BHLHE40/41 regulate Microglia and Peripheral Macrophage Responses Associated With Alzheimer's Disease and Other Disorders of Lipid‐rich Tissues
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Genetic and experimental evidence suggests that Alzheimer’s disease (AD) risk alleles and genes may influence disease susceptibility by altering the transcriptional and cellular responses of macrophages, including microglia, to damage of lipid-rich tissues like the brain. Recently, sc/nRNA sequencing studies identified similar transcriptional activation states in subpopulations of macrophages in aging and degenerating brains and in other diseased lipid-rich tissues. We collectively refer to these subpopulations of microglia and peripheral macrophages as DLAMs. Using macrophage sc/nRNA-seq data from healthy and diseased human and mouse lipid-rich tissues, we reconstructed gene regulatory networks and identified 11 strong candidate transcriptional regulators of the DLAM response across species. Loss or reduction of two of these transcription factors, BHLHE40/41, in iPSC-derived microglia and human THP-1 macrophages as well as loss of Bhlhe40/41 in mouse microglia, resulted in increased expression of DLAM genes involved in cholesterol clearance and lysosomal processing, increased cholesterol efflux and storage, and increased lysosomal mass and degradative capacity. These findings provide targets for therapeutic modulation of macrophage/microglial function in AD and other disorders affecting lipid-rich tissues.
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BHLHE40/41 regulate genes involved in lipid clearance (ABCA1, APOE, LPL), lysosomal processing (CTSD, PSAP, LAMP-1 and -2), TREM2, metabolism (PPARγ, LXR), and efferocytosis.
“Specifically, BHLHE40/41 regulate genes involved in lipid clearance (ABCA1, APOE, LPL), lysosomal processing (CTSD, PSAP, LAMP‐ 1 and ‐2), TREM2, metabolism (PPARγ, LXR), and efferocytosis (the process by which apoptotic cells are cleared by phagocytic cells) [53].”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [53]
The Results report that loss of BHLHE40/41 increased expression of genes involved in cholesterol clearance and lysosomal processing in human iPSC-derived microglia; Fig. 5 specifically identifies APOE and ABCA1. The Discussion describes opposition to LXR:RXR-regulated pathways. Our copy does not establish BHLHE40/41 regulation of every gene listed—particularly LPL, CTSD, PSAP, LAMP-1/2, and TREM2—or of efferocytosis; it discusses efferocytosis in other contexts. (LLM, conf=0.87)
Experimental — accuracy not yet measuredBHLHE40/41 bind to open chromatin at promoters and enhancers of LXR:RXR and MiT/TFE family transcriptional factors, acting as transcriptional repressors and modulating cholesterol/lipid efflux genes and lysosomal genes, thereby influencing cellular clearance functions.
“BHLHE40/41 bind to open chromatin at promoters and enhancers of LXR:RXR and MiT/TFE family transcriptional factors, acting as transcriptional repressors and modulating cholesterol/lipid efflux genes and lysosomal genes, thereby influencing cellular clearance functions (Figure 1 and Table 2) [53, 54].”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [53]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredPU.1, IRF8, and BHLHE40/41 regulate multiple downstream targets that orchestrate microglial immune response functions, including phagocytosis, cytokine production, and inflammatory signaling.
“PU.1, IRF8, and BHLHE40/41 regulates multiple downstream targets that orchestrate microglial immune response functions, including phagocytosis, cytokine production, and inflammatory signaling”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [53]
The Results section on DLAM gene promoters identifies BHLHE41 and SPI1/PU.1 regulons enriched for likely direct targets. Other Results sections link BHLHE40/41 knockout in human iPSC-derived microglia to predicted changes in cell engulfment and measured changes in cytokine secretion. The paper’s shortlist of candidate regulators does not include IRF8, and these passages do not establish the claimed downstream regulation by all three factors or specifically demonstrate inflammatory signaling. (LLM, conf=0.86)
Experimental — accuracy not yet measuredMEF2C functions as a counterbalance by suppressing excessive pro-inflammatory responses.
“MEF2C functions as a counterbalance by suppressing excessive pro‐inflammatory responses”
From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [53]
The Results section on candidate DLAM transcription factors names MEF2C as a candidate regulator of macrophage and microglial responses (page unavailable). It does not say that MEF2C suppresses excessive pro-inflammatory responses; the Results passage on reduced pro-inflammatory cytokines concerns BHLHE40/41 knockout, not MEF2C. (LLM, conf=0.82)
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Ou, L., Han, S., Hao, T., Ding, G., Mai, K., & Ai, Q. (2026) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2026.111763
Metabolic reprogramming in macrophages: the central role of lipid metabolism in bone homeostasis
Li, L., Zhang, Y., Huang, S., Xiao, Y., Liu, G., Wu, Z., Hu, Y., Gong, S., 冒静, Song, K., et al. (2026) · Bone Research · doi:10.1038/s41413-026-00590-w
- Authors
- Podleśny-Drabiniok, A., Novikova, G., Liu, Y., Dunst, J., Temizer, R., Giannarelli, C., Marro, S., Kreslavsky, T., Marcora, E., & Goate, A. M.
- Affiliations
- Genentech (US)
- Icahn School of Medicine at Mount Sinai (US)
- Karolinska University Hospital (SE)
- New York University (US)
- Corresponding author
- Marcora, Edoardo
- Goate, Alison Mary
- ORCID
- Venue
- Nature Communications
- Published
- 2024-03-06
- Volume
- 15
- Issue
- 1
- Pages
- 2058-2058
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10917780
- OpenAlex
- W4392503471
- Cited by
- 52
- References
- 101
- Citations by year
- 2026: 25 · 2025: 18 · 2024: 9
- FWCI
- 8.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- American Heart Association (20SFRN35210252)
- New York State Department of Health (NYSTEM-C32561GG)
- BrightFocus Foundation (A2021014F)
- JPB Foundation (U01AG058635)
- New York State Stem Cell Science (NYSTEM‐C32561GG, C32561GG)
- Graduate Women in Science
- Georgia Clinical and Translational Science Alliance (UL1TR004419)
- National Institutes of Health (1r56ag081417-01, 1s10od026880-01, 1s10od030463-01, UL1TR004419)
- National Institute on Aging (U01AG058635, U01AG066757, R56 AG081417, RF1AG054011, P30AG066514)
- National Heart, Lung, and Blood Institute (R01HL153712)
- National Center for Advancing Translational Sciences (S10OD026880, S10OD030463)
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Keywords
- microglia, peripheral macrophages, Alzheimer's disease, gene regulatory networks, cholesterol efflux, lysosomal function, macrophage heterogeneity, iPSC-derived microglia, THP-1 macrophages, transcription factors
- MeSH terms
- Alzheimer Disease, Animals, Cholesterol, Humans, Lipids, Macrophages, Microglia, Homeodomain Proteins, Mice, Basic Helix-Loop-Helix Transcription Factors, Basic Helix-Loop-Helix Proteins
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