377, 2P01AI039671, 5U24AI118672, 2RM1HG006193, and 1R33CA202820), and the Bill and Melinda Gates Foundation (grants OPP1139972 and BMGF OPP1116944). J.O.M. is an HHMI Damon Runyon Cancer Research Foundation Fellow (DRG-2274-16). A.R. and P.A.D. were supported by NIH grant R01 DK047987. Further support was provided by NIH grants R01 DK099559 and NIHR01 AR064036 (F.D.C.). B.J.P.-M. and F.D.C. conceived the study; B.J.P.-M. and M.T.D. designed, performed, and analyzed experiments and prepared figures; A.A. aided in single-cell figure generation and performed all scRNA-seq computational analysis and additional statistical analysis with direction from B.J.P.-M. and M.T.D. under the supervision of A.v.O.; J.O.-M. performed “Seq-Well” hepatocyte capture, library preparation, and sequencing and pre-processed sequencing data under the supervision of A.K.S.; Y.M. A.R. and A.S. performed experiments on collaborative mouse models under the supervision of N.O. P.A.D. and S.A.; and M.M. performed experiments on collaborative mouse models. F.D.C. supervised the study. B.J.P.-M. and M.T.D. wrote the manuscript, which was edited by all co-authors. The authors declare no competing interests. Funding Information: The authors are grateful to Ronald Mathieu and Mahnaz Paktinat for assistance with FACS and Luigi Terracciano for his assistance in evaluation of histopathology. The authors thank Charles Murtaugh for Hes1 CreER mice and the members of the Camargo laboratory for helpful discussion. This work was supported by a National Science Foundation Predoctoral Award and NIH grant F31 DK107049-01A1 (B.J.P.-M.); Swiss National Science Foundation fellowships P2BSP3_161941 and P300PB_171568 and the Eugen and Elisabeth Schellenberg-Stiftung (M.T.D.); European Research Council Advanced grant ERC-AdG 742225-IntScOmics ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek TOP award NWO-CW 714.016.001 ; and the Foundation for Fundamental Research on Matter, financially supported by the NWO ( FOM-14NOISE01 ) (A.v.O.). A.K.S. was supported by the Searle Scholars Program , the Beckman Young Investigator Program , the Alfred P. Sloan Foundation , the NIH (grants 1DP2GM119419 , 2U19AI089992 , 1U54CA217377 , 2P01AI039671 , 5U24AI118672 , 2RM1HG006193 , and 1R33CA202820 ), and the Bill and Melinda Gates Foundation (grants OPP1139972 and BMGF OPP1116944 ). J.O.M. is an HHMI Damon Runyon Cancer Research Foundation Fellow ( DRG-2274-16 ). A.R. and P.A.D. were supported by NIH grant R01 DK047987 . Further support was provided by NIH grants R01 DK099559 and NIHR01 AR064036 (F.D.C.). Publisher Copyright: © 2019 Elsevier Inc.
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