Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

Emmanuel L. Gautiar, Tal Shay, Jennifer Miller, Melanie Greter, Claudia Jakubzick, Stoyan Ivanov, Julie Helft, Andrew Chow, Kutlu G. Elpek, Simon Gordonov, Amin R. Mazloom, Avi Ma'Ayan, Wei Jen Chua, Ted H. Hansen, Shannon J. Turley, Miriam Merad, Gwendalyn J. Randolph, Adam J. Best, Jamie Knell, Ananda GoldrathBrian Brown, Vladimir Jojic, Daphne Koller, Nadia Cohen, Michael Brenner, Aviv Regev, Anne Fletcher, Angelique Bellemare-Pelletier, Deepali Malhotra, Radu Jianu, David Laidlaw, Jim Collins, Kavitha Narayan, Katelyn Sylvia, Joonsoo Kang, Roi Gazit, Brian S. Garrison, Derrick J. Rossi, Francis Kim, Tata Nageswara Rao, Amy Wagers, Susan A. Shinton, Richard R. Hardy, Paul Monach, Natalie A. Bezman, Joseph C. Sun, Charlie C. Kim, Lewis L. Lanier, Tracy Heng, Taras Kreslavsky, Michio Painter, Jeffrey Ericson, Scott Davis, Diane Mathis, Christophe Benoist

Research output: Contribution to journalArticlepeer-review

1510 Scopus citations


We assessed gene expression in tissue macrophages from various mouse organs. The diversity in gene expression among different populations of macrophages was considerable. Only a few hundred mRNA transcripts were selectively expressed by macrophages rather than dendritic cells, and many of these were not present in all macrophages. Nonetheless, well-characterized surface markers, including MerTK and FcγR1 (CD64), along with a cluster of previously unidentified transcripts, were distinctly and universally associated with mature tissue macrophages. TCEF3, C/EBP-α, Bach1 and CREG-1 were among the transcriptional regulators predicted to regulate these core macrophage-associated genes. The mRNA encoding other transcription factors, such as Gata6, was associated with single macrophage populations. We further identified how these transcripts and the proteins they encode facilitated distinguishing macrophages from dendritic cells.

Original languageEnglish (US)
Pages (from-to)1118-1128
Number of pages11
JournalNature immunology
Issue number11
StatePublished - Nov 2012

Bibliographical note

Funding Information:
We thank our colleagues of the ImmGen Project consortium; V. Jojic, J. Ericson, S. Davis and C. Benoist for contributions; eBioscience and Affymetrix for material support of the ImmGen Project; and M. Colonna (Washington University School of Medicine) for monoclonal antibodies (including anti-Siglec-H) and other reagents. Supported by the National Institute of Allergy and Infectious Diseases of the US National Institutes of Health (R24 AI072073 to fund the ImmGen Project, spearheaded by C. Benoist), the US National Institutes of Health (R01AI049653 and R01AI061741 to G.J.R.; P50GM071558-03 and R01DK08854 to A.M.; and5T32DA007135-27 to A.R.M.) and the American Heart Association (10POST4160140 to E.L.G.).


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