biostudies-literatureUnknownPodlesny-Drabiniok ANIA NIH HHSNHLBI NIH HHS<h4>Background</h4>Genetic and experimental evidence strongly implicates myeloid cells in the etiology of AD and suggests that AD-associated alleles and genes may modulate disease risk by altering the transcriptional and cellular responses of macrophages (like microglia) to damage of lipid-rich tissues (like the brain). Specifically, recent single-cell/nucleus RNA sequencing (sc/nRNA-seq) studies identified a transcriptionally distinct state of subsets of macrophages in aging or degenerating brains (usually referred to as disease-associated microglia or DAM) and in other diseased lipid-rich tissues (e.g., obese adipose tissue, fatty liver, and atherosclerotic plaques). We collectively refer to these subpopulations as lipid-associated macrophages or LAMs. Importantly, this particular activation state is characterized by increased expression of genes involved in the phagocytic clearance of lipid-rich cellular debris (efferocytosis), including several AD risk genes.<h4>Methods</h4>We used sc/nRNA-seq data from human and mouse microglia from healthy and diseased brains and macrophages from other lipid-rich tissues to reconstruct gene regulatory networks and identify transcriptional regulators whose regulons are enriched for LAM response genes (LAM TFs) across species. We then used gene knock-down/knock-out strategies to validate some of these LAM TFs in human THP-1 macrophages and iPSC-derived microglia <i>in vitro</i>, as well as mouse microglia <i>in vivo</i>.<h4>Results</h4>We nominate 11 strong candidate LAM TFs shared across human and mouse networks (<i>BHLHE41</i>, <i>HIF1A</i>, <i>ID2</i>, <i>JUNB</i>, <i>MAF</i>, <i>MAFB</i>, <i>MEF2A</i>, <i>MEF2C</i>, <i>NACA, POU2F2</i> and <i>SPI1</i>). We also demonstrate a strong enrichment of AD risk alleles in the cistrome of <i>BHLHE41</i> (and its close homolog <i>BHLHE40</i>), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction of <i>BHLHE40/41</i> expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss of <i>Bhlhe40</i>/<i>41</i> in mouse microglia led to increased expression of LAM response genes, specifically those involved in cholesterol clearance and lysosomal processing, with a concomitant increase in cholesterol efflux and storage, as well as lysosomal mass and degradative capacity.<h4>Conclusions</h4>Taken together, this study nominates transcriptional regulators of the LAM response, experimentally validates BHLHE40/41 in human and mouse macrophages/microglia, and provides novel targets for therapeutic modulation of macrophage/microglia function in AD and other disorders of lipid-rich tissues.bioRxiv : the preprint server for biology2023.02.13.528372https://www.ebi.ac.uk/biostudies/studies/S-EPMC9948946biostudies-literatureBHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer's disease and other disorders of lipid-rich tissues.PMC9948946U01 AG066757RF1 AG054011R01 HL153712U01 AG058635Marcora ELiu YKreslavsky TNovikova GPodlesny-Drabiniok ADunst JTemizer RGoate AMGiannarelli CMarro SfalseBHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer's disease and other disorders of lipid-rich tissues.<h4>Background</h4>Genetic and experimental evidence strongly implicates myeloid cells in the etiology of AD and suggests that AD-associated alleles and genes may modulate disease risk by altering the transcriptional and cellular responses of macrophages (like microglia) to damage of lipid-rich tissues (like the brain). Specifically, recent single-cell/nucleus RNA sequencing (sc/nRNA-seq) studies identified a transcriptionally distinct state of subsets of macrophages in aging or degenerating brains (usually referred to as disease-associated microglia or DAM) and in other diseased lipid-rich tissues (e.g., obese adipose tissue, fatty liver, and atherosclerotic plaques). We collectively refer to these subpopulations as lipid-associated macrophages or LAMs. Importantly, this particular activation state is characterized by increased expression of genes involved in the phagocytic clearance of lipid-rich cellular debris (efferocytosis), including several AD risk genes.<h4>Methods</h4>We used sc/nRNA-seq data from human and mouse microglia from healthy and diseased brains and macrophages from other lipid-rich tissues to reconstruct gene regulatory networks and identify transcriptional regulators whose regulons are enriched for LAM response genes (LAM TFs) across species. We then used gene knock-down/knock-out strategies to validate some of these LAM TFs in human THP-1 macrophages and iPSC-derived microglia <i>in vitro</i>, as well as mouse microglia <i>in vivo</i>.<h4>Results</h4>We nominate 11 strong candidate LAM TFs shared across human and mouse networks (<i>BHLHE41</i>, <i>HIF1A</i>, <i>ID2</i>, <i>JUNB</i>, <i>MAF</i>, <i>MAFB</i>, <i>MEF2A</i>, <i>MEF2C</i>, <i>NACA, POU2F2</i> and <i>SPI1</i>). We also demonstrate a strong enrichment of AD risk alleles in the cistrome of <i>BHLHE41</i> (and its close homolog <i>BHLHE40</i>), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction of <i>BHLHE40/41</i> expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss of <i>Bhlhe40</i>/<i>41</i> in mouse microglia led to increased expression of LAM response genes, specifically those involved in cholesterol clearance and lysosomal processing, with a concomitant increase in cholesterol efflux and storage, as well as lysosomal mass and degradative capacity.<h4>Conclusions</h4>Taken together, this study nominates transcriptional regulators of the LAM response, experimentally validates BHLHE40/41 in human and mouse macrophages/microglia, and provides novel targets for therapeutic modulation of macrophage/microglia function in AD and other disorders of lipid-rich tissues.2023-01-01T00:00:00Z2023 Feb2026-06-26T03:10:11.813Z2025-04-19T20:51:13.315ZS-EPMC99489463682475210.1101/2023.02.13.528372