Highlights d Myeloid cell diversity in NASH is associated with distinct microanatomical niches d Reprogramming of LXR activity leads to impaired Kupffer cell identify and survival d ATF3 collaborates with LXRs to promote a scar-associated macrophage phenotype d Altered enhancer landscapes enable inference of disease mechanisms

Highlights d Determinants of Kupffer cell identity are inferred from dynamic enhancer landscapes d DLL4 activates poised enhancers to induce Kupffer cell lineage-determining factors d LXRa induced by DLL4 drives subsequent activation of Kupffer cell enhancers d TGF-b and desmosterol regulate SMADs and LXRs to maintain Kupffer cell identity

Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.

Significance Toll-like receptors recognize conserved molecules that are expressed by both harmless (commensal) and harmful (virulent) microbes. Another set of receptors, nucleotide-binding oligomerization domain-like receptors (NLRs), are expressed in the cytosol and recognize virulence factors and toxins from pathogenic microbes. Previous studies on TLRs and NLRs have suggested that TLR signaling primes the NLR inflammasome pathway. Here we discovered that TLRs, via the signaling molecule IL-1 receptor-associated kinase, directly regulate activation of a specific NLR, nucleotide binding and oligomerization, leucine-rich repeat, pyrin domain-containing 3 (NLRP3). This is important because when infection occurs, the virulent/pathogenic microorganisms activate both of these receptors. We also found that simultaneous activation of TLRs and NLRP3 is important for rapid innate immune response by the host.

Toll like receptors (TLRs) use Toll-IL-1 receptor (TIR) domain-containing adapters, such as myeloid differentiation primary response gene 88 (MyD88) and TIR domain-containing adapter inducing IFN-β (TRIF), to induce activation of transcription factors, including NF-κB, MAP kinases, and IFN regulatory factors. TLR signaling also leads to activation of PI3K, but the molecular mechanism is not understood. Here we have discovered a unique role for B-cell adapter for PI3K (BCAP) in the TLR-signaling pathway. We find that BCAP has a functional N-terminal TIR homology domain and links TLR signaling to activation of PI3K. In addition, BCAP negatively regulates proinflammatory cytokine secretion upon TLR stimulation. In vivo, the absence of BCAP leads to exaggerated recruitment of inflammatory myeloid cells following infections and enhanced susceptibility to dextran sulfate sodium-induced colitis. Our results demonstrate that BCAP is a unique TIR domaincontaining TLR signaling adapter crucial for linking TLRs to PI3K activation and regulating the inflammatory response.inflammation | negative regulator | macrophage | innate immunity | pattern recognition receptors