Gene expression profiles and transcriptional regulatory pathways underlying mouse tissue macrophage identity and diversity

Nature Immunology    

Emmanuel L Gautier, Tal Shay, Jennifer Miller, Melanie Greter, Claudia Jakubzick, Stoyan Ivanov, Julie Helft, Andrew Chow, Kutlu G Elpek, Simon Gordonov, Amin R Mazloom, Avi Maayan, Wei-Jen Chua, Ted H Hansen, Shannon J Turley, Miriam Merad, Gwendalyn J Randolph, Immunological Genome Consortium


We assessed tissue macrophage gene expression in different mouse organs. Diversity in gene expression among different populations of macrophages was remarkable. Only a few hundred mRNA transcripts stood out as selectively expressed by macrophages over DCs 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 novel transcripts were distinctly and universally associated with mature tissue macrophages. TCEF3, C/EBPα, BACH1, and CREG-1 were among the top transcriptional regulators predicted to regulate these core macrophage-associated genes. Other transcription factor mRNAs were strongly associated with single macrophage populations. We further illustrate how these transcripts and the proteins they encode facilitate distinguishing macrophage versus DC identity of less characterized populations of mononuclear phagocytes.

Dataset information:

Genomic assay Microarray Samples Microglia, spleen, lung, and peritoneal MFs
Method for deriving gene sets Coefficient of variation & T-test Number of gene sets 4
Figure source Figure 2 Data source Figure 2

Associated gene sets:

Gene set # Description No. of genes
1 Spleen 96
2 Lung 96
3 Peritoneal 95
4 Microglia 50

A total of 337 genes are associated with this dataset.