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Moss CE, Johnston SA, Kimble JV, Clements M, Codd V, Hamby S, Goodall AH, Deshmukh S, Sudbery I, Coca D, Wilson HL, Kiss-Toth E. Aging-related defects in macrophage function are driven by MYC and USF1 transcriptional programs. Cell Rep 2024; 43:114073. [PMID: 38578825 DOI: 10.1016/j.celrep.2024.114073] [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: 10/27/2023] [Revised: 02/15/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
Macrophages are central innate immune cells whose function declines with age. The molecular mechanisms underlying age-related changes remain poorly understood, particularly in human macrophages. We report a substantial reduction in phagocytosis, migration, and chemotaxis in human monocyte-derived macrophages (MDMs) from older (>50 years old) compared with younger (18-30 years old) donors, alongside downregulation of transcription factors MYC and USF1. In MDMs from young donors, knockdown of MYC or USF1 decreases phagocytosis and chemotaxis and alters the expression of associated genes, alongside adhesion and extracellular matrix remodeling. A concordant dysregulation of MYC and USF1 target genes is also seen in MDMs from older donors. Furthermore, older age and loss of either MYC or USF1 in MDMs leads to an increased cell size, altered morphology, and reduced actin content. Together, these results define MYC and USF1 as key drivers of MDM age-related functional decline and identify downstream targets to improve macrophage function in aging.
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Affiliation(s)
- Charlotte E Moss
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Healthy Lifespan Institute, University of Sheffield, Sheffield, UK
| | - Simon A Johnston
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Joshua V Kimble
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Healthy Lifespan Institute, University of Sheffield, Sheffield, UK
| | - Martha Clements
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Healthcare Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Stephen Hamby
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Healthcare Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; National Institute for Healthcare Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Sumeet Deshmukh
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Daniel Coca
- Healthy Lifespan Institute, University of Sheffield, Sheffield, UK; Department of Autonomic Control and Systems Engineering, University of Sheffield, Sheffield, UK
| | - Heather L Wilson
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Healthy Lifespan Institute, University of Sheffield, Sheffield, UK.
| | - Endre Kiss-Toth
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Healthy Lifespan Institute, University of Sheffield, Sheffield, UK; Biological Research Centre, Szeged, Hungary.
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2
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Li Y, Ming M, Li C, Liu S, Zhang D, Song T, Tan J, Zhang J. The emerging role of the hedgehog signaling pathway in immunity response and autoimmune diseases. Autoimmunity 2023; 56:2259127. [PMID: 37740690 DOI: 10.1080/08916934.2023.2259127] [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: 04/09/2023] [Accepted: 09/10/2023] [Indexed: 09/25/2023]
Abstract
The Hedgehog (Hh) family is a prototypical morphogen involved in embryonic patterning, multi-lineage differentiation, self-renewal, morphogenesis, and regeneration. There are studies that have demonstrated that the Hh signaling pathway differentiates developing T cells into MHC-restricted self-antigen tolerant T cells in a concentration-dependent manner in the thymus. Whereas Hh signaling pathway is not required in the differentiation of B cells but is indispensable in maintaining the regeneration of hematopoietic stem cells (HSCs) and the viability of germinal centers (GCs) B cells. The Hh signaling pathway exerts both positive and negative effects on immune responses, which involves activating human peripheral CD4+ T cells, regulating the accumulation of natural killer T (NKT) cells, recruiting and activating macrophages, increasing CD4+Foxp3+ regulatory T cells in the inflammation sites to sustain homeostasis. Hedgehog signaling is involved in the patterning of the embryo, as well as homeostasis of adult tissues. Therefore, this review aims to highlight evidence for Hh signaling in the differentiation, function of immune cells and autoimmune disease. Targeting Hh signaling promises to be a novel, alternative or adjunct approach to treating tumors and autoimmune diseases.
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Affiliation(s)
- Yunfei Li
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, China
| | - Min Ming
- Department of Immunology, Zunyi Medical University, Zunyi, China
- People's Hospital of Qingbaijiang District, Chengdu, China
| | - Chunyang Li
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Songpo Liu
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Dan Zhang
- Zunyi Medical University Library, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
| | - Jun Tan
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
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3
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Glotfelty EJ, Tovar-Y-Romo LB, Hsueh SC, Tweedie D, Li Y, Harvey BK, Hoffer BJ, Karlsson TE, Olson L, Greig NH. The RhoA-ROCK1/ROCK2 Pathway Exacerbates Inflammatory Signaling in Immortalized and Primary Microglia. Cells 2023; 12:1367. [PMID: 37408199 DOI: 10.3390/cells12101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 07/07/2023] Open
Abstract
Neuroinflammation is a unifying factor among all acute central nervous system (CNS) injuries and chronic neurodegenerative disorders. Here, we used immortalized microglial (IMG) cells and primary microglia (PMg) to understand the roles of the GTPase Ras homolog gene family member A (RhoA) and its downstream targets Rho-associated coiled-coil-containing protein kinases 1 and 2 (ROCK1 and ROCK2) in neuroinflammation. We used a pan-kinase inhibitor (Y27632) and a ROCK1- and ROCK2-specific inhibitor (RKI1447) to mitigate a lipopolysaccharide (LPS) challenge. In both the IMG cells and PMg, each drug significantly inhibited pro-inflammatory protein production detected in media (TNF-α, IL-6, KC/GRO, and IL-12p70). In the IMG cells, this resulted from the inhibition of NF-κB nuclear translocation and the blocking of neuroinflammatory gene transcription (iNOS, TNF-α, and IL-6). Additionally, we demonstrated the ability of both compounds to block the dephosphorylation and activation of cofilin. In the IMG cells, RhoA activation with Nogo-P4 or narciclasine (Narc) exacerbated the inflammatory response to the LPS challenge. We utilized a siRNA approach to differentiate ROCK1 and ROCK2 activity during the LPS challenges and showed that the blockade of both proteins may mediate the anti-inflammatory effects of Y27632 and RKI1447. Using previously published data, we show that genes in the RhoA/ROCK signaling cascade are highly upregulated in the neurodegenerative microglia (MGnD) from APP/PS-1 transgenic Alzheimer's disease (AD) mice. In addition to illuminating the specific roles of RhoA/ROCK signaling in neuroinflammation, we demonstrate the utility of using IMG cells as a model for primary microglia in cellular studies.
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Affiliation(s)
- Elliot J Glotfelty
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Luis B Tovar-Y-Romo
- Division of Neuroscience, Institute of Cellular Physiology, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Shih-Chang Hsueh
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yazhou Li
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Brandon K Harvey
- Molecular Mechanisms of Cellular Stress and Inflammation Unit, Integrative Neuroscience Department, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Barry J Hoffer
- Department of Neurosurgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tobias E Karlsson
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lars Olson
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
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4
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Zhao Q, Pan S, Zhang L, Zhang Y, Shahsavari A, Lotey P, Baetge C, Deveau M, Gregory C, Kapler G, Liu F. A Salivary Gland Resident Macrophage Subset Regulating Radiation Responses. J Dent Res 2023; 102:536-545. [PMID: 36883649 PMCID: PMC10150438 DOI: 10.1177/00220345221150005] [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] [Indexed: 03/09/2023] Open
Abstract
Radiotherapy of head and neck cancers frequently leads to irreversible hypofunction of salivary glands, which severely compromises the quality of life and is extremely difficult to treat. We found recently that salivary gland resident macrophages are sensitive to radiation and interact with epithelial progenitors and endothelial cells through homeostatic paracrine factors. Heterogeneous subpopulations of resident macrophages are present in other organs with distinct functions, whereas subpopulations of salivary gland resident macrophages with distinct functions or transcriptional profiles have not been reported yet. Using single-cell RNA sequencing, we found that mouse submandibular glands (SMGs) contain 2 distinct self-renewing resident macrophage subsets, an MHC-IIhi subset present in many other organs and an uncommon Csf2r+ subset. The main source of Csf2 in SMGs are innate lymphoid cells (ILCs) that rely on IL15 for maintenance, while the main source of IL15 protein is Csf2r+ resident macrophages, indicating a homeostatic paracrine interaction between these cells. Csf2r+ resident macrophages are the major source of hepatocyte growth factor (Hgf) that regulates homeostasis of SMG epithelial progenitors. Meanwhile, Csf2r+ resident macrophages are responsive to Hedgehog signaling that can rescue salivary function impaired by radiation. Consistently, irradiation persistently decreased numbers of ILCs and levels of IL15 and Csf2 in SMGs, which were all recovered by transient activation of Hedgehog signaling after radiation. Csf2r+ resident macrophages and MHC-IIhi resident macrophages share transcriptome profiles of perivascular macrophages and macrophages associated with nerves and/or epithelial cells in other organs, respectively, and such niche preferences were supported by lineage tracing and immunofluorescent staining. These findings reveal an uncommon resident macrophage subset that regulates the homeostasis of the salivary gland and is promising as the target to restore salivary gland function impaired by radiation.
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Affiliation(s)
- Q. Zhao
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - S. Pan
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - L. Zhang
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - Y. Zhang
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - A. Shahsavari
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - P. Lotey
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - C.L. Baetge
- Department of Small Animal Clinical Sciences,
College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College
Station, TX, USA
| | - M.A. Deveau
- Department of Small Animal Clinical Sciences,
College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College
Station, TX, USA
| | - C.A. Gregory
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - G.M. Kapler
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
| | - F. Liu
- Cell Biology and Genetics Department, College
of Medicine, Texas A&M University Health Science Center, College Station, TX, USA
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5
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Olivieri F, Marchegiani F, Matacchione G, Giuliani A, Ramini D, Fazioli F, Sabbatinelli J, Bonafè M. Sex/gender-related differences in inflammaging. Mech Ageing Dev 2023; 211:111792. [PMID: 36806605 DOI: 10.1016/j.mad.2023.111792] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Geroscience puts mechanisms of aging as a driver of the most common age-related diseases and dysfunctions. Under this perspective, addressing the basic mechanisms of aging will produce a better understanding than addressing each disease pathophysiology individually. Worldwide, despite greater functional impairment, life expectancy is higher in women than in men. Gender differences in the prevalence of multimorbidity lead mandatory to the understanding of the mechanisms underlying gender-related differences in multimorbidity patterns and disability-free life expectancy. Extensive literature suggested that inflammaging is at the crossroad of aging and age-related diseases. In this review, we highlight the main evidence on sex/gender differences in the mechanisms that foster inflammaging, i.e. the age-dependent triggering of innate immunity, modifications of adaptive immunity, and accrual of senescent cells, underpinning some biomarkers of inflammaging that show sex-related differences. In the framework of the "gender medicine perspective", we will also discuss how sex/gender differences in inflammaging can affect sex differences in COVID-19 severe outcomes.
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Affiliation(s)
- Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy; Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | | | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Francesca Fazioli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy; Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy.
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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6
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Gast M, Nageswaran V, Kuss AW, Tzvetkova A, Wang X, Mochmann LH, Rad PR, Weiss S, Simm S, Zeller T, Voelzke H, Hoffmann W, Völker U, Felix SB, Dörr M, Beling A, Skurk C, Leistner DM, Rauch BH, Hirose T, Heidecker B, Klingel K, Nakagawa S, Poller WC, Swirski FK, Haghikia A, Poller W. tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions. Cells 2022; 11:cells11243970. [PMID: 36552736 PMCID: PMC9777231 DOI: 10.3390/cells11243970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary conserved NEAT1-MALAT1 gene cluster generates large noncoding transcripts remaining nuclear, while tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. Whereas functions have been assigned to the nuclear transcripts, data on biological functions of the small cytosolic transcripts are sparse. We previously found NEAT1-/- and MALAT1-/- mice to display massive atherosclerosis and vascular inflammation. Here, employing selective targeted disruption of menRNA or mascRNA, we investigate the tRNA-like molecules as critical components of innate immunity. CRISPR-generated human ΔmascRNA and ΔmenRNA monocytes/macrophages display defective innate immune sensing, loss of cytokine control, imbalance of growth/angiogenic factor expression impacting upon angiogenesis, and altered cell-cell interaction systems. Antiviral response, foam cell formation/oxLDL uptake, and M1/M2 polarization are defective in ΔmascRNA/ΔmenRNA macrophages, defining first biological functions of menRNA and describing new functions of mascRNA. menRNA and mascRNA represent novel components of innate immunity arising from the noncoding genome. They appear as prototypes of a new class of noncoding RNAs distinct from others (miRNAs, siRNAs) by biosynthetic pathway and intracellular kinetics. Their NEAT1-MALAT1 region of origin appears as archetype of a functionally highly integrated RNA processing system.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - Vanasa Nageswaran
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 12200 Berlin, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Ana Tzvetkova
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Xiaomin Wang
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Liliana H Mochmann
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Pegah Ramezani Rad
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Tanja Zeller
- University Center of Cardiovascular Science, University Heart and Vascular Center, 20246 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, 20246 Hamburg, Germany
| | - Henry Voelzke
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Wolfgang Hoffmann
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan B Felix
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antje Beling
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Institute for Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - David-Manuel Leistner
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Bernhard H Rauch
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Pharmacology, University Medicine Greifswald, 17487 Greifswald, Germany
- Department Human Medicine, Section Pharmacology and Toxicology, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Bettina Heidecker
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Wolfram C Poller
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Filip K Swirski
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
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7
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Maity AK, Hu X, Zhu T, Teschendorff AE. Inference of age-associated transcription factor regulatory activity changes in single cells. NATURE AGING 2022; 2:548-561. [PMID: 37118452 DOI: 10.1038/s43587-022-00233-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/03/2022] [Indexed: 04/30/2023]
Abstract
Transcription factors (TFs) control cell identity and function. How their activity is altered during healthy aging is critical for an improved understanding of aging and disease risk, yet relatively little is known about such changes at cell-type resolution. Here we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs. This revealed an age-associated signature of macrophage dedifferentiation, which is shared across tissue types, and aggravated in tumor-associated macrophages. By extending the analysis to all major cell types, we reveal cell-type and tissue-type-independent age-associated alterations to regulatory factors controlling antigen processing, inflammation, collagen processing and circadian rhythm, that are implicated in age-related diseases. Finally, our study highlights the limitations of using TF expression to infer age-associated changes, underscoring the need to use regulatory activity inference methods.
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Affiliation(s)
- Alok K Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xue Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK.
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