Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

Brian J Pepe-Mooney; Michael T Dill; Anna Alemany; Jose Ordovas-Montanes; Yuki Matsushita; Anuradha Rao; Anushna Sen; Makoto Miyazaki; Sayeepriyadarshini Anakk; Paul A Dawson; Noriaki Ono; Alex K Shalek; Alexander van Oudenaarden; Fernando D Camargo

doi:10.1016/j.stem.2019.04.004

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

Cell Stem Cell. 2019 Jul 3;25(1):23-38.e8. doi: 10.1016/j.stem.2019.04.004. Epub 2019 May 9.

Authors

Affiliations

¹ Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
² Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
³ Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
⁴ Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁵ Department of Orthodontics and Pediatric Dentistry, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA.
⁶ Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
⁷ Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
⁸ Division of Renal Diseases and Hypertension, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA.
⁹ Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA 02139, USA.
¹⁰ Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address: fernando.camargo@childrens.harvard.edu.

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 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.

Keywords: YAP signaling; bile acids; biliary epithelial cells; cellular plasticity; cholangiocytes; hepatocytes; liver biology; liver progenitor cells; regeneration; single-cell RNA sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adaptor Proteins, Signal Transducing / genetics
Adaptor Proteins, Signal Transducing / metabolism*
Animals
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism*
Cell Proliferation
Cell Self Renewal
Chemical and Drug Induced Liver Injury / metabolism*
Chemical and Drug Induced Liver Injury / pathology
Disease Models, Animal
Epithelial Cells / metabolism*
Epithelial Cells / pathology
Female
Hepatocytes / physiology*
Homeostasis
Humans
Liver / pathology*
Liver Regeneration
Male
Mice
Mice, Inbred C57BL
Mice, Knockout
Pyridines / toxicity
Signal Transduction
Single-Cell Analysis
YAP-Signaling Proteins

Substances

3,5-diethoxycarbonyl-1,4-dihydrocollidine
Adaptor Proteins, Signal Transducing
Cell Cycle Proteins
Pyridines
YAP-Signaling Proteins
Yap1 protein, mouse

Abstract

Publication types

MeSH terms

Substances

Grants and funding