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Podleśny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer's disease and other disorders of lipid-rich tissues. Nat Commun 2024; 15:2058. [PMID: 38448474 PMCID: PMC10917780 DOI: 10.1038/s41467-024-46315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
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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Affiliation(s)
- Anna Podleśny-Drabiniok
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gloriia Novikova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- OMNI Bioinformatics Department, Genentech, Inc., South San Francisco, CA, USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rose Temizer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Samuele Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Alison Mary Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Xu L, Min H, Saha A, Gunaratne A, Schwartzman J, Parrott R, Kurtzberg J, Filiano AJ. Mesenchymal stromal cells suppress microglial activation and tumor necrosis factor production. Cytotherapy 2024; 26:185-193. [PMID: 38054911 DOI: 10.1016/j.jcyt.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND AIMS White matter diseases are commonly associated with microglial activation and neuroinflammation. Mesenchymal stromal cells (MSCs) have immunomodulatory properties and thus have the potential to be developed as cell therapy for white matter disease. MSCs interact with resident macrophages to alter the trajectory of inflammation; however, the impact MSCs have on central nervous system macrophages and the effect this has on the progression of white matter disease are unclear. METHODS In this study, we utilized numerous assays of varying complexity to model different aspects of white matter disease. These assays ranged from an in vivo spinal cord acute demyelination model to a simple microglial cell line activation assay. Our goal was to investigate the influence of human umbilical cord tissue MSCs on the activation of microglia. RESULTS MSCs reduced the production of tumor necrosis factor (TNF) by microglia and decreased demyelinated lesions in the spinal cord after acute focal injury. To determine if MSCs could directly suppress the activation of microglia and to develop an efficient potency assay, we utilized isolated primary microglia from mouse brains and the Immortalized MicroGlial Cell Line (IMG). MSCs suppressed the activation of microglia and the release of TNF after stimulation with lipopolysaccharide, a toll-like receptor agonist. CONCLUSIONS In this study, we demonstrated that MSCs altered the immune response after acute injury in the spinal cord. In numerous assays, MSCs suppressed activation of microglia and release of the pro-inflammatory cytokine TNF. Of these assays, IMG could be standardized and used as an effective potency assay to determine the efficacy of MSCs for treating white matter disease or other neuroinflammatory conditions associated with microglial activation.
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Affiliation(s)
- Li Xu
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA
| | - Hyunjung Min
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA
| | - Arjun Saha
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA
| | - Aruni Gunaratne
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA; Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | | | - Roberta Parrott
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA
| | - Joanne Kurtzberg
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA; Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Anthony J Filiano
- Marcus Center for Cellular Cures, Duke University, Durham, North Carolina, USA; Department of Neurosurgery, Duke University, Durham, North Carolina, USA; Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA; Department of Pathology, Duke University, Durham, North Carolina, USA.
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3
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Tripathi S, Nathan CL, Tate MC, Horbinski CM, Templer JW, Rosenow JM, Sita TL, James CD, Deneen B, Miller SD, Heimberger AB. The immune system and metabolic products in epilepsy and glioma-associated epilepsy: emerging therapeutic directions. JCI Insight 2024; 9:e174753. [PMID: 38193532 PMCID: PMC10906461 DOI: 10.1172/jci.insight.174753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Epilepsy has a profound impact on quality of life. Despite the development of new antiseizure medications (ASMs), approximately one-third of affected patients have drug-refractory epilepsy and are nonresponsive to medical treatment. Nearly all currently approved ASMs target neuronal activity through ion channel modulation. Recent human and animal model studies have implicated new immunotherapeutic and metabolomic approaches that may benefit patients with epilepsy. In this Review, we detail the proinflammatory immune landscape of epilepsy and contrast this with the immunosuppressive microenvironment in patients with glioma-related epilepsy. In the tumor setting, excessive neuronal activity facilitates immunosuppression, thereby contributing to subsequent glioma progression. Metabolic modulation of the IDH1-mutant pathway provides a dual pathway for reversing immune suppression and dampening seizure activity. Elucidating the relationship between neurons and immunoreactivity is an area for the prioritization and development of the next era of ASMs.
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Affiliation(s)
- Shashwat Tripathi
- Department of Neurological Surgery
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center
| | | | | | - Craig M. Horbinski
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center
- Department of Pathology, and
| | | | | | - Timothy L. Sita
- Department of Neurological Surgery
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Charles D. James
- Department of Neurological Surgery
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center
| | - Benjamin Deneen
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Stephen D. Miller
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Amy B. Heimberger
- Department of Neurological Surgery
- Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center
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4
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Abstract
Microglia are resident macrophages of the central nervous system that have key functions in its development, homeostasis and response to damage and infection. Although microglia have been increasingly implicated in contributing to the pathology that underpins neurological dysfunction and disease, they also have crucial roles in neurological homeostasis and regeneration. This includes regulation of the maintenance and regeneration of myelin, the membrane that surrounds neuronal axons, which is required for axonal health and function. Myelin is damaged with normal ageing and in several neurodegenerative diseases, such as multiple sclerosis and Alzheimer disease. Given the lack of approved therapies targeting myelin maintenance or regeneration, it is imperative to understand the mechanisms by which microglia support and restore myelin health to identify potential therapeutic approaches. However, the mechanisms by which microglia regulate myelin loss or integrity are still being uncovered. In this Review, we discuss recent work that reveals the changes in white matter with ageing and neurodegenerative disease, how this relates to microglia dynamics during myelin damage and regeneration, and factors that influence the regenerative functions of microglia.
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Affiliation(s)
- Sarah A Kent
- UK Dementia Research Institute at The University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, Chancellor's Building, The University of Edinburgh, Edinburgh, UK
| | - Veronique E Miron
- UK Dementia Research Institute at The University of Edinburgh, Edinburgh, UK.
- Centre for Discovery Brain Sciences, Chancellor's Building, The University of Edinburgh, Edinburgh, UK.
- Barlo Multiple Sclerosis Centre, St Michael's Hospital, Toronto, Ontario, Canada.
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, Ontario, Canada.
- Department of Immunology, The University of Toronto, Toronto, Ontario, Canada.
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Baaklini CS, Ho MFS, Lange T, Hammond BP, Panda SP, Zirngibl M, Zia S, Himmelsbach K, Rana H, Phillips B, Antoszko D, Ibanga J, Lopez M, Lee KV, Keough MB, Caprariello AV, Kerr BJ, Plemel JR. Microglia promote remyelination independent of their role in clearing myelin debris. Cell Rep 2023; 42:113574. [PMID: 38100356 DOI: 10.1016/j.celrep.2023.113574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease characterized by myelin loss. While therapies exist to slow MS progression, no treatment currently exists for remyelination. Remyelination, linked to reduced disability in MS, relies on microglia and monocyte-derived macrophages (MDMs). This study aims to understand the role of microglia during remyelination by lineage tracing and depleting them. Microglial lineage tracing reveals that both microglia and MDMs initially accumulate, but microglia later dominate the lesion. Microglia and MDMs engulf equal amounts of inhibitory myelin debris, but after microglial depletion, MDMs compensate by engulfing more myelin debris. Microglial depletion does, however, reduce the recruitment and proliferation of oligodendrocyte progenitor cells (OPCs) and impairs their subsequent differentiation and remyelination. These findings underscore the essential role of microglia during remyelination and offer insights for enhancing this process by understanding microglial regulation of remyelination.
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Affiliation(s)
- Charbel S Baaklini
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Madelene F S Ho
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tristan Lange
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Brady P Hammond
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Sharmistha P Panda
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Martin Zirngibl
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Sameera Zia
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kassandre Himmelsbach
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Heli Rana
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Braxton Phillips
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Daria Antoszko
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jeremies Ibanga
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Mizuki Lopez
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kelly V Lee
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Michael B Keough
- Division of Neurosurgery, Department of Surgery, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Andrew V Caprariello
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Cumming School of Medicine, Calgary, AB T2N 1N4, Canada
| | - Bradley J Kerr
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada; Department of Anesthesiology & Pain Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jason R Plemel
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada; Department of Medicine, Division of Neurology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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Schröder LJ, Mulenge F, Pavlou A, Skripuletz T, Stangel M, Gudi V, Kalinke U. Dynamics of reactive astrocytes fosters tissue regeneration after cuprizone-induced demyelination. Glia 2023; 71:2573-2590. [PMID: 37455566 DOI: 10.1002/glia.24440] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Demyelination in the central nervous system (CNS) is a hallmark of many neurodegenerative diseases such as multiple sclerosis (MS) and others. Here, we studied astrocytes during de- and remyelination in the cuprizone mouse model. To this end, we exploited the ribosomal tagging (RiboTag) technology that is based on Cre-mediated cell type-selective HA-tagging of ribosomes. Analyses were performed in the corpus callosum of GFAP-Cre+/- Rpl22HA/wt mice 5 weeks after cuprizone feeding, at the peak of demyelination, and 0.5 and 2 weeks after cuprizone withdrawal, when remyelination and tissue repair is initiated. After 5 weeks of cuprizone feeding, reactive astrocytes showed inflammatory signatures with enhanced expression of genes that modulate leukocyte migration (Tlr2, Cd86, Parp14) and they produced the chemokine CXCL10, as verified by histology. Furthermore, demyelination-induced reactive astrocytes expressed numerous ligands including Cx3cl1, Csf1, Il34, and Gas6 that act on homeostatic as well as activated microglia and thus potentially mediate activation and recruitment of microglia and enhancement of their phagocytotic activity. During early remyelination, HA-tagged cells displayed reduced inflammatory response signatures, as indicated by shutdown of CXCL10 production, and enhanced expression of osteopontin (SPP1) as well as of factors that are relevant for tissue remodeling (Timp1), regeneration and axonal repair. During late remyelination, the signatures shifted towards resolving inflammation by active suppression of lymphocyte activation and differentiation and support of glia cell differentiation. In conclusion, we detected highly dynamic astroglial transcriptomic signatures in the cuprizone model, which reflects excessive communication among glia cells and highlights different astrocyte functions during neurodegeneration and regeneration.
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Affiliation(s)
- Lara-Jasmin Schröder
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Felix Mulenge
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | | | - Martin Stangel
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Viktoria Gudi
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience, University of Veterinary Medicine Hannover, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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Guo ML, Roodsari SK, Cheng Y, Dempsey RE, Hu W. Microglia NLRP3 Inflammasome and Neuroimmune Signaling in Substance Use Disorders. Biomolecules 2023; 13:922. [PMID: 37371502 DOI: 10.3390/biom13060922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
During the last decade, substance use disorders (SUDs) have been increasingly recognized as neuroinflammation-related brain diseases. Various types of abused drugs (cocaine, methamphetamine, alcohol, opiate-like drugs, marijuana, etc.) can modulate the activation status of microglia and neuroinflammation levels which are involved in the pathogenesis of SUDs. Several neuroimmune signaling pathways, including TLR/NF-кB, reactive oxygen species, mitochondria dysfunction, as well as autophagy defection, etc., have been implicated in promoting SUDs. Recently, inflammasome-mediated signaling has been identified as playing critical roles in the microglia activation induced by abused drugs. Among the family of inflammasomes, NOD-, LRR-, and pyrin-domain-containing protein 3 (NLRP3) serves the primary research target due to its abundant expression in microglia. NLRP3 has the capability of integrating multiple external and internal inputs and coordinately determining the intensity of microglia activation under various pathological conditions. Here, we summarize the effects of abused drugs on NLRP3 inflammasomes, as well as others, if any. The research on this topic is still at an infant stage; however, the readily available findings suggest that NLRP3 inflammasome could be a common downstream effector stimulated by various types of abused drugs and play critical roles in determining abused-drug-mediated biological effects through enhancing glia-neuron communications. NLRP3 inflammasome might serve as a novel target for ameliorating the development of SUDs.
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Affiliation(s)
- Ming-Lei Guo
- Drug Addiction Laboratory, Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA 23507, USA
- Center for Integrative Neuroscience and Inflammatory Diseases, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Soheil Kazemi Roodsari
- Drug Addiction Laboratory, Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Yan Cheng
- Drug Addiction Laboratory, Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Rachael Elizabeth Dempsey
- Drug Addiction Laboratory, Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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8
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Podlesny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer's disease and other disorders of lipid-rich tissues. bioRxiv 2023:2023.02.13.528372. [PMID: 36824752 PMCID: PMC9948946 DOI: 10.1101/2023.02.13.528372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background 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. Methods 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 in vitro, as well as mouse microglia in vivo. Results We nominate 11 strong candidate LAM TFs shared across human and mouse networks (BHLHE41, HIF1A, ID2, JUNB, MAF, MAFB, MEF2A, MEF2C, NACA, POU2F2 and SPI1). We also demonstrate a strong enrichment of AD risk alleles in the cistrome of BHLHE41 (and its close homolog BHLHE40), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction of BHLHE40/41 expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss of Bhlhe40/41 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. Conclusions 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.
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Affiliation(s)
- Anna Podlesny-Drabiniok
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gloriia Novikova
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- OMNI Bioinformatics Department and Neuroscience Department, Genentech, Inc., South San Francisco, CA, USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rose Temizer
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine (C.G.), Cardiology, NYU Grossman School of Medicine
- Department of Pathology (C.G.), Cardiology, NYU Grossman School of Medicine
| | - Samuele Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alison Mary Goate
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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