Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses by potentiating glucocorticoid receptor activity

Abstract

In macrophages, homeostatic and immune signals induce distinct sets of transcriptional responses, defining cellular identity and functional states. The activity of lineage-specific and signal-induced transcription factors are regulated by chromatin accessibility and other epigenetic modulators. Glucocorticoids are potent antiinflammatory drugs; however, the mechanisms by which they selectively attenuate inflammatory genes are not yet understood. Acting through the glucocorticoid receptor (GR), glucocorticoids directly repress inflammatory responses at transcriptional and epigenetic levels in macrophages. A major unanswered question relates to the sequence of events that result in the formation of repressive regions. In this study, we identify bromodomain containing 9 (BRD9), a component of SWI/SNF chromatin remodeling complex, as a modulator of glucocorticoid responses in macrophages. Inhibition, degradation, or genetic depletion of BRD9 in bone marrow-derived macrophages significantly attenuated their responses to both liposaccharides and interferon inflammatory stimuli. Notably, BRD9-regulated genes extensively overlap with those regulated by the synthetic glucocorticoid dexamethasone. Pharmacologic inhibition of BRD9 potentiated the antiinflammatory responses of dexamethasone, while the genetic deletion of BRD9 in macrophages reduced high-fat diet-induced adipose inflammation. Mechanistically, BRD9 colocalized at a subset of GR genomic binding sites, and depletion of BRD9 enhanced GR occupancy primarily at inflammatory-related genes to potentiate GR-induced repression. Collectively, these findings establish BRD9 as a genomic antagonist of GR at inflammatory-related genes in macrophages, and reveal a potential for BRD9 inhibitors to increase the therapeutic efficacies of glucocorticoids.

Ultra-Rare BRD9 Loss-of-Function Variants Limit the Antiviral Action of Interferon

“…These analyses suggest that human BRD9 is well conserved, and may indicate that rare BRD9 missense variants are not readily tolerated in humans. This would be consistent with the critical role of BRD9 in the gene expression regulatory functions of the ncBAF chromatin remodeling complex 20 , and potentially also the antiviral IFN system [16][17][18] .…”

“…BRD9 defines the ncBAF chromatin remodeling complex that, together with the canonical STAT1-STAT2-IRF9 transcription factor complex, has previously been identified as an important contributor to efficient IFN-stimulated gene transcription and antiviral immunity [16][17][18] . Our evaluation of BRD9 genetic variants has now identified that severely truncated ultra-rare BRD9 LOF alleles exist in the human population, and revealed that under conditions where only these alleles are present there is compromised ability of IFN to fully protect cells against virus infection.…”

“…Our rationale was that loss-of-function missense genetic variants may exist in human populations and have the potential to compromise IFN-mediated antiviral immunity, but have not yet been identified due to their extreme rarity or recessive nature, or due to their existence in non-canonical IFN signaling pathway components that are not part of most targeted analyses. In this latter regard, we therefore focused our attention on bromodomain-containing protein 9 (BRD9), an epigenetic reader and defining subunit of non-canonical BAF (ncBAF) chromatin remodeling complexes, that we and others have newly characterized as a cellular contributor to efficient ISG expression and antiviral immunity [16][17][18] . We now explore a range of rare human BRD9 genetic variants that are predicted to be deleterious in human genomes, and use functional reconstitution experiments in BRD9 knock-out cells to assess their impact on IFN-mediated antiviral activity.…”

BRD9 regulates interferon-stimulated genes during macrophage activation via cooperation with BET protein BRD4

“…Notably, most DEGs are down-regulated by inhibitor treatment, in agreement with the cluster results showing dampened induction of genes 4 h post Lipid A stimulation. Finally, to determine how well each BRD9 inhibitor treatment correlated with Brd9 genetic deletion, we made use of an RNA-seq dataset comparing LPS + IFN-γ treatment in BMDM derived from wild-type or Brd9f/f;LysM-Cre animals, in which Brd9 is conditionally deleted in the myeloid lineage ( 22 ). Using gene set enrichment analysis (GSEA), we found that genes down-regulated in BI-9564-, dBRD9-, and I-BRD9-treated Lipid A-induced macrophages were positively correlated with genes down-regulated in LPS+IFN-γ–treated Brd9 knockout macrophages with normalized enrichment scores (NES) of 2.47, 2.33, and 2.35, respectively ( Fig.…”

“…Publicly available data were processed using HOMER version 4.10 (Christopher Benner, HOMER, http://homer.ucsd.edu/homer/index.html ). The following database deposition numbers are given: for RNA-seq of Irf3 −/− , Ifnar −/− , Trif −/− , Myd88 −/− , Pam3, and CHX treatment, GEO GSE67355 ( 2 ); for RNA-seq of LysM-Cre BRD9 knockout, Sequence Read Archive (SRA) PRJNA731887 ( 22 ); for ChIP-seq of IRF3, GEO GSE67357 ( 2 ); IRF9, STAT1, and STAT2 in IFNb stimulation, GEO GSE115435 ( 19 ); PU.1, GEO GSE38379 ( 25 ); and p65, GEO GSE106701 ( 26 ).…”