Deciphering microglia phenotypes in health and disease

Abstract

Microglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent transcription factors interact to select and regulate the ensembles of enhancers that determine microglia development and function. We then highlight recent findings that advance these concepts and conclude with a consideration of open questions that represent some of the major hurdles to be addressed in the future.

Figure 1.. Human microglia undergo rapid changes upon in vitro culturing.

(a) Schematic showing the number of genes that are differentially expressed upon culturing primary ex vivo human microglia isolated from cortical brain tissue for the indicated amount of time. Data are derived from Gosselin et al., 2017. Created with BioRender.com. (b) Expression of SALL1 (left, transcripts per million (TPM)) and read coverage of H3K27ac ChIP-seq (right) in primary ex vivo human microglia and human microglia cultured for 7 days. Data are derived from Gosselin et al., 2017. Image of browser track was generated from the UCSC Genome Browser.

Figure 2.. Collaborative-hierarchical model of enhancer activation in microglia.

(a) (left) Lineage-determining transcription factors (LDTFs, blue and green) recognize their respective motifs (rectangles) in the closed chromatin conformation. Collaborative binding effects of LDTFs displace nucleosomes and open chromatin, generating primed enhancers marked by H3K4 mono- and/or di-methylation (H3K4me1/2). Subsequent cellular sensing of homeostatic or pathogenic environmental signals, such as CSF1 / IL34 / TGFβ or Pathogen / Damage-associated molecular patterns (PAMPs/DAMPs), respectively, leads to the activation of signal-dependent transcription factors (SDTFs, red) that bind to the primed enhancers. These concerted actions result in the recruitment of co-activators, acetylation of nearby histones (e.g., H3K27ac), enhancer activation and promotion of gene transcription. (right) Examples of core macrophage LDTFs (blue), microglia LDTFs (green), and SDTFs (red) shown as a Venn diagram to emphasize the concept that SDTFs and LDTFs can be interchangeably dependent on cell-type and environment context. *SALL1 and MEF2C can recognize highly related motifs, as determined by machine-learning approaches (Fixsen et al., 2023), but the two factors also have independent binding sites. Figure created in BioRender.com. (b) Motifs recognized by transcription factor families that are detected in the active enhancers of primary human microglia (left), human fetal microglia (center), or human postnatal microglia (right).

Figure 3.. Interaction of SALL1 and SMAD4 to regulate microglia-specific genes.

In mice, TGFβ signaling in microglia results in the activation of SMADs which bind to the Sall1 super-enhancer promoting its expression. Accordingly, the absence of SMADs leads to loss of Sall1 expression (Fixsen et al., 2023). This signaling axis is evolutionarily conserved through the orthologues Dpp and Mad which allow for cell-specific expression of Spalt in the Drosophila wing. SALL1 subsequently directs SMAD activity by interacting with SMADs to activate microglia-specific enhancers (bottom left). In parallel, SALL1 prevents SMAD binding at other genomic loci resulting in repression of gene activity (bottom right). Figure created in BioRender.com.