Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations

Abstract

The proliferation, differentiation and survival of mononuclear phagocytes depend on signals from the receptor for macrophage colony-stimulating factor, CSF1R. The mammalian Csf1r locus contains a highly conserved super-enhancer, the fms -intronic regulatory element (FIRE). Here we show that genomic deletion of FIRE in mice selectively impacts CSF1R expression and tissue macrophage development in specific tissues. Deletion of FIRE ablates macrophage development from murine embryonic stem cells. Csf1r ΔFIRE/ΔFIRE mice lack macrophages in the embryo, brain microglia and resident macrophages in the skin, kidney, heart and peritoneum. The homeostasis of other macrophage populations and monocytes is unaffected, but monocytes and their progenitors in bone marrow lack surface CSF1R. Finally, Csf1r ΔFIRE/ΔFIRE mice are healthy and fertile without the growth, neurological or developmental abnormalities reported in Csf1r −/− rodents. Csf1r ΔFIRE/ΔFIRE mice thus provide a model to explore the homeostatic, physiological and immunological functions of tissue-specific macrophage populations in adult animals.

Transcriptional network analysis of transcriptomic diversity in resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system

“…Genes in Cluster 4 were strongly expressed in samples from brain and include microglia-enriched markers that are depleted in brains of Csf1r-deficient mice and rats such as Cx3cr1, Tmem119, P2ry12 and the key transcription factor genes Sall1, Sall2 and Sall3 [16,61]. Cluster 9 contains the S phase transcription factor gene Foxm1 and numerous cell cycle-associated transcripts [62] and the GO term enrichment supports the cell cycle association.…”

“…Transcripts in Cluster 4 were enriched in the resident kidney macrophages compared to both splenic macrophages and other kidney myeloid populations. Interestingly, the resident kidney macrophage cluster includes many genes that are also highly-expressed in microglia and depleted in the brain in Csf1r mutant mice and rats, including Cx3cr1, C1qa/b/c, Csf3r, Ctss, Fcrls, Hexb, Laptm5, Tgfbr1, Tmem119 and Trem2 [16,61]. These were also detected in the isolated kidney macrophages in Table S1.…”

“…Both populations of interstitial lung macrophages (and all the samples from other tissues in this BioProject) expressed very high levels of all of the IEG transcripts in Cluster 41. Whereas macrophageexpressed transcripts such as Adgre1 are readily detected in total tissue mRNA, and are CSF1Rdependent, inflammatory cytokines and IEG are not [16,61]. Accordingly, in each of these studies, the expression of IEG and inducible cytokines is most likely an artefact of tissue disaggregation.…”

“…Epidermal Langerhans cells (LC) have at times been considered as DC-like because of their migratory and APC properties but are now considered to be a specialized resident tissue macrophage [94]. Unlike most classical DC in lymphoid tissue, they are clearly Csf1r-dependent and share with several other macrophage populations dependence on the conserved enhancer in the Csf1r locus [16]. Cluster 43 did not include a transcriptional regulator specific to LC.…”

“…At least some of these transcription factors act by regulating Csf1r expression. Deletion of a conserved enhancer in the mouse Csf1r gene leads to selective loss of some tissue macrophage populations, whereas others express Csf1r normally [16]. In the mouse embryo, where abundant macrophage populations are engaged with phagocytosis of apoptotic cells [17], the macrophage transcriptome does not differ greatly between organs.…”