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Pannetta M, Smal M, Ferravante C, Eletto D, Di Rosa D, Alexandrova E, Rizzo F, Voli A, Tosco A, Weisz A, Porta A. Transcriptome analysis of macrophages during Brucella abortus infection clarifies the survival mechanisms of the bacteria. Diagn Microbiol Infect Dis 2024; 110:116401. [PMID: 38878343 DOI: 10.1016/j.diagmicrobio.2024.116401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 07/30/2024]
Abstract
Brucellosis is a critical zoonotic disease impacting humans and animals globally, causing symptoms like fever and arthritis in humans and reproductive issues in animals. The disease stems from the Brucella genus, adept at evading the immune system and proliferating within host cells. This study explores how Brucella abortus manipulates host cellular mechanisms to sustain infection, focusing on the interaction with murine macrophages over 24 h. Initial host defenses involve innate immune responses, while Brucella's survival strategies include evading lysosomal degradation and modulating host cell functions through various pathways. The research identified significant transcriptional changes in macrophages post-infection, highlighting pathways such as cytokine storm, pyroptosis signaling, Toll-like receptor pathways, and LXRs/RXRs signaling. The findings shed light on Brucella's complex mechanisms to undermine host defenses and underscore the need for further investigation into therapeutic targets to combat brucellosis.
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Affiliation(s)
- Martina Pannetta
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy; Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, SA, Italy
| | - Marharyta Smal
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy
| | - Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy; Medical Genomics Program and Division of Oncology, AOU "S. Giovanni di Dio e Ruggi d'Aragona", University of Salerno, Salerno, Italy
| | - Daniela Eletto
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Domenico Di Rosa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy; Medical Genomics Program and Division of Oncology, AOU "S. Giovanni di Dio e Ruggi d'Aragona", University of Salerno, Salerno, Italy; Genome Research Center for Health-CRGS, Campus of Medicine of the University of Salerno, Baronissi, SA, Italy
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy; Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, SA, Italy
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana" University of Salerno, Baronissi, SA, Italy; Medical Genomics Program and Division of Oncology, AOU "S. Giovanni di Dio e Ruggi d'Aragona", University of Salerno, Salerno, Italy; Genome Research Center for Health-CRGS, Campus of Medicine of the University of Salerno, Baronissi, SA, Italy
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy.
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Iwata A, Maruyama J, Natsuki S, Nishiyama A, Tamura T, Tanaka M, Shichino S, Seki T, Komai T, Okamura T, Fujio K, Tanaka M, Asano K. Egr2 drives the differentiation of Ly6C hi monocytes into fibrosis-promoting macrophages in metabolic dysfunction-associated steatohepatitis in mice. Commun Biol 2024; 7:681. [PMID: 38831027 PMCID: PMC11148031 DOI: 10.1038/s42003-024-06357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH), previously called non-alcoholic steatohepatitis (NASH), is a growing concern worldwide, with liver fibrosis being a critical determinant of its prognosis. Monocyte-derived macrophages have been implicated in MASH-associated liver fibrosis, yet their precise roles and the underlying differentiation mechanisms remain elusive. In this study, we unveil a key orchestrator of this process: long chain saturated fatty acid-Egr2 pathway. Our findings identify the transcription factor Egr2 as the driving force behind monocyte differentiation into hepatic lipid-associated macrophages (hLAMs) within MASH liver. Notably, Egr2-deficiency reroutes monocyte differentiation towards a macrophage subset resembling resident Kupffer cells, hampering hLAM formation. This shift has a profound impact, suppressing the transition from benign steatosis to liver fibrosis, demonstrating the critical pro-fibrotic role played by hLAMs in MASH pathogenesis. Long-chain saturated fatty acids that accumulate in MASH liver emerge as potent inducers of Egr2 expression in macrophages, a process counteracted by unsaturated fatty acids. Furthermore, oral oleic acid administration effectively reduces hLAMs in MASH mice. In conclusion, our work not only elucidates the intricate interplay between saturated fatty acids, Egr2, and monocyte-derived macrophages but also highlights the therapeutic promise of targeting the saturated fatty acid-Egr2 axis in monocytes for MASH management.
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Grants
- 22H05190 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H05064 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JPMXP0618217493, JPMXP0622717006, and JPMXP0723833149 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H03473 Japan Society for the Promotion of Science London (JSPS London)
- 21K06877 Japan Society for the Promotion of Science London (JSPS London)
- JP18gm1210002 Japan Agency for Medical Research and Development (AMED)
- JP21gm6210025 Japan Agency for Medical Research and Development (AMED)
- Ono Medical Research Foundation
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Affiliation(s)
- Ayaka Iwata
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Juri Maruyama
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Shibata Natsuki
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, 236-0004, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, 236-0004, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, 236-0004, Japan
| | - Minoru Tanaka
- Department of Regenerative Medicine, Research Institute National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, 278-0022, Japan
| | - Takao Seki
- Department of Biochemistry, Toho University School of Medicine, Tokyo, 143-8540, Japan
| | - Toshihiko Komai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Masato Tanaka
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan.
| | - Kenichi Asano
- Laboratory of Immune Regulation, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan.
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Nagy G, Bojcsuk D, Tzerpos P, Cseh T, Nagy L. Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression. Nucleic Acids Res 2024; 52:4234-4256. [PMID: 38348998 PMCID: PMC11077085 DOI: 10.1093/nar/gkae088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 05/09/2024] Open
Abstract
Mammalian promoters consist of multifarious elements, which make them unique and support the selection of the proper transcript variants required under diverse conditions in distinct cell types. However, their direct DNA-transcription factor (TF) interactions are mostly unidentified. Murine bone marrow-derived macrophages (BMDMs) are a widely used model for studying gene expression regulation. Thus, this model serves as a rich source of various next-generation sequencing data sets, including a large number of TF cistromes. By processing and integrating the available cistromic, epigenomic and transcriptomic data from BMDMs, we characterized the macrophage-specific direct DNA-TF interactions, with a particular emphasis on those specific for promoters. Whilst active promoters are enriched for certain types of typically methylatable elements, more than half of them contain non-methylatable and prototypically promoter-distal elements. In addition, circa 14% of promoters-including that of Csf1r-are composed exclusively of 'distal' elements that provide cell type-specific gene regulation by specialized TFs. Similar to CG-rich promoters, these also contain methylatable CG sites that are demethylated in a significant portion and show high polymerase activity. We conclude that this unusual class of promoters regulates cell type-specific gene expression in macrophages, and such a mechanism might exist in other cell types too.
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Affiliation(s)
- Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Dóra Bojcsuk
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Petros Tzerpos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tímea Cseh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
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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] [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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5
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Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
- Present address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Andy Y. Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Wenxi Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhuang Miao
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Present address: Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Present address: Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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6
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Deochand DK, Dacic M, Bale MJ, Daman AW, Josefowicz SZ, Oliver D, Chinenov Y, Rogatsky I. Mechanisms of Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580560. [PMID: 38405750 PMCID: PMC10888924 DOI: 10.1101/2024.02.16.580560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Macrophages adopt distinct phenotypes in response to environmental cues, with type-2 cytokine interleukin-4 promoting a tissue-repair homeostatic state (M2IL4). Glucocorticoids, widely used anti-inflammatory therapeutics, reportedly impart a similar phenotype (M2GC), but how such disparate pathways may functionally converge is unknown. We show using integrative functional genomics that M2IL4 and M2GC transcriptomes share a striking overlap mirrored by a shift in chromatin landscape in both common and signal-specific gene subsets. This core homeostatic program is enacted by transcriptional effectors KLF4 and the GC receptor, whose genome-wide occupancy and actions are integrated in a stimulus-specific manner by the nuclear receptor cofactor GRIP1. Indeed, many of the M2IL4:M2GC-shared transcriptomic changes were GRIP1-dependent. Consistently, GRIP1 loss attenuated phagocytic activity of both populations in vitro and macrophage tissue-repair properties in the murine colitis model in vivo. These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform anti-inflammatory drug design.
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Affiliation(s)
- Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Marija Dacic
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - David Oliver
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Yurii Chinenov
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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7
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Mu Z, Shen T, Deng H, Zeng B, Huang C, Mao Z, Xie Y, Pei Y, Guo L, Hu R, Chen L, Zhou Y. Enantiomer-Dependent Supramolecular Immunosuppressive Modulation for Tissue Reconstruction. ACS NANO 2024; 18:5051-5067. [PMID: 38306400 DOI: 10.1021/acsnano.3c11601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Modulating the properties of biomaterials in terms of the host immune response is critical for tissue repair and regeneration. However, it is unclear how the preference for the cellular microenvironment manipulates the chiral immune responses under physiological or pathological conditions. Here, we reported that in vivo and in vitro oligopeptide immunosuppressive modulation was achieved by manipulation of macrophage polarization using chiral tetrapeptide (Ac-FFFK-OH, marked as FFFK) supramolecular polymers. The results suggested that chiral FFFK nanofibers can serve as a defense mechanism in the restoration of tissue homeostasis by upregulating macrophage M2 polarization via the Src-STAT6 axis. More importantly, transiently acting STAT6, insufficient to induce a sustained polarization program, then passes the baton to EGR2, thereby continuously maintaining the M2 polarization program. It is worth noting that the L-chirality exhibits a more potent effect in inducing macrophage M2 polarization than does the D-chirality, leading to enhanced tissue reconstruction. These findings elucidate the crucial molecular signals that mediate chirality-dependent supramolecular immunosuppression in damaged tissues while also providing an effective chiral supramolecular strategy for regulating macrophage M2 polarization and promoting tissue injury repair based on the self-assembling chiral peptide design.
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Affiliation(s)
- Zhixiang Mu
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Tianxi Shen
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Hui Deng
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Bairui Zeng
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Chen Huang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Zhengjin Mao
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Yuyu Xie
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325000, P. R. China
| | - Yu Pei
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325000, P. R. China
| | - Liting Guo
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325000, P. R. China
| | - Rongdang Hu
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Limin Chen
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, P. R. China
| | - Yunlong Zhou
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, P. R. China
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8
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Sharma D, Sharma A, Hu L, Chen TA, Voon S, Bayless KJ, Goldman J, Walsh AJ, Zhao F. Perfusability and immunogenicity of implantable pre-vascularized tissues recapitulating features of native capillary network. Bioact Mater 2023; 30:184-199. [PMID: 37589031 PMCID: PMC10425689 DOI: 10.1016/j.bioactmat.2023.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023] Open
Abstract
Vascularization is a key pre-requisite to engineered anatomical scale three dimensional (3-D) constructs to ensure their nutrient and oxygen supply upon implantation. Presently, engineered pre-vascularized 3-D tissues are limited to only micro-scale hydrogels, which meet neither the anatomical scale needs nor the complexity of natural extracellular matrix (ECM) environments. Anatomical scale perfusable constructs are critically needed for translational applications. To overcome this challenge, we previously developed pre-vascularized ECM sheets with long and oriented dense microvascular networks. The present study further evaluated the patency, perfusability and innate immune response toward these pre-vascularized constructs. Macrophage-co-cultured pre-vascularized constructs were evaluated in vitro to confirm micro-vessel patency and perturbations in macrophage metabolism. Subcutaneously implanted pre-vascularized constructs remained viable and formed a functional anastomosis with host vasculature within 3 days of implantation. This completely biological pre-vascularized construct holds great potential as a building block to engineer perfusable anatomical scale tissues.
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Affiliation(s)
- Dhavan Sharma
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Archita Sharma
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Linghao Hu
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Te-An Chen
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Sarah Voon
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Kayla J. Bayless
- School of Medicine, Texas A&M University, College Station, TX, United States
| | - Jeremy Goldman
- Department of Biomedical Engineering, Michigan Technological University, Houghton, MI, United States
| | - Alex J. Walsh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Feng Zhao
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
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9
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Inclan-Rico JM, Napuri CM, Lin C, Hung LY, Ferguson AA, Wu Q, Pastore CF, Stephenson A, Femoe UM, Rossi HL, Reed DR, Luo W, Abdus-Saboor I, Herbert DR. "MrgprA3 neurons selectively control myeloid-derived cytokines for IL-17 dependent cutaneous immunity". RESEARCH SQUARE 2023:rs.3.rs-3644984. [PMID: 38076920 PMCID: PMC10705600 DOI: 10.21203/rs.3.rs-3644984/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Skin employs interdependent cellular networks to facilitate barrier integrity and host immunity through ill-defined mechanisms. This study demonstrates that manipulation of itch-sensing neurons bearing the Mas-related G protein-coupled receptor A3 (MrgprA3) drives IL-17+ γδ T cell expansion, epidermal thickening, and resistance to the human pathogen Schistosoma mansoni through mechanisms that require myeloid antigen presenting cells (APC). Activated MrgprA3 neurons instruct myeloid APCs to downregulate interleukin 33 (IL-33) and up-regulate TNFα partially through the neuropeptide calcitonin gene related peptide (CGRP). Strikingly, cell-intrinsic deletion of IL-33 in myeloid APC basally alters chromatin accessibility at inflammatory cytokine loci and promotes IL-17/23-dependent epidermal thickening, keratinocyte hyperplasia, and resistance to helminth infection. Our findings reveal a previously undescribed mechanism of intercellular cross-talk wherein "itch" neuron activation reshapes myeloid cytokine expression patterns to alter skin composition for cutaneous immunity against invasive pathogens.
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Affiliation(s)
- Juan M. Inclan-Rico
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Camila M. Napuri
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cailu Lin
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA
| | - Li-Yin Hung
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Annabel A. Ferguson
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Qinxue Wu
- Department of Neuroscience, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher F. Pastore
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adriana Stephenson
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ulrich M. Femoe
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Heather L. Rossi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Wenqin Luo
- Department of Neuroscience, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Regenerative Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ishmail Abdus-Saboor
- Department of Biological Sciences, Zuckerman Mind, Brain, Behavior Institute, Columbia University, New York, New York, USA
| | - De’Broski R. Herbert
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Han CZ, Li RZ, Hansen E, Trescott S, Fixsen BR, Nguyen CT, Mora CM, Spann NJ, Bennett HR, Poirion O, Buchanan J, Warden AS, Xia B, Schlachetzki JCM, Pasillas MP, Preissl S, Wang A, O'Connor C, Shriram S, Kim R, Schafer D, Ramirez G, Challacombe J, Anavim SA, Johnson A, Gupta M, Glass IA, Levy ML, Haim SB, Gonda DD, Laurent L, Hughes JF, Page DC, Blurton-Jones M, Glass CK, Coufal NG. Human microglia maturation is underpinned by specific gene regulatory networks. Immunity 2023; 56:2152-2171.e13. [PMID: 37582369 PMCID: PMC10529991 DOI: 10.1016/j.immuni.2023.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/11/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.
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Affiliation(s)
- Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Hansen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Celina T Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Cristina M Mora
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter R Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Bing Xia
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Shreya Shriram
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Roy Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Gabriela Ramirez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Jean Challacombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel A Anavim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Avalon Johnson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Mihir Gupta
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sharona Ben Haim
- Department of Neurosurgery, University of California, San Diego, La Jolla, CA 92037, USA
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92696, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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11
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Ghorbani P, Kim SY, Smith TKT, Minarrieta L, Robert-Gostlin V, Kilgour MK, Ilijevska M, Alecu I, Snider SA, Margison KD, Nunes JRC, Woo D, Pember C, O’Dwyer C, Ouellette J, Kotchetkov P, St-Pierre J, Bennett SAL, Lacoste B, Blais A, Nair MG, Fullerton MD. Choline metabolism underpins macrophage IL-4 polarization and RELMα up-regulation in helminth infection. PLoS Pathog 2023; 19:e1011658. [PMID: 37747879 PMCID: PMC10553840 DOI: 10.1371/journal.ppat.1011658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/05/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023] Open
Abstract
Type 2 cytokines like IL-4 are hallmarks of helminth infection and activate macrophages to limit immunopathology and mediate helminth clearance. In addition to cytokines, nutrients and metabolites critically influence macrophage polarization. Choline is an essential nutrient known to support normal macrophage responses to lipopolysaccharide; however, its function in macrophages polarized by type 2 cytokines is unknown. Using murine IL-4-polarized macrophages, targeted lipidomics revealed significantly elevated levels of phosphatidylcholine, with select changes to other choline-containing lipid species. These changes were supported by the coordinated up-regulation of choline transport compared to naïve macrophages. Pharmacological inhibition of choline metabolism significantly suppressed several mitochondrial transcripts and dramatically inhibited select IL-4-responsive transcripts, most notably, Retnla. We further confirmed that blocking choline metabolism diminished IL-4-induced RELMα (encoded by Retnla) protein content and secretion and caused a dramatic reprogramming toward glycolytic metabolism. To better understand the physiological implications of these observations, naïve or mice infected with the intestinal helminth Heligmosomoides polygyrus were treated with the choline kinase α inhibitor, RSM-932A, to limit choline metabolism in vivo. Pharmacological inhibition of choline metabolism lowered RELMα expression across cell-types and tissues and led to the disappearance of peritoneal macrophages and B-1 lymphocytes and an influx of infiltrating monocytes. The impaired macrophage activation was associated with some loss in optimal immunity to H. polygyrus, with increased egg burden. Together, these data demonstrate that choline metabolism is required for macrophage RELMα induction, metabolic programming, and peritoneal immune homeostasis, which could have important implications in the context of other models of infection or cancer immunity.
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Affiliation(s)
- Peyman Ghorbani
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sang Yong Kim
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California, United States of America
| | - Tyler K. T. Smith
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Lucía Minarrieta
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Victoria Robert-Gostlin
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marisa K. Kilgour
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Maja Ilijevska
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Irina Alecu
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Shayne A. Snider
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kaitlyn D. Margison
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Julia R. C. Nunes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Woo
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California, United States of America
| | - Ciara Pember
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Conor O’Dwyer
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Ouellette
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Pavel Kotchetkov
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie St-Pierre
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Steffany A. L. Bennett
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Baptiste Lacoste
- Neuroscience Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Alexandre Blais
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Brain and Mind Institute, University of Ottawa, Ottawa, Ontario, Canada
- Éric Poulin Centre for Neuromuscular Disease, Ottawa, Ontario, Canada
| | - Meera G. Nair
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, California, United States of America
| | - Morgan D. Fullerton
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada
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12
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Czimmerer Z, Nagy L. Epigenomic regulation of macrophage polarization: Where do the nuclear receptors belong? Immunol Rev 2023; 317:152-165. [PMID: 37074820 PMCID: PMC10524119 DOI: 10.1111/imr.13209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/20/2023]
Abstract
Our laboratory has a long-standing research interest in understanding how lipid-activated transcription factors, nuclear hormone receptors, contribute to dendritic cell and macrophage gene expression regulation, subtype specification, and responses to a changing extra and intracellular milieu. This journey in the last more than two decades took us from identifying target genes for various RXR heterodimers to systematically mapping nuclear receptor-mediated pathways in dendritic cells to identifying hierarchies of transcription factors in alternative polarization in macrophages to broaden the role of nuclear receptors beyond strictly ligand-regulated gene expression. We detail here the milestones of the road traveled and draw conclusions regarding the unexpectedly broad role of nuclear hormone receptors as epigenomic components of dendritic cell and macrophage gene regulation as we are getting ready for the next challenges.
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Affiliation(s)
- Zsolt Czimmerer
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Laszlo Nagy
- Departments Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, and Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St Petersburg, FL, United States
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13
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Distéfano-Gagné F, Bitarafan S, Lacroix S, Gosselin D. Roles and regulation of microglia activity in multiple sclerosis: insights from animal models. Nat Rev Neurosci 2023:10.1038/s41583-023-00709-6. [PMID: 37268822 DOI: 10.1038/s41583-023-00709-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
As resident macrophages of the CNS, microglia are critical immune effectors of inflammatory lesions and associated neural dysfunctions. In multiple sclerosis (MS) and its animal models, chronic microglial inflammatory activity damages myelin and disrupts axonal and synaptic activity. In contrast to these detrimental effects, the potent phagocytic and tissue-remodelling capabilities of microglia support critical endogenous repair mechanisms. Although these opposing capabilities have long been appreciated, a precise understanding of their underlying molecular effectors is only beginning to emerge. Here, we review recent advances in our understanding of the roles of microglia in animal models of MS and demyelinating lesions and the mechanisms that underlie their damaging and repairing activities. We also discuss how the structured organization and regulation of the genome enables complex transcriptional heterogeneity within the microglial cell population at demyelinating lesions.
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Affiliation(s)
- Félix Distéfano-Gagné
- Axe Neuroscience, Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire de la Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Sara Bitarafan
- Axe Neuroscience, Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire de la Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Steve Lacroix
- Axe Neuroscience, Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada
- Département de Médecine Moléculaire de la Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - David Gosselin
- Axe Neuroscience, Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.
- Département de Médecine Moléculaire de la Faculté de Médecine, Université Laval, Québec, Québec, Canada.
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14
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Domokos A, Varga Z, Jambrovics K, Caballero-Sánchez N, Szabo E, Nagy G, Scholtz B, Halasz L, Varadi E, Bene KP, Mazlo A, Bacsi A, Jeney V, Szebeni GJ, Nagy L, Czimmerer Z. The transcriptional control of the VEGFA-VEGFR1 (FLT1) axis in alternatively polarized murine and human macrophages. Front Immunol 2023; 14:1168635. [PMID: 37215144 PMCID: PMC10192733 DOI: 10.3389/fimmu.2023.1168635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction Macrophages significantly contribute to the regulation of vessel formation under physiological and pathological conditions. Although the angiogenesis-regulating role of alternatively polarized macrophages is quite controversial, a growing number of evidence shows that they can participate in the later phases of angiogenesis, including vessel sprouting and remodeling or regression. However, the epigenetic and transcriptional regulatory mechanisms controlling this angiogenesis-modulating program are not fully understood. Results Here we show that IL-4 can coordinately regulate the VEGFA-VEGFR1 (FLT1) axis via simultaneously inhibiting the proangiogenic Vegfa and inducing the antiangiogenic Flt1 expression in murine bone marrow-derived macrophages, which leads to the attenuated proangiogenic activity of alternatively polarized macrophages. The IL-4-activated STAT6 and IL-4-STAT6 signaling pathway-induced EGR2 transcription factors play a direct role in the transcriptional regulation of the Vegfa-Flt1 axis. We demonstrated that this phenomenon is not restricted to the murine bone marrow-derived macrophages, but can also be observed in different murine tissue-resident macrophages ex vivo and parasites-elicited macrophages in vivo with minor cell type-specific differences. Furthermore, IL-4 exposure can modulate the hypoxic response of genes in both murine and human macrophages leading to a blunted Vegfa/VEGFA and synergistically induced Flt1/FLT1 expression. Discussion Our findings establish that the IL-4-activated epigenetic and transcriptional program can determine angiogenesis-regulating properties in alternatively polarized macrophages under normoxic and hypoxic conditions.
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Affiliation(s)
- Apolka Domokos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Karoly Jambrovics
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Noemí Caballero-Sánchez
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Eniko Szabo
- Laboratory of Functional Genomics, Biological Research Centre Eotvos Lorand Research Network, Szeged, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beata Scholtz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Eszter Varadi
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Krisztian P. Bene
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anett Mazlo
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Viktoria Jeney
- MTA-DE Lendület Vascular Pathophysiology Research Group, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gabor J. Szebeni
- Laboratory of Functional Genomics, Biological Research Centre Eotvos Lorand Research Network, Szeged, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Institute of Genetics, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
- Department of Immunology, Albert Szent-Györgyi Medical School, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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15
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Caratti G, Stifel U, Caratti B, Jamil AJM, Chung KJ, Kiehntopf M, Gräler MH, Blüher M, Rauch A, Tuckermann JP. Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance. Nat Commun 2023; 14:2271. [PMID: 37080971 PMCID: PMC10119112 DOI: 10.1038/s41467-023-37831-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/01/2023] [Indexed: 04/22/2023] Open
Abstract
Insulin resistance (IR) during obesity is linked to adipose tissue macrophage (ATM)-driven inflammation of adipose tissue. Whether anti-inflammatory glucocorticoids (GCs) at physiological levels modulate IR is unclear. Here, we report that deletion of the GC receptor (GR) in myeloid cells, including macrophages in mice, aggravates obesity-related IR by enhancing adipose tissue inflammation due to decreased anti-inflammatory ATM leading to exaggerated adipose tissue lipolysis and severe hepatic steatosis. In contrast, GR deletion in Kupffer cells alone does not alter IR. Co-culture experiments show that the absence of GR in macrophages directly causes reduced phospho-AKT and glucose uptake in adipocytes, suggesting an important function of GR in ATM. GR-deficient macrophages are refractory to alternative ATM-inducing IL-4 signaling, due to reduced STAT6 chromatin loading and diminished anti-inflammatory enhancer activation. We demonstrate that GR has an important function in macrophages during obesity by limiting adipose tissue inflammation and lipolysis to promote insulin sensitivity.
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Affiliation(s)
- Giorgio Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ulrich Stifel
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Bozhena Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Ali J M Jamil
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kyoung-Jin Chung
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Michael Kiehntopf
- SG Sepsis Research Clinic for Anesthesiology and Intensive Care, Jena University Hospital, Jena, Germany
| | - Markus H Gräler
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Matthias Blüher
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Alexander Rauch
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark.
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
- Steno Diabetes Center Odense, Odense, Denmark.
| | - Jan P Tuckermann
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany.
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Alternative signal priming enhances the inflammatory response in macrophages. Cell Mol Immunol 2023:10.1038/s41423-023-00984-4. [PMID: 36806397 DOI: 10.1038/s41423-023-00984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
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17
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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18
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Daniel B, Belk JA, Meier SL, Chen AY, Sandor K, Czimmerer Z, Varga Z, Bene K, Buquicchio FA, Qi Y, Kitano H, Wheeler JR, Foster DS, Januszyk M, Longaker MT, Chang HY, Satpathy AT. Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. Mol Cell 2023; 83:121-138.e7. [PMID: 36521490 PMCID: PMC9831293 DOI: 10.1016/j.molcel.2022.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Cell cycle (CC) facilitates cell division via robust, cyclical gene expression. Protective immunity requires the expansion of pathogen-responsive cell types, but whether CC confers unique gene expression programs that direct the subsequent immunological response remains unclear. Here, we demonstrate that single macrophages (MFs) adopt different plasticity states in CC, which leads to heterogeneous cytokine-induced polarization, priming, and repolarization programs. Specifically, MF plasticity to interferon gamma (IFNG) is substantially reduced during S-G2/M, whereas interleukin 4 (IL-4) induces S-G2/M-biased gene expression, mediated by CC-biased enhancers. Additionally, IL-4 polarization shifts the CC-phase distribution of MFs toward the G2/M phase, providing a subpopulation-specific mechanism for IL-4-induced, dampened IFNG responsiveness. Finally, we demonstrate CC-dependent MF responses in murine and human disease settings in vivo, including Th2-driven airway inflammation and pulmonary fibrosis, where MFs express an S-G2/M-biased tissue remodeling gene program. Therefore, MF inflammatory and regenerative responses are gated by CC in a cyclical, phase-dependent manner.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Stefanie L Meier
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Andy Y Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary; Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary
| | - Krisztian Bene
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen 4032, Hungary
| | - Frank A Buquicchio
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hugo Kitano
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Joshua R Wheeler
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA 94305, USA; Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Program in Immunology, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
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19
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Huang Z, Efthymiadou A, Liang N, Fan R, Treuter E. Antagonistic action of GPS2 and KDM1A at enhancers governs alternative macrophage activation by interleukin 4. Nucleic Acids Res 2023; 51:1067-1086. [PMID: 36610795 PMCID: PMC9943668 DOI: 10.1093/nar/gkac1230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/24/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
The Th2 cytokine interleukin 4 (IL4) promotes macrophage differentiation into alternative subtypes and plays important roles in physiology, in metabolic and inflammatory diseases, in cancer and in tissue regeneration. While the regulatory transcription factor networks governing IL4 signaling are already well-characterized, it is currently less understood which transcriptional coregulators are involved and how they operate mechanistically. In this study, we discover that G protein pathway suppressor 2 (GPS2), a core subunit of the HDAC3 corepressor complex assembled by SMRT and NCOR, represses IL4-dependent enhancer activation in mouse macrophages. Our genome-wide and gene-specific characterization revealed that, instead of directly repressing STAT6, chromatin-bound GPS2 cooperates with SMRT and NCOR to antagonize enhancer activation by lysine demethylase 1A (KDM1A, LSD1). Mechanistically, corepressor depletion increased KDM1A recruitment to enhancers linked to IL4-induced genes, accompanied by demethylation of the repressive histone marks H3K9me2/3 without affecting H3K4me1/2, the classic KDM1A substrates for demethylation in other cellular contexts. This in turn caused enhancer and gene activation already in the absence of IL4/STAT6 and sensitized the STAT6-dependent IL4 responsiveness of macrophages. Thus, our work identified with the antagonistic action of a GPS2-containing corepressor complex and the lysine demethylase KDM1A a hitherto unknown epigenetic corepressor-coactivator switching mechanism that governs alternative macrophage activation.
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Affiliation(s)
- Zhiqiang Huang
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Astradeni Efthymiadou
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Ning Liang
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Rongrong Fan
- Correspondence may also be addressed to Rongrong Fan. Tel: +46 8 524 81161;
| | - Eckardt Treuter
- To whom correspondence should be addressed. Tel: +46 8 524 81060;
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20
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Li W, Tan J, He S, Yue Y, Liu H, Li R, Wang X, Wang G, Fan W, Zhao C, Zhou Q, Yang P, Hou S. iPSC-based model of Vogt-Koyanagi-Harada disease for phenotype recapitulation and drug screening. Clin Immunol 2023; 246:109205. [PMID: 36509389 DOI: 10.1016/j.clim.2022.109205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Vogt-Koyanagi-Harada (VKH) disease, a major blinding eye disease, is characterized by an autoimmune response against melanocytes in multiple organs throughout the body. Currently, the aetiology and pathogenesis of VKH disease are unclear, and the treatment strategy needs to be further optimized. The retinal pigment epithelium (RPE), a monolayer of pigmented cells of the fundus, is essential for maintaining normal visual function and is involved in both the acute and chronic stages of VKH disease. Therefore, the functions of the RPE may play a critical role in the aetiology and treatment of VKH disease. Herein, we established a human induced pluripotent stem cell (hiPSC) RPE model of VKH disease by reprogramming peripheral blood mononuclear cells (PBMCs) into iPSCs and then differentiating them into RPE cells. Patient-derived RPE cells exhibited barrier disruption, impaired phagocytosis, and depigmentation compared with those from normal controls, which was consistent with the features of VKH disease. Furthermore, a small molecular compound targeting EGR2 was found to rescue the barrier and phagocytic functions of the hiPSC-RPE cells through high-throughput virtual screening and functional studies, suggesting a promising strategy for the treatment of VKH disease.
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Affiliation(s)
- Wanqian Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Jun Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Siyuan He
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Yingying Yue
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Huan Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Ruonan Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Guoqing Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Wei Fan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Chenyang Zhao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Qian Zhou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China..
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Ophthalmology, Chongqing, China; Chongqing Eye Institute, Chongqing, China; Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular Diseases, Chongqing, China..
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21
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Hu X, Wu M, Ma T, Zhang Y, Zou C, Wang R, Zhang Y, Ren Y, Li Q, Liu H, Li H, Wang T, Sun X, Yang Y, Tang M, Li X, Li J, Gao X, Li T, Zhou X. Single-cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of Pseudomonas aeruginosa. MedComm (Beijing) 2022; 3:e193. [PMID: 36514779 PMCID: PMC9732387 DOI: 10.1002/mco2.193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the changes in the immune microenvironment during pulmonary bacterial acute and chronic infections is limited. The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. Here, we describe a single immune cell atlas of mouse lungs after acute and chronic Pseudomonas aeruginosa infection using single-cell transcriptomics, multiplex immunohistochemistry, and flow cytometry. Our single-cell transcriptomic analysis revealed large-scale comprehensive changes in immune cell composition and high variation in cell-cell interactions after acute and chronic P. aeruginosa infection. Bacterial infection reprograms the genetic architecture of immune cell populations. We identified specific immune cell types, including Cxcl2+ B cells and interstitial macrophages, in response to acute and chronic infection, such as their proportions, distribution, and functional status. Importantly, the patterns of immune cell response are drastically different between acute and chronic infection models. The distinct molecular signatures highlight the importance of the highly dynamic cell-cell interaction process in different pathological conditions, which has not been completely revealed previously. These findings provide a comprehensive and unbiased immune cellular landscape for respiratory pathogenesis in mice, enabling further understanding of immunologic mechanisms in infection and inflammatory diseases.
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Affiliation(s)
- Xueli Hu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Mingbo Wu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Teng Ma
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yige Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Chaoyu Zou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Ruihuan Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yongxin Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yuan Ren
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina,State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Qianqian Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Huan Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Heyue Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taolin Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xiaolong Sun
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Miao Tang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xuefeng Li
- Department of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jing Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xiang Gao
- Department of Neurosurgery and Institute of NeurosurgeryState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taiwen Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
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22
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Czimmerer Z, Halasz L, Daniel B, Varga Z, Bene K, Domokos A, Hoeksema M, Shen Z, Berger WK, Cseh T, Jambrovics K, Kolostyak Z, Fenyvesi F, Varadi J, Poliska S, Hajas G, Szatmari I, Glass CK, Bacsi A, Nagy L. The epigenetic state of IL-4-polarized macrophages enables inflammatory cistromic expansion and extended synergistic response to TLR ligands. Immunity 2022; 55:2006-2026.e6. [PMID: 36323312 PMCID: PMC9649892 DOI: 10.1016/j.immuni.2022.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 07/11/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Prior exposure to microenvironmental signals could fundamentally change the response of macrophages to subsequent stimuli. It is believed that T helper-2 (Th2)-cell-type cytokine interleukin-4 (IL-4) and Toll-like receptor (TLR) ligand-activated transcriptional programs mutually antagonize each other, and no remarkable convergence has been identified between them. In contrast, here, we show that IL-4-polarized macrophages established a hyperinflammatory gene expression program upon lipopolysaccharide (LPS) exposure. This phenomenon, which we termed extended synergy, was supported by IL-4-directed epigenomic remodeling, LPS-activated NF-κB-p65 cistrome expansion, and increased enhancer activity. The EGR2 transcription factor contributed to the extended synergy in a macrophage-subtype-specific manner. Consequently, the previously alternatively polarized macrophages produced increased amounts of immune-modulatory factors both in vitro and in vivo in a murine Th2 cell-type airway inflammation model upon LPS exposure. Our findings establish that IL-4-induced epigenetic reprogramming is responsible for the development of inflammatory hyperresponsiveness to TLR activation and contributes to lung pathologies.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,These authors contributed equally
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,Present address: Stanford University School of Medicine, Department of Pathology, Stanford, CA, USA
| | - Bence Daniel
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,These authors contributed equally,Present address: Stanford University School of Medicine, Department of Pathology, Stanford, CA, USA
| | - Zsofia Varga
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztian Bene
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Apolka Domokos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Molecular Cell and Immunobiology Doctoral School, Faculty of Medicine, University of Debrecen 4032, Debrecen, Hungary
| | - Marten Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA,Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Wilhelm K. Berger
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Timea Cseh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Karoly Jambrovics
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Kolostyak
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Molecular Cell and Immunobiology Doctoral School, Faculty of Medicine, University of Debrecen 4032, Debrecen, Hungary
| | - Ferenc Fenyvesi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Judit Varadi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gyorgy Hajas
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA,Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,ELKH-DE Allergology Research Group, Debrecen, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary,Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA,Lead contact,Correspondence:
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23
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Aegerter H, Lambrecht BN, Jakubzick CV. Biology of lung macrophages in health and disease. Immunity 2022; 55:1564-1580. [PMID: 36103853 DOI: 10.1016/j.immuni.2022.08.010] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
Tissue-resident alveolar and interstitial macrophages and recruited macrophages are critical players in innate immunity and maintenance of lung homeostasis. Until recently, assessing the differential functional contributions of tissue-resident versus recruited macrophages has been challenging because they share overlapping cell surface markers, making it difficult to separate them using conventional methods. This review describes how scRNA-seq and spatial transcriptomics can separate these subpopulations and help unravel the complexity of macrophage biology in homeostasis and disease. First, we provide a guide to identifying and distinguishing lung macrophages from other mononuclear phagocytes in humans and mice. Second, we outline emerging concepts related to the development and function of the various lung macrophages in the alveolar, perivascular, and interstitial niches. Finally, we describe how different tissue states profoundly alter their functions, including acute and chronic lung disease, cancer, and aging.
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Affiliation(s)
- Helena Aegerter
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Claudia V Jakubzick
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH, USA.
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24
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Zhou D, Wu Z, Park JG, Fiches GN, Li TW, Ma Q, Huang H, Biswas A, Martinez-Sobrido L, Santoso NG, Zhu J. FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling. Nucleic Acids Res 2022; 50:8700-8718. [PMID: 35904816 PMCID: PMC9410884 DOI: 10.1093/nar/gkac645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 06/26/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated in both epithelial and natural killer (NK) cells. The histone acetyltransferase TIP60 contributes to the acetylation of SUPT16H middle domain (MD) at lysine 674 (K674). Such acetylation of SUPT16H is recognized by bromodomain protein BRD4, which promotes protein stability of SUPT16H in both epithelial and NK cells. We further demonstrated that SUPT16H-BRD4 associates with histone modification enzymes (HDAC1, EZH2), and further regulates their activation status and/or promoter association as well as affects the relevant histone marks (H3ac, H3K9me3 and H3K27me3). BRD4 is known to profoundly regulate interferon (IFN) signaling, while such function of SUPT16H has never been explored. Surprisingly, our results revealed that SUPT16H genetic knockdown via RNAi or pharmacological inhibition by using its inhibitor, curaxin 137 (CBL0137), results in the induction of IFNs and interferon-stimulated genes (ISGs). Through this mechanism, depletion or inhibition of SUPT16H is shown to efficiently inhibit infection of multiple viruses, including Zika, influenza, and SARS-CoV-2. Furthermore, we demonstrated that depletion or inhibition of SUPT16H also causes the remarkable activation of IFN signaling in NK cells, which promotes the NK-mediated killing of virus-infected cells in a co-culture system using human primary NK cells. Overall, our studies unraveled the previously un-appreciated role of FACT complex in coordinating with BRD4 and regulating IFN signaling in both epithelial and NK cells, and also proposed the novel application of the FACT inhibitor CBL0137 to treat viral infections.
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Affiliation(s)
- Dawei Zhou
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Zhenyu Wu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jun-Gyu Park
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Guillaume N Fiches
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Tai-Wei Li
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Huachao Huang
- Department of Medicine, Columbia University Medical Center, NY, NY 10032, USA
| | - Ayan Biswas
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - Netty G Santoso
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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25
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Gopalakrishnan A, Joseph J, Shirey KA, Keegan AD, Boukhvalova MS, Vogel SN, Blanco JCG. Protection against influenza-induced Acute Lung Injury (ALI) by enhanced induction of M2a macrophages: possible role of PPARγ/RXR ligands in IL-4-induced M2a macrophage differentiation. Front Immunol 2022; 13:968336. [PMID: 36052067 PMCID: PMC9424652 DOI: 10.3389/fimmu.2022.968336] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many respiratory viruses cause lung damage that may evolve into acute lung injury (ALI), a cytokine storm, acute respiratory distress syndrome, and ultimately, death. Peroxisome proliferator activated receptor gamma (PPARγ), a member of the nuclear hormone receptor (NHR) family of transcription factors, regulates transcription by forming heterodimers with another NHR family member, Retinoid X Receptor (RXR). Each component of the heterodimer binds specific ligands that modify transcriptional capacity of the entire heterodimer by recruiting different co-activators/co-repressors. However, the role of PPARγ/RXR ligands in the context of influenza infection is not well understood. PPARγ is associated with macrophage differentiation to an anti-inflammatory M2 state. We show that mice lacking the IL-4Rα receptor, required for M2a macrophage differentiation, are more susceptible to mouse-adapted influenza (A/PR/8/34; "PR8")-induced lethality. Mice lacking Ptgs2, that encodes COX-2, a key proinflammatory M1 macrophage mediator, are more resistant. Blocking the receptor for COX-2-induced Prostaglandin E2 (PGE2) was also protective. Treatment with pioglitazone (PGZ), a PPARγ ligand, increased survival from PR8 infection, decreased M1 macrophage gene expression, and increased PPARγ mRNA in lungs. Conversely, conditional knockout mice expressing PPARγ-deficient macrophages were significantly more sensitive to PR8-induced lethality. These findings were extended in cotton rats: PGZ blunted lung inflammation and M1 cytokine gene expression after challenge with non-adapted human influenza. To study mechanisms by which PPARγ/RXR transcription factors induce canonical M2a genes, WT mouse macrophages were treated with IL-4 in the absence or presence of rosiglitazone (RGZ; PPARγ ligand), LG100754 (LG; RXR ligand), or both. IL-4 dose-dependently induced M2a genes Arg1, Mrc1, Chil3, and Retnla. Treatment of macrophages with IL-4 and RGZ and/or LG differentially affected induction of Arg1 and Mrc1 vs. Chil3 and Retnla gene expression. In PPARγ-deficient macrophages, IL-4 alone failed to induce Arg1 and Mrc1 gene expression; however, concurrent treatment with LG or RGZ + LG enhanced IL-4-induced Arg1 and Mrc1 expression, but to a lower level than in WT macrophages, findings confirmed in the murine alveolar macrophage cell line, MH-S. These findings support a model in which PPARγ/RXR heterodimers control IL-4-induced M2a differentiation, and suggest that PPARγ/RXR agonists should be considered as important tools for clinical intervention against influenza-induced ALI.
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Affiliation(s)
- Archana Gopalakrishnan
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
| | - John Joseph
- Sigmovir Biosystems, Inc., Rockville, MD, United States
| | - Kari Ann Shirey
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
| | - Achsah D. Keegan
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
- Center for Vascular and Inflammatory Diseases, University of Maryland, School of Medicine, Baltimore, MD, United States
| | | | - Stefanie N. Vogel
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, MD, United States
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26
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Halimani N, Nesterchuk M, Andreichenko IN, Tsitrina AA, Elchaninov A, Lokhonina A, Fatkhudinov T, Dashenkova NO, Brezgina V, Zatsepin TS, Mikaelyan AS, Kotelevtsev YV. Phenotypic Alteration of BMDM In Vitro Using Small Interfering RNA. Cells 2022; 11:cells11162498. [PMID: 36010574 PMCID: PMC9406732 DOI: 10.3390/cells11162498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022] Open
Abstract
Autologous macrophage transfer is an emerging platform for cell therapy. It is anticipated that conventional macrophage reprogramming based on ex vivo polarization using cytokines and ligands of TLRs may enhance the therapeutic effect. We describe an alternative approach based on small interfering RNA (siRNA) knockdown of selected molecular cues of macrophage polarization, namely EGR2, IRF3, IRF5, and TLR4 in Raw264.7 monocyte/macrophage cell line and mouse-bone-marrow-derived macrophages (BMDMs). The impact of IRF5 knockdown was most pronounced, curtailing the expression of other inflammatory mediators such as IL-6 and NOS2, especially in M1-polarized macrophages. Contrary to IRF5, EGR2 knockdown potentiated M1-associated markers while altogether abolishing M2 marker expression, which is indicative of the principal role of EGR2 in the maintenance of alternative phenotypes. IRF3 knockdown suppressed M1 polarization but upregulated Arg 1, a canonical marker of alternative polarization in M1 macrophages. As anticipated, the knockdown of TLR4 also attenuated the M1 phenotype but, akin to IRF3, significantly induced Arginase 1 in M0 and M1, driving the phenotype towards M2. This study validates RNAi as a viable option for the alteration and maintenance of macrophage phenotypes.
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Affiliation(s)
- Noreen Halimani
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
- Correspondence: (N.H.); (Y.V.K.)
| | - Mikhail Nesterchuk
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Irina N. Andreichenko
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Alexandra A. Tsitrina
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow 119334, Russia
| | - Andrey Elchaninov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov, Russian Federation, 4 Oparina Street, Moscow 117997, Russia
- Department of Histology, Pirogov Russian National Research Medical University, Ministry of Healthcare of The Russian Federation, 1 Ostrovitianov Street, Moscow 117997, Russia
| | - Anastasia Lokhonina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov, Russian Federation, 4 Oparina Street, Moscow 117997, Russia
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
| | - Timur Fatkhudinov
- Department of Histology, Pirogov Russian National Research Medical University, Ministry of Healthcare of The Russian Federation, 1 Ostrovitianov Street, Moscow 117997, Russia
- Scientific Research Institute of Human Morphology, 3 Tsurupa Street, Moscow 117418, Russia
| | - Nataliya O. Dashenkova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow 119334, Russia
| | - Vera Brezgina
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Timofei S. Zatsepin
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Arsen S. Mikaelyan
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow 119334, Russia
| | - Yuri V. Kotelevtsev
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
- Correspondence: (N.H.); (Y.V.K.)
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27
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Kamerkar S, Leng C, Burenkova O, Jang SC, McCoy C, Zhang K, Dooley K, Kasera S, Zi T, Sisó S, Dahlberg W, Sia CL, Patel S, Schmidt K, Economides K, Soos T, Burzyn D, Sathyanarayanan S. Exosome-mediated genetic reprogramming of tumor-associated macrophages by exoASO-STAT6 leads to potent monotherapy antitumor activity. SCIENCE ADVANCES 2022; 8:eabj7002. [PMID: 35179953 PMCID: PMC8856615 DOI: 10.1126/sciadv.abj7002] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/23/2021] [Indexed: 05/04/2023]
Abstract
Effectiveness of checkpoint immunotherapy in cancer can be undermined by immunosuppressive tumor-associated macrophages (TAMs) with an M2 phenotype. Reprogramming TAMs toward a proinflammatory M1 phenotype is a novel approach to induce antitumor immunity. The M2 phenotype is controlled by key transcription factors such as signal transducer and activator of transcription 6 (STAT6), which have been "undruggable" selectively in TAMs. We describe an engineered exosome therapeutic candidate delivering an antisense oligonucleotide (ASO) targeting STAT6 (exoASO-STAT6), which selectively silences STAT6 expression in TAMs. In syngeneic models of colorectal cancer and hepatocellular carcinoma, exoASO-STAT6 monotherapy results in >90% tumor growth inhibition and 50 to 80% complete remissions. Administration of exoASO-STAT6 leads to induction of nitric oxide synthase 2 (NOS2), an M1 macrophage marker, resulting in remodeling of the tumor microenvironment and generation of a CD8 T cell-mediated adaptive immune response. Collectively, exoASO-STAT6 represents the first platform targeting transcription factors in TAMs in a highly selective manner.
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Affiliation(s)
| | - Charan Leng
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | | | - Su Chul Jang
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | | | - Kelvin Zhang
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | - Kevin Dooley
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | | | - Tong Zi
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | - Sílvia Sisó
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | | | | | - Shil Patel
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | - Karl Schmidt
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | | | - Timothy Soos
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
| | - Dalia Burzyn
- Codiak BioSciences Inc., Cambridge, MA 02140, USA
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28
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McCowan J, Fercoq F, Kirkwood PM, T’Jonck W, Hegarty LM, Mawer CM, Cunningham R, Mirchandani AS, Hoy A, Humphries DC, Jones GR, Hansen CG, Hirani N, Jenkins SJ, Henri S, Malissen B, Walmsley SR, Dockrell DH, Saunders PTK, Carlin LM, Bain CC. The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair. Sci Immunol 2021; 6:eabj2132. [PMID: 34797692 PMCID: PMC7612216 DOI: 10.1126/sciimmunol.abj2132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alveolar macrophages are the most abundant macrophages in the healthy lung where they play key roles in homeostasis and immune surveillance against airborne pathogens. Tissue-specific differentiation and survival of alveolar macrophages rely on niche-derived factors, such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor–β (TGF-β). However, the nature of the downstream molecular pathways that regulate the identity and function of alveolar macrophages and their response to injury remain poorly understood. Here, we identify that the transcription factor EGR2 is an evolutionarily conserved feature of lung alveolar macrophages and show that cell-intrinsic EGR2 is indispensable for the tissue-specific identity of alveolar macrophages. Mechanistically, we show that EGR2 is driven by TGF-β and GM-CSF in a PPAR-γ–dependent manner to control alveolar macrophage differentiation. Functionally, EGR2 was dispensable for the regulation of lipids in the airways but crucial for the effective handling of the respiratory pathogen Streptococcus pneumoniae. Last, we show that EGR2 is required for repopulation of the alveolar niche after sterile, bleomycin-induced lung injury and demonstrate that EGR2-dependent, monocyte-derived alveolar macrophages are vital for effective tissue repair after injury. Collectively, we demonstrate that EGR2 is an indispensable component of the transcriptional network controlling the identity and function of alveolar macrophages in health and disease.
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Affiliation(s)
- Jack McCowan
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | | | - Phoebe M. Kirkwood
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Wouter T’Jonck
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Lizi M. Hegarty
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Connar M. Mawer
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
| | - Richard Cunningham
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Ananda S. Mirchandani
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Anna Hoy
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
| | - Duncan C. Humphries
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Gareth-Rhys Jones
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Carsten G. Hansen
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Nik Hirani
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Stephen J. Jenkins
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, INSERM, U1104, CNRS UMR7280, 13288 Marseille, France
| | - Sarah R. Walmsley
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - David H. Dockrell
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Philippa T. K. Saunders
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - Leo M. Carlin
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Calum C. Bain
- University of Edinburgh Centre for Inflammation Research, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4TJ, UK
- Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
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29
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Chu YB, Li J, Jia P, Cui J, Zhang R, Kang X, Lv M, Zhang S. Irf1- and Egr1-activated transcription plays a key role in macrophage polarization: A multiomics sequencing study with partial validation. Int Immunopharmacol 2021; 99:108072. [PMID: 34426111 DOI: 10.1016/j.intimp.2021.108072] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Macrophage polarization has a causal role in the pathogenesis and resolution of various clinical diseases. DNA-binding transcription factors (TFs) have been identified as essential factors during gene transcription. Better insight into the TFs that regulate macrophage polarization could provide novel therapeutic targets. METHODS IFN-γ (50 ng/mL) or IL4 (20 ng/mL) was utilized to stimulate bone marrow-derived macrophages from mice for 24 h for M1- and M2-polarized macrophage model construction, respectively. First, ATAC-seq (Assay for Targeting Accessible-Chromatin with high throughout sequencing) and motif analysis were conducted to identify potential transcription factors (TFs) involved in M1 and M2 macrophage polarization. Second, essential TFs were identified through RNA-seq, after which, their expression was compared between M0-polarized and M1/M2-polarized macrophages. Furthermore, a multiomic analysis of RNA-seq (siRNA knock down of the identified TFs), ChIP-seq and ATAC-seq was utilized to explore the TF-regulated molecular network. GO and KEGG analyses were used to expound the main functions of the TF-regulated molecular network. Finally, the top 5 TF-regulated genes were validated through flow cytometry, ELISA and qPCR. The cut-off values for high-throughput sequencing and qPCR were FDR < 0.05 and P < 0.05, respectively. RESULTS Compared with M0 macrophages, 10,771 and 4,848 peaks were identified by ATAC-seq during M1 and M2 macrophage polarization, respectively (FDR < 0.05). Fifty and 62 TF binding motifs were identified for the TFs that participate in M1 and M2 macrophage polarization, respectively. The most significantly highly expressed TFs in M1 and M2 macrophages were identified by RNA-seq as Irf1 and Egr1, with LogFC values of 3.2 and 2.8, respectively. Multiomic analyses further found that Irf1 regulated the transcription of 90 genes and that Egr1 regulated the transcription of 116 genes. The Irf1-regulated molecular network played a key role in the inflammatory response and viral defence of M1 macrophages, and 116 Egr1-regulated genes included anti-inflammatory and cell proliferation genes. Validation experiments indicated that IFN-γ-induced Gbp5, Nos2, CD86, Cxcl10 and Cxcl5 expression was significantly downregulated in siIrf1-BMDMs, and IL4-induced Itgax, Nipal1, Bhlhe40, CD206 and Ffar4 expression was significantly downregulated in siEgr1-BMDMs (P < 0.05). CONCLUSIONS Through multiomic analyses of epigenetic sequencing and RNA-seq with partial validation, the current study found that Irf1- and Egr1-induced transcription plays key roles in M1 and M2 macrophage polarization, respectively.
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Affiliation(s)
- Yan-Biao Chu
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Pingdong Jia
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Jiyun Cui
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Ronghua Zhang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Xueli Kang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Meng Lv
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Shi Zhang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China; Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
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Abstract
This Outlook discusses findings by Daniel et al. identifying EGR2 as a downstream regulator of STAT6 with broad functionality that further induces many transcription factors associated with alternative polarization. Alternative polarization of macrophages induced by IL-4 is important for homeostasis and tissue repair. Downstream from IL-4 receptor signaling, STAT6 activation is transient, but induces stable transcriptional changes. These data suggest that STAT6 induces second messengers to carry out the alternative transcriptional program. In this issue of Genes & Development, Daniel and colleagues (pp. 1474–1492) identify EGR2 as a downstream regulator of STAT6 with broad functionality that further induces many transcription factors associated with alternative polarization. Identification of high EGR2 expression in a subset of mouse and human alveolar macrophages further highlights EGR2 as a conserved marker of alternatively activated macrophages.
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Affiliation(s)
- Jingwen Liao
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA.,Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Diana C Hargreaves
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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Hoeksema MA, Shen Z, Holtman IR, Zheng A, Spann NJ, Cobo I, Gymrek M, Glass CK. Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. SCIENCE ADVANCES 2021; 7:7/25/eabf9808. [PMID: 34134993 PMCID: PMC8208725 DOI: 10.1126/sciadv.abf9808] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/29/2021] [Indexed: 05/24/2023]
Abstract
Mechanisms by which noncoding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. Here, we evaluated effects of >50 million single-nucleotide polymorphisms and short insertions/deletions provided by five inbred strains of mice on the responses of macrophages to interleukin-4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage-determining and signal-dependent transcription factors driving IL-4 enhancer activation. These studies further revealed mechanisms by which noncoding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity.
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Affiliation(s)
- Marten A Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - An Zheng
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Isidoro Cobo
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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Karpathiou G, Papoudou-Bai A, Ferrand E, Dumollard JM, Peoc'h M. STAT6: A review of a signaling pathway implicated in various diseases with a special emphasis in its usefulness in pathology. Pathol Res Pract 2021; 223:153477. [PMID: 33991851 DOI: 10.1016/j.prp.2021.153477] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/17/2022]
Abstract
Signal Transducer and Activator of Transcription 6 (STAT6), belonging to a family of seven similar members is primarily stimulated by interleukin(IL)-4 and IL-13, and acts as a T helper type 2 (Th2)-inducing factor. Thus, it is implicated in the pathophysiology of various allergic conditions, such as asthma, atopic dermatitis, eosinophilic esophagitis and food allergies, but also in tumor microenvironment regulation. Furthermore, certain forms of lymphomas, notably the Hodgkin lymphoma group, the primary mediastinal and primary central nervous system lymphoma, as well as some follicular and T cell lymphomas are associated with dysregulation of the STAT6 pathway. STAT6 immunohistochemical expression also serves as a surrogate marker in the diagnosis of solitary fibrous tumor, despite not directly responsible for the tumorigenic effect. These pathophysiological implications of the STAT6 pathway, its diagnostic or prognostic role in pathology, as well its immunohistochemical detection with different antibodies will be discussed in this review.
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Affiliation(s)
| | | | - Elise Ferrand
- Pathology Department, University Hospital of Saint-Etienne, France
| | | | - Michel Peoc'h
- Pathology Department, University Hospital of Saint-Etienne, France
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The epigenetic pioneer EGR2 initiates DNA demethylation in differentiating monocytes at both stable and transient binding sites. Nat Commun 2021; 12:1556. [PMID: 33692344 PMCID: PMC7946903 DOI: 10.1038/s41467-021-21661-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The differentiation of human blood monocytes (MO), the post-mitotic precursors of macrophages (MAC) and dendritic cells (moDC), is accompanied by the active turnover of DNA methylation, but the extent, consequences and mechanisms of DNA methylation changes remain unclear. Here, we profile and compare epigenetic landscapes during IL-4/GM-CSF-driven MO differentiation across the genome and detect several thousand regions that are actively demethylated during culture, both with or without accompanying changes in chromatin accessibility or transcription factor (TF) binding. We further identify TF that are globally associated with DNA demethylation processes. While interferon regulatory factor 4 (IRF4) is found to control hallmark dendritic cell functions with less impact on DNA methylation, early growth response 2 (EGR2) proves essential for MO differentiation as well as DNA methylation turnover at its binding sites. We also show that ERG2 interacts with the 5mC hydroxylase TET2, and its consensus binding sequences show a characteristic DNA methylation footprint at demethylated sites with or without detectable protein binding. Our findings reveal an essential role for EGR2 as epigenetic pioneer in human MO and suggest that active DNA demethylation can be initiated by the TET2-recruiting TF both at stable and transient binding sites. DNA methylation turnover is an essential epigenetic process during development. Here, the authors look at the changes in DNA methylation during the differentiation of post-mitotic human monocytes (MO), and find that EGR2 interacts with TET2 and is required for DNA demethylation at its binding sites; revealing EGR2 as an epigenetic pioneer factor in human MO.
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Czimmerer Z, Halasz L, Nagy L. Unorthodox Transcriptional Mechanisms of Lipid-Sensing Nuclear Receptors in Macrophages: Are We Opening a New Chapter? Front Endocrinol (Lausanne) 2020; 11:609099. [PMID: 33362723 PMCID: PMC7758493 DOI: 10.3389/fendo.2020.609099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022] Open
Abstract
Work over the past 30 years has shown that lipid-activated nuclear receptors form a bridge between metabolism and immunity integrating metabolic and inflammatory signaling in innate immune cells. Ligand-induced direct transcriptional activation and protein-protein interaction-based transrepression were identified as the most common mechanisms of liganded-nuclear receptor-mediated transcriptional regulation. However, the integration of different next-generation sequencing-based methodologies including chromatin immunoprecipitation followed by sequencing and global run-on sequencing allowed to investigate the DNA binding and ligand responsiveness of nuclear receptors at the whole-genome level. Surprisingly, these studies have raised the notion that a major portion of lipid-sensing nuclear receptor cistromes are not necessarily responsive to ligand activation. Although the biological role of the ligand insensitive portion of nuclear receptor cistromes is largely unknown, recent findings indicate that they may play roles in the organization of chromatin structure, in the regulation of transcriptional memory, and the epigenomic modification of responsiveness to other microenvironmental signals in macrophages. In this review, we will provide an overview and discuss recent advances of our understanding of lipid-activated nuclear receptor-mediated non-classical or unorthodox actions in macrophages.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
- *Correspondence: Laszlo Nagy,
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