Nature and nurture of tissue-specific macrophage phenotypes

Abstract

Macrophages are key players in immunity and tissue homeostasis but can also contribute to a diverse range of human diseases, including cardiovascular diseases. Enhancers, cis-acting DNA elements regulating gene activity, have been shown to be crucial for control of macrophage development and function. The selection and activities of macrophage-specific enhancers are regulated by the combined actions of lineage determining transcription factors (LDTFs) and signal dependent transcription factors (SDTFs) that are specified by developmental origin and tissue-specific signals. As a consequence, each tissue resident macrophage population adopts a distinct phenotype. In this review, we discuss recent work on how environmental factors affect the activation status of enhancers and can lead to long-lasting epigenetic changes resulting in innate immune memory. Furthermore, we discuss how non-coding genetic variation affects gene expression by altering transcription factor binding through local and domain-wide mechanisms. These findings have implications for interpretation of non-coding risk alleles that are associated with human disease and efforts to target macrophages for therapeutic purposes.

Keywords: Enhancer; Genetic variation; Macrophage; Tissue environment.

Fig 1.

Stimulus-dependent macrophage enhancer activation. Macrophage enhancers marked by H3K4me1/2 require macrophage lineage determining transcription factors (LDTFs) like PU.1 and collaborating transcriptions like AP-1 and RUNX1. Enhancers frequently require signal-dependent transcription factor (SDTF) binding to gain H3K27 acetylation before they become active and transcribe enhancer RNAs (eRNA) and/or interact with target gene promoters.

Fig 2.

Environmental factors shape the macrophage enhancer landscape. (A) Tissue macrophages like microglia and peritoneal macrophages (PM) share the majority of macrophage core enhancers, while a subset of enhancers is specific for the tissue they reside in. (B) Environmental factors present in the tissue activate signal dependent transcription factors (SDTFs). In the peritoneum, retinoic acid (RA) activates GATA6 in peritoneal macrophages (PM), while in the brain, factors like TGF-β induce transcription factors SMADs and SALL1 that are specific for microglia.

Fig 3.

Different strains of mice as a tool to study the effects of genetic variation on enhancer activation and gene expression. (A and B) Variation in gene expression scales with underlying genetic variation, variation in LDTF PU.1 binding exceeds the differences seen on the gene expression level. (C) Weighted correlation network analysis (WGCNA) analysis of RNA-seq on macrophages from different strains treated with or without Kdo2-Lipid A (KLA) shows that differentially expressed genes are associated with diverse cellular functions, adapted from Link et al..

Fig 4.

Effects of collaborating transcription factor motif mutations on LDTF binding. (A) Apoe gene expression, as measured with RNA-seq in bone marrow derived macrophages from five strains and strain specific PU.1 binding at the Apoe locus with corresponding H3K27 acetylation in the strains where PU.1 binds. (B) Top 14 of 48 motifs correlated with binding of PU.1 as determined by motif mutation analysis. The node size is the fraction of PU.1 peaks containing the indicated motif, and edge thickness is proportional to the effect size of motif mutations. Nodes indicate motifs in which mutations result in reduced PU.1 binding (red) or in which mutations result in increased PU.1 binding (blue), adapted from Link et al..

Fig 5.

Mechanisms underlying strain-specific transcription factor binding patterns. Only 10–30% of the strain-specific LDTF binding can be explained by mutations in the actual LDTF (PU.1) motif itself, the majority of the variation is explained by mutations in collaborating transcription factor (cTF) motifs. The remaining strain-specific LDTF binding are mostly located in cis-regulatory domains.