Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

Sonya A. MacParland, Jeff C. Liu, Xue Zhong Ma, Brendan T. Innes, Agata M. Bartczak, Blair K. Gage, Justin Manuel, Nicholas Khuu, Juan Echeverri, Ivan Linares, Rahul Gupta, Michael L. Cheng, Lewis Y. Liu, Damra Camat, Sai W. Chung, Rebecca K. Seliga, Zigong Shao, Elizabeth Lee, Shinichiro Ogawa, Mina OgawaMichael D. Wilson, Jason E. Fish, Markus Selzner, Anand Ghanekar, David Grant, Paul Greig, Gonzalo Sapisochin, Nazia Selzner, Neil Winegarden, Oyedele Adeyi, Gordon Keller, Gary D. Bader, Ian D. McGilvray

Research output: Contribution to journalArticlepeer-review

790 Scopus citations


The liver is the largest solid organ in the body and is critical for metabolic and immune functions. However, little is known about the cells that make up the human liver and its immune microenvironment. Here we report a map of the cellular landscape of the human liver using single-cell RNA sequencing. We provide the transcriptional profiles of 8444 parenchymal and non-parenchymal cells obtained from the fractionation of fresh hepatic tissue from five human livers. Using gene expression patterns, flow cytometry, and immunohistochemical examinations, we identify 20 discrete cell populations of hepatocytes, endothelial cells, cholangiocytes, hepatic stellate cells, B cells, conventional and non-conventional T cells, NK-like cells, and distinct intrahepatic monocyte/macrophage populations. Together, our study presents a comprehensive view of the human liver at single-cell resolution that outlines the characteristics of resident cells in the liver, and in particular provides a map of the human hepatic immune microenvironment.

Original languageEnglish (US)
Article number4383
JournalNature communications
Issue number1
StatePublished - Dec 1 2018

Bibliographical note

Funding Information:
This research was funded in part by the University of Toronto’s Medicine by Design initiative, which receives funding from the Canada First Research Excellence Fund (CFREF) to IDM and by start-up funds from the Multi-Organ transplant program at the UHN to SAM. We would like to acknowledge Dr. M. Guilliams (VIB, Ghent University) and Dr. I.N. Crispe (University of Washington) for discussions of macrophage ontogeny. We would like to thank Joy Qu [] for generating the illustration in Fig. 10. This work was supported by NRNB (U.S. National Institutes of Health, grant P41 GM103504) to GDB.

Publisher Copyright:
© 2018, The Author(s).

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't


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