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

1535 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
Pages (from-to)1118-1128
Number of pages11
JournalNature immunology
Issue number11
StatePublished - Nov 2012


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