1
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Zandigohar M, Pang J, Rodrigues A, Roberts RE, Dai Y, Koh TJ. Transcription Factor Activity Regulating Macrophage Heterogeneity during Skin Wound Healing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:506-518. [PMID: 38940624 PMCID: PMC11300156 DOI: 10.4049/jimmunol.2400172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024]
Abstract
Monocytes and macrophages (Mos/Mϕs) play diverse roles in wound healing by adopting a spectrum of functional phenotypes; however, the regulation of such heterogeneity remains poorly defined. We enhanced our previously published Bayesian inference TF activity model, incorporating both single-cell RNA sequencing and single-cell ATAC sequencing data to infer transcription factor (TF) activity in Mos/Mϕs during skin wound healing. We found that wound Mos/Mϕs clustered into early-stage Mos/Mϕs, late-stage Mϕs, and APCs, and that each cluster showed differential chromatin accessibility and differential predicted TF activity that did not always correlate with mRNA or protein expression. Network analysis revealed two highly connected large communities involving a total of 19 TFs, highlighting TF cooperation in regulating wound Mos/Mϕs. This analysis also revealed a small community populated by NR4A1 and NFKB1, supporting a proinflammatory link between these TFs. Importantly, we validated a proinflammatory role for NR4A1 activity during wound healing, showing that Nr4a1 knockout mice exhibit decreased inflammatory gene expression in early-stage wound Mos/Mϕs, along with delayed wound re-epithelialization and impaired granulation tissue formation. In summary, our study provides insight into TF activity that regulates Mo/Mϕ heterogeneity during wound healing and provides a rational basis for targeting Mo/Mϕ TF networks to alter phenotypes and improve healing.
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Affiliation(s)
- Mehrdad Zandigohar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612
| | - Jingbo Pang
- Center for Wound Healing and Tissue Regeneration, Department of Kinesiology and Nutrition
| | - Alannah Rodrigues
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612
| | - Rita E. Roberts
- Center for Wound Healing and Tissue Regeneration, Department of Kinesiology and Nutrition
| | - Yang Dai
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612
| | - Timothy J. Koh
- Center for Wound Healing and Tissue Regeneration, Department of Kinesiology and Nutrition
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2
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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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3
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Vladimir de la Rosa J, Tabraue C, Huang Z, Orizaola MC, Martin‐Rodríguez P, Steffensen KR, Zapata JM, Boscá L, Tontonoz P, Alemany S, Treuter E, Castrillo A. Reprogramming of the LXRα Transcriptome Sustains Macrophage Secondary Inflammatory Responses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307201. [PMID: 38549193 PMCID: PMC11132038 DOI: 10.1002/advs.202307201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/01/2024] [Indexed: 05/29/2024]
Abstract
Macrophages regulate essential aspects of innate immunity against pathogens. In response to microbial components, macrophages activate primary and secondary inflammatory gene programs crucial for host defense. The liver X receptors (LXRα, LXRβ) are ligand-dependent nuclear receptors that direct gene expression important for cholesterol metabolism and inflammation, but little is known about the individual roles of LXRα and LXRβ in antimicrobial responses. Here, the results demonstrate that induction of LXRα transcription by prolonged exposure to lipopolysaccharide (LPS) supports inflammatory gene expression in macrophages. LXRα transcription is induced by NF-κB and type-I interferon downstream of TLR4 activation. Moreover, LPS triggers a reprogramming of the LXRα cistrome that promotes cytokine and chemokine gene expression through direct LXRα binding to DNA consensus sequences within cis-regulatory regions including enhancers. LXRα-deficient macrophages present fewer binding of p65 NF-κB and reduced histone H3K27 acetylation at enhancers of secondary inflammatory response genes. Mice lacking LXRα in the hematopoietic compartment show impaired responses to bacterial endotoxin in peritonitis models, exhibiting reduced neutrophil infiltration and decreased expansion and inflammatory activation of recruited F4/80lo-MHC-IIhi peritoneal macrophages. Together, these results uncover a previously unrecognized function for LXRα-dependent transcriptional cis-activation of secondary inflammatory gene expression in macrophages and the host response to microbial ligands.
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Affiliation(s)
- Juan Vladimir de la Rosa
- Unidad de Biomedicina (Unidad Asociada al CSIC)Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS) de la Universidad de Las Palmas de Gran CanariaLas Palmas35016Spain
| | - Carlos Tabraue
- Unidad de Biomedicina (Unidad Asociada al CSIC)Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS) de la Universidad de Las Palmas de Gran CanariaLas Palmas35016Spain
- Departamento de MorfologíaUniversidad de Las Palmas de Gran CanariaLas Palmas35016Spain
| | - Zhiqiang Huang
- Department of Biosciences and NutritionKarolinska Institutet, NEOHuddinge14183Sweden
- Center for Translational Medicine and Jiangsu Key Laboratory of Molecular MedicineMedical SchoolNanjing UniversityNanjing210093P. R. China
| | - Marta C. Orizaola
- Department of Metabolic and Immune Diseases. Instituto de Investigaciones Biomédicas Sols‐MorrealeCentro Mixto Consejo Superior de Investigaciones Científicas CSIC‐Universidad Autónoma de MadridMadrid28029Spain
| | - Patricia Martin‐Rodríguez
- Unidad de Biomedicina (Unidad Asociada al CSIC)Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS) de la Universidad de Las Palmas de Gran CanariaLas Palmas35016Spain
| | - Knut R. Steffensen
- Division of Clinical Chemistry, Department of Laboratory MedicineKarolinska InstituteHuddinge14186Sweden
| | - Juan Manuel Zapata
- Department of Metabolic and Immune Diseases. Instituto de Investigaciones Biomédicas Sols‐MorrealeCentro Mixto Consejo Superior de Investigaciones Científicas CSIC‐Universidad Autónoma de MadridMadrid28029Spain
| | - Lisardo Boscá
- Department of Metabolic and Immune Diseases. Instituto de Investigaciones Biomédicas Sols‐MorrealeCentro Mixto Consejo Superior de Investigaciones Científicas CSIC‐Universidad Autónoma de MadridMadrid28029Spain
- Centro de Investigación Biomedica en Red sobre Enfermedades Cardiovasculares (CIBERCV)Madrid28029Spain
| | - Peter Tontonoz
- Department of Pathology and Laboratory MedicineUniversity of California Los AngelesUCLACalifornia90095USA
| | - Susana Alemany
- Department of Metabolic and Immune Diseases. Instituto de Investigaciones Biomédicas Sols‐MorrealeCentro Mixto Consejo Superior de Investigaciones Científicas CSIC‐Universidad Autónoma de MadridMadrid28029Spain
| | - Eckardt Treuter
- Department of Biosciences and NutritionKarolinska Institutet, NEOHuddinge14183Sweden
| | - Antonio Castrillo
- Unidad de Biomedicina (Unidad Asociada al CSIC)Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS) de la Universidad de Las Palmas de Gran CanariaLas Palmas35016Spain
- Department of Metabolic and Immune Diseases. Instituto de Investigaciones Biomédicas Sols‐MorrealeCentro Mixto Consejo Superior de Investigaciones Científicas CSIC‐Universidad Autónoma de MadridMadrid28029Spain
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4
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Hiebert P, Antoniazzi G, Aronoff M, Werner S, Wennemers H. A lysyl oxidase-responsive collagen peptide illuminates collagen remodeling in wound healing. Matrix Biol 2024; 128:11-20. [PMID: 38382767 DOI: 10.1016/j.matbio.2024.02.006] [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: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Tissue repair and fibrosis involve the dynamic remodeling of collagen, and accurate detection of these sites is of utmost importance. Here, we use a collagen peptide sensor (1) to visualize collagen formation and remodeling during wound healing in mice and humans. We show that the probe binds selectively to sites of collagen formation and remodeling at different stages of healing. Compared to conventional methods, the peptide sensor localizes preferentially to areas of collagen synthesis and remodeling at the wound edge and not in matured fibrillar collagen. We also demonstrate its applicability for in vivo wound imaging and for discerning differential remodeling in wounds of transgenic mice with altered collagen dynamics. Our findings show the value of 1 as a diagnostic tool to rapidly identify the sites of matrix remodeling in tissue sections, which will aid in the conception of new therapeutic strategies for fibrotic disorders and defective tissue repair.
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Affiliation(s)
- Paul Hiebert
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, Zurich 8093, Switzerland
| | - Giuseppe Antoniazzi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog Weg 3, Zurich 8093, Switzerland
| | - Matthew Aronoff
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog Weg 3, Zurich 8093, Switzerland
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, Zurich 8093, Switzerland.
| | - Helma Wennemers
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog Weg 3, Zurich 8093, Switzerland.
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5
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Simkin J, Aloysius A, Adam M, Safaee F, Donahue RR, Biswas S, Lakhani Z, Gensel JC, Thybert D, Potter S, Seifert AW. Tissue-resident macrophages specifically express Lactotransferrin and Vegfc during ear pinna regeneration in spiny mice. Dev Cell 2024; 59:496-516.e6. [PMID: 38228141 PMCID: PMC10922778 DOI: 10.1016/j.devcel.2023.12.017] [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: 01/17/2022] [Revised: 05/30/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
The details of how macrophages control different healing trajectories (regeneration vs. scar formation) remain poorly defined. Spiny mice (Acomys spp.) can regenerate external ear pinnae tissue, whereas lab mice (Mus musculus) form scar tissue in response to an identical injury. Here, we used this dual species system to dissect macrophage phenotypes between healing modes. We identified secreted factors from activated Acomys macrophages that induce a pro-regenerative phenotype in fibroblasts from both species. Transcriptional profiling of Acomys macrophages and subsequent in vitro tests identified VEGFC, PDGFA, and Lactotransferrin (LTF) as potential pro-regenerative modulators. Examining macrophages in vivo, we found that Acomys-resident macrophages secreted VEGFC and LTF, whereas Mus macrophages do not. Lastly, we demonstrate the requirement for VEGFC during regeneration and find that interrupting lymphangiogenesis delays blastema and new tissue formation. Together, our results demonstrate that cell-autonomous mechanisms govern how macrophages react to the same stimuli to differentially produce factors that facilitate regeneration.
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Affiliation(s)
- Jennifer Simkin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Department of Orthopaedic Surgery, LSU Health-New Orleans, New Orleans, LA 70112, USA.
| | - Ajoy Aloysius
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mike Adam
- Department of Pediatrics, University of Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - Fatemeh Safaee
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Renée R Donahue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Shishir Biswas
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Zohaib Lakhani
- Department of Orthopaedic Surgery, LSU Health-New Orleans, New Orleans, LA 70112, USA
| | - John C Gensel
- Department of Physiology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA
| | - David Thybert
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Steven Potter
- Department of Pediatrics, University of Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA.
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6
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [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: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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7
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Ganesh GV, Ramkumar KM. Pterostilbene accelerates wound healing response in diabetic mice through Nrf2 regulation. Mol Immunol 2023; 164:17-27. [PMID: 37926050 DOI: 10.1016/j.molimm.2023.10.010] [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: 06/29/2023] [Revised: 08/31/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Pterostilbene (PTS), known for its diverse beneficial effects via Nuclear factor erythroid-2 related factor (Nrf2) activation, holds potential for Diabetic Foot Ulcer (DFU) treatment. However, PTS-mediated Nrf2 regulation in diabetic wounds has yet to be elucidated. We used IC21 macrophage-conditioned media to simulate complex events that can influence the fibroblast phenotype using L929 cells during the wound healing process under a hyperglycemic microenvironment. We found that PTS attenuated fibroblast migration and alpha-smooth muscle actin (α-SMA) levels and hypoxia-inducible factor- 1 alpha (HIF1α). Furthermore, we demonstrated that wounds in diabetic mice characterized by impaired wound closure in a heightened inflammatory milieu, such as the NOD-like receptor P3 (NLRP3) and intercellular adhesion molecule 1 (ICAM1), and deficient Nrf2 response accompanying lowered Akt signaling and heme oxygenase1 (HO1) expression along with the impaired macrophage M2 marker CD206 expression, was rescued by administration of PTS. Such an elicited response was also compared favorably with the standard treatment using Regranex, a commercially available topical formulation for treating DFUs. Our findings suggest that PTS regulates Nrf2 in diabetic wounds, triggering a pro-wound healing response mediated by macrophages. This insight holds the potential for developing targeted therapies to heal chronic wounds, including DFUs.
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Affiliation(s)
- Goutham V Ganesh
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Kunka Mohanram Ramkumar
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India.
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Yang Z, Man J, Liu Y, Zhang H, Wu D, Shao D, Hao B, Wang S. Study on the Alleviating Effect and Potential Mechanism of Ethanolic Extract of Limonium aureum (L.) Hill. on Lipopolysaccharide-Induced Inflammatory Responses in Macrophages. Int J Mol Sci 2023; 24:16272. [PMID: 38003461 PMCID: PMC10671607 DOI: 10.3390/ijms242216272] [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: 10/23/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Inflammation is the host response of immune cells during infection and traumatic tissue injury. An uncontrolled inflammatory response leads to inflammatory cascade, which in turn triggers a variety of diseases threatening human and animal health. The use of existing inflammatory therapeutic drugs is constrained by their high cost and susceptibility to systemic side effects, and therefore new therapeutic candidates for inflammatory diseases need to be urgently developed. Natural products are characterized by wide sources and rich pharmacological activities, which are valuable resources for the development of new drugs. This study aimed to uncover the alleviating effect and potential mechanism of natural product Limonium aureum (LAH) on LPS-induced inflammatory responses in macrophages. The experimental results showed that the optimized conditions for LAH ultrasound-assisted extraction via response surface methodology were an ethanol concentration of 72%, a material-to-solvent ratio of 1:37 g/mL, an extraction temperature of 73 °C, and an extraction power of 70 W, and the average extraction rate of LAH total flavonoids was 0.3776%. Then, data of 1666 components in LAH ethanol extracts were obtained through quasi-targeted metabolomics analysis. The ELISA showed that LAH significantly inhibited the production of pro-inflammatory cytokines while promoting the secretion of anti-inflammatory cytokines. Finally, combined with the results of network pharmacology analysis and protein expression validation of hub genes, it was speculated that LAH may alleviate LPS-induced inflammatory responses of macrophages through the AKT1/RELA/PTGS2 signaling pathway and the MAPK3/JUN signaling pathway. This study preliminarily revealed the anti-inflammatory activity of LAH and the molecular mechanism of its anti-inflammatory action, and provided a theoretical basis for the development of LAH as a new natural anti-inflammatory drug.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Jingyuan Man
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yu Liu
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Hongjuan Zhang
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Di Wu
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Dan Shao
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Baocheng Hao
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
| | - Shengyi Wang
- Key Laboratory of New Animal Drug Project, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agriculture Sciences, Lanzhou 730050, China; (Z.Y.); (Y.L.); (H.Z.); (D.W.); (D.S.)
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9
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Bennett H, Troutman TD, Zhou E, Spann NJ, Link VM, Seidman JS, Nickl CK, Abe Y, Sakai M, Pasillas MP, Marlman JM, Guzman C, Hosseini M, Schnabl B, Glass CK. Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes. Nat Immunol 2023; 24:1825-1838. [PMID: 37735593 PMCID: PMC10602851 DOI: 10.1038/s41590-023-01631-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Noncoding genetic variation drives phenotypic diversity, but underlying mechanisms and affected cell types are incompletely understood. Here, investigation of effects of natural genetic variation on the epigenomes and transcriptomes of Kupffer cells derived from inbred mouse strains identified strain-specific environmental factors influencing Kupffer cell phenotypes, including leptin signaling in Kupffer cells from a steatohepatitis-resistant strain. Cell-autonomous and non-cell-autonomous effects of genetic variation were resolved by analysis of F1 hybrid mice and cells engrafted into an immunodeficient host. During homeostasis, non-cell-autonomous trans effects of genetic variation dominated control of Kupffer cells, while strain-specific responses to acute lipopolysaccharide injection were dominated by actions of cis-acting effects modifying response elements for lineage-determining and signal-dependent transcription factors. These findings demonstrate that epigenetic landscapes report on trans effects of genetic variation and serve as a resource for deeper analyses into genetic control of transcription in Kupffer cells and macrophages in vitro.
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Affiliation(s)
- Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Division of Allergy and Immunology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Enchen Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christian K Nickl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin M Marlman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carlos Guzman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mojgan Hosseini
- Department of Pathology, University of California, San Diego, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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10
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Sarad K, Stefańska M, Kraszewska I, Szade K, Sluimer JC, Błyszczuk P, Dulak J, Jaźwa-Kusior A. Single-cell transcriptomics reveals subtype-specific molecular profiles in Nrf2-deficient macrophages from murine atherosclerotic aortas. Front Immunol 2023; 14:1249379. [PMID: 37965327 PMCID: PMC10641521 DOI: 10.3389/fimmu.2023.1249379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcriptional regulator of antioxidant and anti-inflammatory response in all cell types. It also activates the transcription of genes important for macrophage function. Nrf2 activity declines with age and has been closely linked to atherosclerosis, but its specific role in this vascular pathology is not clear. Atherosclerotic plaques contain several macrophage subsets with distinct, yet not completely understood, functions in the lesion development. The aim of this study was to analyze the transcriptome of diverse Nrf2-deficient macrophage subpopulations from murine atherosclerotic aortas. Mice with transcriptionally inactive Nrf2 in Cdh5-expressing cells (Nrf2 Cdh5tKO) were used in the experiments. These mice lack transcriptional Nrf2 activity in endothelial cells, but also in a proportion of leukocytes. We confirmed that the bone marrow-derived and tissue-resident macrophages isolated from Nrf2 Cdh5tKO mice exhibit a significant decline in Nrf2 activity. Atherosclerosis was induced in Nrf2 Cdh5tKO and appropriate control mice via adeno-associated viral vector (AAV)-mediated overexpression of murine proprotein convertase subtilisin/kexin type 9 (Pcsk9) in the liver and high-fat diet feeding. After 21 weeks, live aortic cells were sorted on FACS and single-cell RNA sequencing (scRNA-seq) was performed. Unsupervised clustering singled out 13 distinct aortic cell types. Among macrophages, 9 subclusters were identified. Differential gene expression analysis revealed cell subtype-specific expression patterns. A subset of inflammatory macrophages from atherosclerotic Nrf2 Cdh5tKO mice demonstrated downregulation of DNA replication genes (e.g. Mcm7, Lig1, Pola1) concomitant with upregulation of DNA damage sensor Atr gene. Atherosclerotic Nrf2 Cdh5tKO Lyve1+ resident macrophages showed strong upregulation of IFN-stimulated genes, as well as changes in the expression of death pathways-associated genes (Slc40a1, Bcl2a1). Furthermore, we observed subtype-specific expression of core ferroptosis genes (e.g. Cp, Hells, Slc40a1) in inflammatory versus tissue resident macrophages. This observation suggested a link between ferroptosis and inflammatory microenvironment appearing at a very early stage of atherogenesis. Our findings indicate that Nrf2 deficiency in aortic macrophages leads to subtype-specific transcriptomic changes associated with inflammation, iron homeostasis, cell injury or death pathways. This may help understanding the role of aging-associated decline of Nrf2 activity and the function of specific macrophage subtypes in atherosclerotic lesion development.
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Affiliation(s)
- Katarzyna Sarad
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Kraków, Poland
| | - Monika Stefańska
- Department of Clinical Immunology, Jagiellonian University Medical College, Kraków, Poland
| | - Izabela Kraszewska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Krzysztof Szade
- Laboratory of Stem Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Judith C. Sluimer
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
- BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Przemysław Błyszczuk
- Department of Clinical Immunology, Jagiellonian University Medical College, Kraków, Poland
- Department of Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Agnieszka Jaźwa-Kusior
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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11
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Bogen KT. Ultrasensitive dose-response for asbestos cancer risk implied by new inflammation-mutation model. ENVIRONMENTAL RESEARCH 2023; 230:115047. [PMID: 36965808 DOI: 10.1016/j.envres.2022.115047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/09/2022] [Indexed: 05/30/2023]
Abstract
Alterations in complex cellular phenotype each typically involve multistep activation of an ultrasensitive molecular switch (e.g., to adaptively initiate an apoptosis, inflammasome, Nrf2-ARE anti-oxidant, or heat-shock activation pathway) that triggers expression of a suite of target genes while efficiently limiting false-positive switching from a baseline state. Such switches exhibit nonlinear signal-activation relationships. In contrast, a linear no-threshold (LNT) dose-response relationship is expected for damage that accumulates in proportion to dose, as hypothesized for increased risk of cancer in relation to genotoxic dose according to the multistage somatic mutation/clonal-expansion theory of cancer, e.g., as represented in the Moolgavkar-Venzon-Knudsen (MVK) cancer model by a doubly stochastic nonhomogeneous Poisson process. Mesothelioma and lung cancer induced by exposure to carcinogenic (e.g., certain asbestos) fibers in humans and experimental animals are thought to involve modes of action driven by mutations, cytotoxicity-associated inflammation, or both, rendering ambiguous expectations concerning the nature of model-implied shape of the low-dose response for above-background increase in risk of incurring these endpoints. A recent Inflammation Somatic Mutation (ISM) theory of cancer posits instead that tissue-damage-associated inflammation that epigenetically recruits, activates and orchestrates stem cells to engage in tissue repair does not merely promote cancer, but rather is a requisite co-initiator (acting together with as few as two somatic mutations) of the most efficient pathway to any type of cancer in any reparable tissue (Dose-Response 2019; 17(2):1-12). This theory is reviewed, implications of this theory are discussed in relation to mesothelioma and lung cancer associated with chronic asbestos inhalation, one of the two types of ISM-required mutations is here hypothesized to block or impede inflammation resolution (e.g., by doing so for GPCR-mediated signal transduction by one or more endogenous autacoid specialized pro-resolving mediators or SPMs), and supporting evidence for this hypothesis is discussed.
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Affiliation(s)
- Kenneth T Bogen
- 9832 Darcy Forest Drive, Silver Spring, MD, 20910, United States.
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12
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Zhang Y, Gao Y, Ding Y, Jiang Y, Chen H, Zhan Z, Liu X. Targeting KAT2A inhibits inflammatory macrophage activation and rheumatoid arthritis through epigenetic and metabolic reprogramming. MedComm (Beijing) 2023; 4:e306. [PMID: 37313329 PMCID: PMC10258526 DOI: 10.1002/mco2.306] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic regulation of inflammatory macrophages governs inflammation initiation and resolution in the pathogenesis of rheumatoid arthritis (RA). Nevertheless, the mechanisms underlying macrophage-mediated arthritis injuries remain largely obscure. Here, we found that increased expression of lysine acetyltransferase 2A (KAT2A) in synovial tissues was closely correlated with inflammatory joint immunopathology in both RA patients and experimental arthritis mice. Administration of MB-3, the KAT2A-specific chemical inhibitor, significantly ameliorated the synovitis and bone destruction in collagen-induced arthritis model. Both pharmacological inhibition and siRNA silencing of KAT2A, not only suppressed innate stimuli-triggered proinflammatory gene (such as Il1b and Nlrp3) transcription but also impaired NLR family pyrin domain containing 3 (NLRP3) inflammasome activation in vivo and in vitro. Mechanistically, KAT2A facilitated macrophage glycolysis reprogramming through suppressing nuclear factor-erythroid 2-related factor 2 (NRF2) activity as well as downstream antioxidant molecules, which supported histone 3 lysine 9 acetylation (H3K9ac) and limited NRF2-mediated transcriptional repression of proinflammatory genes. Our study proves that acetyltransferase KAT2A licenses metabolic and epigenetic reprogramming for NLRP3 inflammasome activation in inflammatory macrophages, thereby targeting KAT2A represents a potential therapeutic approach for patients suffering from RA and relevant inflammatory diseases.
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Affiliation(s)
- Yunkai Zhang
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
- National Key Laboratory of Immunity & InflammationNaval Medical UniversityShanghaiChina
| | - Ying Gao
- Department of RheumatologyChanghai Hospital, Naval Medical UniversityShanghaiChina
- Key Laboratory of Arrhythmias of the Ministry of Education of ChinaShanghai East Hospital, Tongji University School of MedicineShanghaiChina
| | - Yingying Ding
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
| | - Yuyu Jiang
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
| | - Huiying Chen
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
| | - Zhenzhen Zhan
- Key Laboratory of Arrhythmias of the Ministry of Education of ChinaShanghai East Hospital, Tongji University School of MedicineShanghaiChina
- Department of Liver Surgery, Shanghai Institute of TransplantationRenji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xingguang Liu
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
- National Key Laboratory of Immunity & InflammationNaval Medical UniversityShanghaiChina
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13
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Benjamin DI, Brett JO, Both P, Benjamin JS, Ishak HL, Kang J, Kim S, Chung M, Arjona M, Nutter CW, Tan JH, Krishnan AK, Dulay H, Louie SM, de Morree A, Nomura DK, Rando TA. Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging. Cell Metab 2023; 35:472-486.e6. [PMID: 36854304 PMCID: PMC10015599 DOI: 10.1016/j.cmet.2023.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/14/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
With age, skeletal muscle stem cells (MuSCs) activate out of quiescence more slowly and with increased death, leading to defective muscle repair. To explore the molecular underpinnings of these defects, we combined multiomics, single-cell measurements, and functional testing of MuSCs from young and old mice. The multiomics approach allowed us to assess which changes are causal, which are compensatory, and which are simply correlative. We identified glutathione (GSH) metabolism as perturbed in old MuSCs, with both causal and compensatory components. Contrary to young MuSCs, old MuSCs exhibit a population dichotomy composed of GSHhigh cells (comparable with young MuSCs) and GSHlow cells with impaired functionality. Mechanistically, we show that antagonism between NRF2 and NF-κB maintains this bimodality. Experimental manipulation of GSH levels altered the functional dichotomy of aged MuSCs. These findings identify a novel mechanism of stem cell aging and highlight glutathione metabolism as an accessible target for reversing MuSC aging.
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Affiliation(s)
- Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jamie O Brett
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Pieter Both
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Joel S Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Heather L Ishak
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingyu Chung
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Arjona
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Nutter
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jenna H Tan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Ananya K Krishnan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Hunter Dulay
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon M Louie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Neurology Service, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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14
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Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients. Cell Rep Med 2023; 4:100935. [PMID: 36758547 PMCID: PMC9874047 DOI: 10.1016/j.xcrm.2023.100935] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/08/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.
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Affiliation(s)
- Michael Tun Yin Lam
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Pulmonary and Critical Care Section, VA San Diego Healthcare System, La Jolla, CA 92161, USA.
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA
| | - Mazen F Odish
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiep D Le
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emily A Hansen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Celina T Nguyen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Samantha Trescott
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Roy Kim
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shaunak Deota
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Max W Chang
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arjun Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Hepokoski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Rolfsen
- Internal Medicine Residency Program, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Perofsky
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Anna S Warden
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | | | - Sydney I Ramirez
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Robert K Abbott
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shane Crotty
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Laura E Crotty Alexander
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Pulmonary and Critical Care Section, VA San Diego Healthcare System, La Jolla, CA 92161, USA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Satchidananda Panda
- Laboratory of Regulatory Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher W Benner
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Hospital, San Diego, CA 92123, USA
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15
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Kong T, Laranjeira ABA, Yang K, Fisher DAC, Yu L, Poittevin De La Frégonnière L, Wang AZ, Ruzinova MB, Fowles JS, Fulbright MC, Cox MJ, Celik H, Challen GA, Huang S, Oh ST. DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression. NATURE CANCER 2023; 4:108-127. [PMID: 36581736 PMCID: PMC11288645 DOI: 10.1038/s43018-022-00486-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/08/2022] [Indexed: 12/31/2022]
Abstract
Myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed single-cell RNA sequencing on serial MPN and sAML patient stem and progenitor cells, identifying aberrantly increased expression of DUSP6 underlying disease transformation. Pharmacologic dual-specificity phosphatase (DUSP)6 targeting led to inhibition of S6 and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling while also reducing inflammatory cytokine production. DUSP6 perturbation further inhibited ribosomal S6 kinase (RSK)1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 mediated JAK2-inhibitor resistance and exacerbated disease severity in patient-derived xenograft (PDX) models. Contrastingly, DUSP6 inhibition potently suppressed disease development across Jak2V617F and MPLW515L MPN mouse models and sAML PDXs without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and highlight the DUSP6-RSK1 axis as a vulnerable, druggable pathway in myeloid malignancies.
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Affiliation(s)
- Tim Kong
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Angelo B A Laranjeira
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kangning Yang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - LaYow Yu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Laure Poittevin De La Frégonnière
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Anthony Z Wang
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Marianna B Ruzinova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jared S Fowles
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mary C Fulbright
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Cox
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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16
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Maassen S, Coenen B, Ioannidis M, Harber K, Grijpstra P, Van den Bossche J, van den Bogaart G. Itaconate promotes a wound resolving phenotype in pro-inflammatory macrophages. Redox Biol 2022; 59:102591. [PMID: 36574745 PMCID: PMC9800195 DOI: 10.1016/j.redox.2022.102591] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
Pathological conditions associated with dysfunctional wound healing are characterized by impaired remodelling of extracellular matrix (ECM), increased macrophage infiltration, and chronic inflammation. Macrophages also play an important role in wound healing as they drive wound closure by secretion of molecules like transforming growth factor beta-1 (TGF-β). As the functions of macrophages are regulated by their metabolism, local administration of small molecules that alter this might be a novel approach for treatment of wound-healing disorders. Itaconate is a tricarboxylic acid (TCA) cycle-derived metabolite that has been associated with resolution of macrophage-mediated inflammation. However, its effects on macrophage wound healing functions are unknown. In this study, we investigated the effects of the membrane-permeable 4-octyl itaconate (4-OI) derivative on ECM scavenging by cultured human blood monocyte-derived macrophages (hMDM). We found that 4-OI reduced signalling of p38 mitogen-activated protein kinase (MAPK) induced by the canonical immune stimulus lipopolysaccharide (LPS). Likely as a consequence of this, the production of the inflammatory mediators like tumor necrosis factor (TNF)-α and cyclooxygenase (COX)-2 were also reduced. On the transcriptional level, 4-OI increased expression of the gene coding for TGF-β (TGFB1), whereas expression of the collagenase matrix metalloprotease-8 (MMP8) was reduced. Furthermore, surface levels of the anti-inflammatory marker CD36, but not CD206 and CD11c, were increased in these cells. To directly investigate the effect of 4-OI on scavenging of ECM by macrophages, we developed an assay to measure uptake of fibrous collagen. We observed that LPS promoted collagen uptake and that this was reversed by 4-OI-induced signaling of nuclear factor erythroid 2-related factor 2 (NRF2), a regulator of cellular resistance to oxidative stress and the reduced glycolytic capacity of the macrophage. These results indicate that 4-OI lowers macrophage inflammation, likely promoting a more wound-resolving phenotype.
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Affiliation(s)
- Sjors Maassen
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, the Netherlands
| | - Britt Coenen
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, the Netherlands
| | - Melina Ioannidis
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, the Netherlands
| | - Karl Harber
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Institute for Infection and Immunity, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Grijpstra
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, the Netherlands
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Institute for Infection and Immunity, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, the Netherlands; Department of Medical Biology and Pathology, University Medical Center Groningen, Groningen, the Netherlands.
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17
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Cobo I, Tanaka TN, Chandra Mangalhara K, Lana A, Yeang C, Han C, Schlachetzki J, Challcombe J, Fixsen BR, Sakai M, Li RZ, Fields H, Mokry M, Tsai RG, Bejar R, Prange K, de Winther M, Shadel GS, Glass CK. DNA methyltransferase 3 alpha and TET methylcytosine dioxygenase 2 restrain mitochondrial DNA-mediated interferon signaling in macrophages. Immunity 2022; 55:1386-1401.e10. [PMID: 35931086 PMCID: PMC9718507 DOI: 10.1016/j.immuni.2022.06.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022]
Abstract
Deleterious somatic mutations in DNA methyltransferase 3 alpha (DNMT3A) and TET mehtylcytosine dioxygenase 2 (TET2) are associated with clonal expansion of hematopoietic cells and higher risk of cardiovascular disease (CVD). Here, we investigated roles of DNMT3A and TET2 in normal human monocyte-derived macrophages (MDM), in MDM isolated from individuals with DNMT3A or TET2 mutations, and in macrophages isolated from human atherosclerotic plaques. We found that loss of function of DNMT3A or TET2 resulted in a type I interferon response due to impaired mitochondrial DNA integrity and activation of cGAS signaling. DNMT3A and TET2 normally maintained mitochondrial DNA integrity by regulating the expression of transcription factor A mitochondria (TFAM) dependent on their interactions with RBPJ and ZNF143 at regulatory regions of the TFAM gene. These findings suggest that targeting the cGAS-type I IFN pathway may have therapeutic value in reducing risk of CVD in patients with DNMT3A or TET2 mutations.
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Affiliation(s)
- Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffany N Tanaka
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | | | - Addison Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Calvin Yeang
- University of California San Diego, Sulpizio Cardiovascular Center, La Jolla, CA, USA
| | - Claudia Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Johannes Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jean Challcombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Fields
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, 3584 EA Utrecht, the Netherlands
| | - Randy G Tsai
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Rafael Bejar
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Koen Prange
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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18
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Poole J, Ray D. The Role of Circadian Clock Genes in Critical Illness: The Potential Role of Translational Clock Gene Therapies for Targeting Inflammation, Mitochondrial Function, and Muscle Mass in Intensive Care. J Biol Rhythms 2022; 37:385-402. [PMID: 35880253 PMCID: PMC9326790 DOI: 10.1177/07487304221092727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Earth's 24-h planetary rotation, with predictable light and heat cycles, has driven profound evolutionary adaptation, with prominent impacts on physiological mechanisms important for surviving critical illness. Pathways of interest include inflammation, mitochondrial function, energy metabolism, hypoxic signaling, apoptosis, and defenses against reactive oxygen species. Regulation of these by the cellular circadian clock (BMAL-1 and its network) has an important influence on pulmonary inflammation; ventilator-associated lung injury; septic shock; brain injury, including vasospasm; and overall mortality in both animals and humans. Whether it is cytokines, the inflammasome, or mitochondrial biogenesis, circadian medicine represents exciting opportunities for translational therapy in intensive care, which is currently lacking. Circadian medicine also represents a link to metabolic determinants of outcome, such as diabetes and cardiovascular disease. More than ever, we are appreciating the problem of circadian desynchrony in intensive care. This review explores the rationale and evidence for the importance of the circadian clock in surviving critical illness.
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Affiliation(s)
- Joanna Poole
- Anaesthetics and Critical Care, Gloucestershire Royal Hospital, Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
| | - David Ray
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
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19
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SR9009 Regulates Acute Lung Injury in Mice Induced by Sepsis. Can Respir J 2022; 2022:5802938. [PMID: 35814267 PMCID: PMC9270156 DOI: 10.1155/2022/5802938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/13/2022] [Accepted: 04/21/2022] [Indexed: 12/03/2022] Open
Abstract
Rev-Erbα is a nuclear heme receptor, transcriptional repressor, and critical component of the molecular clock that drives daily rhythms of metabolism. However, the roles of Rev-Erbα in acute lung injury (ALI) remain unclarified. Hence, the effect of Rev-Erbα on lung injury of sepsis mice is investigated here. The mice sepsis model is established using lipopolysaccharide (LPS) injection, and the expression levels of proinflammatory cytokines, such as tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and interleukin-10 (IL-10) in both RAW246.7 cells and lung tissues, are tested. The inflammatory response is obviously enhanced in LPS-constructed sepsis mice and alleviated by SR9009 agonist treatment. Cell-based experiments reveal that pharmacological activation of Rev-Erbα via SR9009 attenuates the LPS-induced inflammatory response by suppressing TLR4-regulated NF-κB activation. Sepsis induces the increase in W/D ratio; promotes the levels of malondialdehyde (MDA), lactic acid (LA), and superoxide dismutase (SOD); and inhibits the levels of glutathione (GSH), whereas SR9009 treatment could effectively yield beneficial effects on metabolism. In addition, SR9009 treatment ameliorates acidosis and hypoxemia by efficiently decreasing arterial PaCO2 and increasing arterial PaO2, SO2, HCO3–, lactic acid concentration, and blood PH. These findings confirm that SR9009 treatment can alleviate the sepsis-induced lung injury and targeting Rev-Erbα may represent a promising approach for the prevention and management of ALI.
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20
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Chen B, Li R, Hernandez SC, Hanna A, Su K, Shinde AV, Frangogiannis NG. Differential effects of Smad2 and Smad3 in regulation of macrophage phenotype and function in the infarcted myocardium. J Mol Cell Cardiol 2022; 171:1-15. [PMID: 35780861 DOI: 10.1016/j.yjmcc.2022.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 02/08/2023]
Abstract
TGF-βs regulate macrophage responses, by activating Smad2/3. We have previously demonstrated that macrophage-specific Smad3 stimulates phagocytosis and mediates anti-inflammatory macrophage transition in the infarcted heart. However, the role of macrophage Smad2 signaling in myocardial infarction remains unknown. We studied the role of macrophage-specific Smad2 signaling in healing mouse infarcts, and we explored the basis for the distinct effects of Smad2 and Smad3. In infarct macrophages, Smad3 activation preceded Smad2 activation. In contrast to the effects of Smad3 loss, myeloid cell-specific Smad2 disruption had no effects on mortality, ventricular dysfunction and adverse remodeling, after myocardial infarction. Macrophage Smad2 loss modestly, but transiently increased myofibroblast density in the infarct, but did not affect phagocytic removal of dead cells, macrophage infiltration, collagen deposition, and scar remodeling. In isolated macrophages, TGF-β1, -β2 and -β3, activated both Smad2 and Smad3, whereas BMP6 triggered only Smad3 activation. Smad2 and Smad3 had similar patterns of nuclear translocation in response to TGF-β1. RNA-sequencing showed that Smad3, and not Smad2, was the main mediator of transcriptional effects of TGF-β on macrophages. Smad3 loss resulted in differential expression of genes associated with RAR/RXR signaling, cholesterol biosynthesis and lipid metabolism. In both isolated bone marrow-derived macrophages and in infarct macrophages, Smad3 mediated synthesis of Nr1d2 and Rara, two genes encoding nuclear receptors, that may be involved in regulation of their phagocytic and anti-inflammatory properties. In conclusion, the in vivo and in vitro effects of TGF-β on macrophage function involve Smad3, and not Smad2.
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Affiliation(s)
- Bijun Chen
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Ruoshui Li
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Silvia C Hernandez
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Anis Hanna
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Kai Su
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Arti V Shinde
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Nikolaos G Frangogiannis
- The Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY, United States of America.
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21
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Monosodium urate crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response. Cell Rep 2022; 38:110489. [PMID: 35263587 DOI: 10.1016/j.celrep.2022.110489] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/20/2021] [Accepted: 02/14/2022] [Indexed: 12/21/2022] Open
Abstract
Monosodium urate crystals (MSUc) induce inflammation in vivo without prior priming, raising the possibility of an initial cell-autonomous phase. Here, using genome-wide transcriptomic analysis and biochemical assays, we demonstrate that MSUc alone induce a metabolic-inflammatory transcriptional program in non-primed human and murine macrophages that is markedly distinct to that induced by LPS. Genes uniquely upregulated in response to MSUc belong to lipid and amino acid metabolism, glycolysis, and SLC transporters. This upregulation leads to a metabolic rewiring in sera from individuals and mice with acute gouty arthritis. Mechanistically, the initiating inflammatory-metabolic changes in acute gout flares are regulated through a persistent expression and increased binding of JUN to the promoter of target genes through JNK signaling-but not P38-in a process that is different than after LPS stimulation and independent of inflammasome activation. Finally, pharmacological JNK inhibition limits MSUc-induced inflammation in animal models of acute gouty inflammation.
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22
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Fagiani F, Di Marino D, Romagnoli A, Travelli C, Voltan D, Mannelli LDC, Racchi M, Govoni S, Lanni C. Molecular regulations of circadian rhythm and implications for physiology and diseases. Signal Transduct Target Ther 2022; 7:41. [PMID: 35136018 PMCID: PMC8825842 DOI: 10.1038/s41392-022-00899-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/11/2022] Open
Abstract
The term “circadian rhythms” describes endogenous oscillations with ca. 24-h period associated with the earth’s daily rotation and light/dark cycle. Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues. At the molecular level, the circadian clock consists of multiple sets of transcription factors resulting in autoregulatory transcription-translation feedback loops. Notably, in addition to their primary role as generator of circadian rhythm, the biological clock plays a key role in controlling physiological functions of almost all tissues and organs. It regulates several intracellular signaling pathways, ranging from cell proliferation, DNA damage repair and response, angiogenesis, metabolic and redox homeostasis, to inflammatory and immune response. In this review, we summarize findings showing the crosstalk between the circadian molecular clock and some key intracellular pathways, describing a scenario wherein their reciprocal regulation impinges upon several aspects of mammalian physiology. Moreover, based on evidence indicating that circadian rhythms can be challenged by environmental factors, social behaviors, as well as pre-existing pathological conditions, we discuss implications of circadian misalignment in human pathologies, such as cancer and inflammatory diseases. Accordingly, disruption of circadian rhythm has been reported to affect several physiological processes that are relevant to human diseases. Expanding our understanding of this field represents an intriguing and transversal medicine challenge in order to establish a circadian precision medicine.
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Affiliation(s)
- Francesca Fagiani
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Travelli
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Davide Voltan
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | | | - Marco Racchi
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Stefano Govoni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy.
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23
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Cui L, Xu F, Jiang Z, Wang S, Li X, Ding Y, Zhang Y, Du M. Melatonin regulates proliferation and apoptosis of endometrial stromal cells via MT1. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1333-1341. [PMID: 34343226 DOI: 10.1093/abbs/gmab108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
Endometrial dysfunction is an important factor for implantation failure. The function of the endometrium is regulated by multiple factors like sex hormones and circadian rhythms. Endometrial stromal cells (ESCs) are a major cellular component in the endometrium, which is essential for proper physiological activities of the endometrium and the establishment of pregnancy. Melatonin, as a circadian-controlled hormone, plays beneficial roles in the regulation of reproductive processes. MT1, a melatonin receptor, can regulate cell proliferation and apoptosis. Whether melatonin-MT1 signal affects biological function of ESCs remains unknown. Here, we showed that MT1 was expressed in human ESCs (hESCs), which could be regulated by estrogen and progesterone. MT1 knockdown inhibited proliferative activity and promoted apoptosis of hESCs by activating caspase-3 and upregulating the Bax/Bcl2 ratio. Melatonin could reverse the effect of MT1 knockdown on proliferative activity and apoptosis of hESCs. Melatonin could promote proliferative activity of hESCs via the JNK/P38 signal pathway and repress the apoptosis of hESCs via the JNK signal pathway. Moreover, in vivo experiments showed that MT1 expression was decreased in endometrial cells from mice with disrupted circadian rhythm, accompanied by increased apoptosis and suppressed proliferative activity, which could be alleviated by administration of melatonin. These results showed the regulatory effect of melatonin-MT1 signal on biological behaviors of ESCs, which might provide a novel therapeutic strategy for endometrial dysfunction induced by disrupted circadian rhythm.
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Affiliation(s)
- Liyuan Cui
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Feng Xu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Zhuxuan Jiang
- Department of Gynecology and Obstetrics, The First People’s Hospital of Yangzhou, Yangzhou Medical University, Yangzhou 225000, China
| | - Songcun Wang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Xinyi Li
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Yan Ding
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Ying Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
| | - Meirong Du
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai 200090, China
- Department of Obstetrics and Gynecology, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
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24
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Mok DZL, Chan CYY, Ooi EE, Chan KR. The effects of aging on host resistance and disease tolerance to SARS-CoV-2 infection. FEBS J 2021; 288:5055-5070. [PMID: 33124149 PMCID: PMC8518758 DOI: 10.1111/febs.15613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 01/08/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a large-scale pandemic that is afflicting millions of individuals in over 200 countries. The clinical spectrum caused by SARS-CoV-2 infections can range from asymptomatic infection to mild undifferentiated febrile illness to severe respiratory disease with multiple complications. Elderly patients (aged 60 and above) with comorbidities such as cardiovascular diseases and diabetes mellitus appear to be at highest risk of a severe disease outcome. To protect against pulmonary immunopathology caused by SARS-CoV-2 infection, the host primarily depends on two distinct defense strategies: resistance and disease tolerance. Resistance is the ability of the host to suppress and eliminate incoming viruses. By contrast, disease tolerance refers to host responses that promote host health regardless of their impact on viral replication. Disruption of either resistance or disease tolerance mechanisms or both could underpin predisposition to elevated risk of severe disease during viral infection. Aging can disrupt host resistance and disease tolerance by compromising immune functions, weakening of the unfolded protein response, progressive mitochondrial dysfunction, and altering metabolic processes. A comprehensive understanding of the molecular mechanisms underlying declining host defense in elderly individuals could thus pave the way to provide new opportunities and approaches for the treatment of severe COVID-19.
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Affiliation(s)
- Darren Z. L. Mok
- Emerging Infectious Diseases ProgramDuke‐NUS Medical SchoolSingaporeSingapore
| | | | - Eng Eong Ooi
- Emerging Infectious Diseases ProgramDuke‐NUS Medical SchoolSingaporeSingapore
- Viral Research & Experimental Medicine Center @ SingHealth/Duke‐NUS (ViREMiCS)SingaporeSingapore
- Singapore‐MIT Alliance in Research and TechnologyAntimicrobial Resistance Interdisciplinary Research GroupSingaporeSingapore
- Saw Swee Hock School of Public HealthNational University of SingaporeSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Kuan Rong Chan
- Emerging Infectious Diseases ProgramDuke‐NUS Medical SchoolSingaporeSingapore
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25
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Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.24.457187. [PMID: 34462742 PMCID: PMC8404884 DOI: 10.1101/2021.08.24.457187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the 'active cistrome,' offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID- 19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.
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Affiliation(s)
- Michael Tun Yin Lam
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Sascha H. Duttke
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Mazen F. Odish
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Hiep D. Le
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Emily A. Hansen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | | | - Samantha Trescott
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Roy Kim
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Shaunak Deota
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Max W. Chang
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Arjun Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mark Hepokoski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mark Rolfsen
- Internal Medicine Residency Program, Department of Medicine, UC San Diego, CA, USA
| | - Katherine Perofsky
- Department of Pediatrics, University of California, San Diego, CA, USA
- Rady Children’s Hospital, San Diego, CA
| | - Anna S. Warden
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | | | - Sydney I Ramirez
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Jennifer M. Dan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Robert K Abbott
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
- Consortium for HIV/AIDS Vaccine Development (CHVAD), The Scripps Research Institute, La Jolla, CA, USA
| | - Shane Crotty
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Laura E Crotty Alexander
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Satchidananda Panda
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Christopher W. Benner
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Nicole G. Coufal
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
- Rady Children’s Hospital, San Diego, CA
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26
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Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.24.457187. [PMID: 34462742 DOI: 10.1101/2021.10.28.466336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the 'active cistrome,' offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID- 19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.
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Affiliation(s)
- Michael Tun Yin Lam
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Sascha H Duttke
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Mazen F Odish
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Hiep D Le
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Emily A Hansen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Celina T Nguyen
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Samantha Trescott
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Roy Kim
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Shaunak Deota
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Max W Chang
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Arjun Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mark Hepokoski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Mark Rolfsen
- Internal Medicine Residency Program, Department of Medicine, UC San Diego, CA, USA
| | - Katherine Perofsky
- Department of Pediatrics, University of California, San Diego, CA, USA
- Rady Children's Hospital, San Diego, CA
| | - Anna S Warden
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | | | - Sydney I Ramirez
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Jennifer M Dan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Robert K Abbott
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
- Consortium for HIV/AIDS Vaccine Development (CHVAD), The Scripps Research Institute, La Jolla, CA, USA
| | - Shane Crotty
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA
| | - Laura E Crotty Alexander
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, San Diego, CA USA
| | - Satchidananda Panda
- Laboratory of Regulatory Biology, Salk Institute of Biological Studies, La Jolla, CA, USA
| | - Christopher W Benner
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, CA, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, CA, USA
- Rady Children's Hospital, San Diego, CA
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Bene K, Halasz L, Nagy L. Transcriptional repression shapes the identity and function of tissue macrophages. FEBS Open Bio 2021; 11:3218-3229. [PMID: 34358410 PMCID: PMC8634859 DOI: 10.1002/2211-5463.13269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 12/22/2022] Open
Abstract
The changing extra‐ and intracellular microenvironment calls for rapid cell fate decisions that are precisely and primarily regulated at the transcriptional level. The cellular components of the immune system are excellent examples of how cells respond and adapt to different environmental stimuli. Innate immune cells such as macrophages are able to modulate their transcriptional programs and epigenetic regulatory networks through activation and repression of particular genes, allowing them to quickly respond to a rapidly changing environment. Tissue macrophages are essential components of different immune‐ and nonimmune cell‐mediated physiological mechanisms in mammals and are widely used models for investigating transcriptional regulatory mechanisms. Therefore, it is critical to unravel the distinct sets of transcription activators, repressors, and coregulators that play roles in determining tissue macrophage identity and functions during homeostasis, as well as in diseases affecting large human populations, such as metabolic syndromes, immune‐deficiencies, and tumor development. In this review, we will focus on transcriptional repressors that play roles in tissue macrophage development and function under physiological conditions.
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Affiliation(s)
- Krisztian Bene
- Department of Biochemistry and Molecular Biology, Nuclear Receptor Research Laboratory, 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, USA
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Nuclear Receptor Research Laboratory, 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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28
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Hong J, Shi Z, Li C, Ji X, Li S, Chen Y, Jiang G, Shi M, Wang W, Zhang Y, Hu B, Yan S. Virtual screening identified natural Keap1-Nrf2 PPI inhibitor alleviates inflammatory osteoporosis through Nrf2-mir214-Traf3 axis. Free Radic Biol Med 2021; 171:365-378. [PMID: 34000381 DOI: 10.1016/j.freeradbiomed.2021.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023]
Abstract
Overactive osteoclastogenesis is involved in the inflammatory bone loss and could be target for therapy. Here, we applied transcription factor enrichment analysis using public inflammatory osteolysis datasets and identified Nrf2 as the potential therapeutic target. Additionally, in-silico screening was performed to dig out Nrf2-Keap1 PPI inhibitor and Forsythoside-β was found to be the best-performing PHG compound. We firstly tested the effect of Forsythoside-β in inflammatory osteoporosis models and found it was able to attenuate the bone loss by inhibiting osteoclastogenesis and activating Nrf2-signaling in vivo. Forsythoside-β was capable to suppress the differentiation of osteoclast in time and dose-dependent manners in vitro. Further, Forsythoside-β could inhibit the production of reactive oxygen species and induce Nrf2 nuclear-translocation by interrupting Nrf2-Keap1 PPI. Recently, Nrf2 was identified as the epigenetic regulator modulating levels of miRNA in various diseases. We discovered that Forsythoside-β could suppress the expression of mir-214-3p, one of most variable miRNAs during osteoclastogenesis. To clarify the undermining mechanism, by utilizing chip-seq dataset, we found that Nrf2 could bind to promoter of mir-214-3p and further regulate this miRNA. Collectively, Forsythoside-β was able to prevent bone loss through Nrf2-mir-214-3p-Traf3 axis, which could be a promising candidate for treating inflammatory bone loss in the future.
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Affiliation(s)
- Jianqiao Hong
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Zhongli Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Congsun Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Xiaoxiao Ji
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Sihao Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Yazhou Chen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Guangyao Jiang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Mingmin Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Wei Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China
| | - Yongxing Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China.
| | - Bin Hu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China.
| | - Shigui Yan
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Orthopedic Research Institute of Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province Hangzhou, Zhejiang, China.
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Choudhury ME, Miyanishi K, Takeda H, Tanaka J. Microglia and the Aging Brain: Are Geriatric Microglia Linked to Poor Sleep Quality? Int J Mol Sci 2021; 22:ijms22157824. [PMID: 34360590 PMCID: PMC8345993 DOI: 10.3390/ijms22157824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
Poor sleep quality and disrupted circadian behavior are a normal part of aging and include excessive daytime sleepiness, increased sleep fragmentation, and decreased total sleep time and sleep quality. Although the neuronal decline underlying the cellular mechanism of poor sleep has been extensively investigated, brain function is not fully dependent on neurons. A recent antemortem autographic study and postmortem RNA sequencing and immunohistochemical studies on aged human brain have investigated the relationship between sleep fragmentation and activation of the innate immune cells of the brain, microglia. In the process of aging, there are marked reductions in the number of brain microglial cells, and the depletion of microglial cells disrupts circadian rhythmicity of brain tissue. We also showed, in a previous study, that pharmacological suppression of microglial function induced sleep abnormalities. However, the mechanism underlying the contribution of microglial cells to sleep homeostasis is only beginning to be understood. This review revisits the impact of aging on the microglial population and activation, as well as microglial contribution to sleep maintenance and response to sleep loss. Most importantly, this review will answer questions such as whether there is any link between senescent microglia and age-related poor quality sleep and how this exacerbates neurodegenerative disease.
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Affiliation(s)
- Mohammed E. Choudhury
- Department of Molecular and Cellular Physiology, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
- Correspondence: (M.E.C.); (J.T.)
| | - Kazuya Miyanishi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan;
| | - Haruna Takeda
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Aoba, Sendai 980-8575, Miyagi, Japan;
| | - Junya Tanaka
- Department of Molecular and Cellular Physiology, Ehime University Graduate School of Medicine, Shitsukawa, Toon 791-0295, Ehime, Japan
- Correspondence: (M.E.C.); (J.T.)
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30
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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: 25] [Impact Index Per Article: 8.3] [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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Harnessing the Benefits of Neuroinflammation: Generation of Macrophages/Microglia with Prominent Remyelinating Properties. J Neurosci 2021; 41:3366-3385. [PMID: 33712513 DOI: 10.1523/jneurosci.1948-20.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Excessive inflammation within the CNS is injurious, but an immune response is also required for regeneration. Macrophages and microglia adopt different properties depending on their microenvironment, and exposure to IL4 and IL13 has been used to elicit repair. Unexpectedly, while LPS-exposed macrophages and microglia killed neural cells in culture, the addition of LPS to IL4/IL13-treated macrophages and microglia profoundly elevated IL10, repair metabolites, heparin binding epidermal growth factor trophic factor, antioxidants, and matrix-remodeling proteases. In C57BL/6 female mice, the generation of M(LPS/IL4/IL13) macrophages required TLR4 and MyD88 signaling, downstream activation of phosphatidylinositol-3 kinase/mTOR and MAP kinases, and convergence on phospho-CREB, STAT6, and NFE2. Following mouse spinal cord demyelination, local LPS/IL4/IL13 deposition markedly increased lesional phagocytic macrophages/microglia, lactate and heparin binding epidermal growth factor, matrix remodeling, oligodendrogenesis, and remyelination. Our data show that a prominent reparative state of macrophages/microglia is generated by the unexpected integration of pro- and anti-inflammatory activation cues. The results have translational potential, as the LPS/IL4/IL13 mixture could be locally applied to a focal CNS injury to enhance neural regeneration and recovery.SIGNIFICANCE STATEMENT The combination of LPS and regulatory IL4 and IL13 signaling in macrophages and microglia produces a previously unknown and particularly reparative phenotype devoid of pro-inflammatory neurotoxic features. The local administration of LPS/IL4/IL13 into spinal cord lesion elicits profound oligodendrogenesis and remyelination. The careful use of LPS and IL4/IL13 mixture could harness the known benefits of neuroinflammation to enable repair in neurologic insults.
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32
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Apaza Ticona L, Rumbero Sánchez Á, Sánchez Sánchez-Corral J, Iglesias Moreno P, Ortega Domenech M. Anti-inflammatory, pro-proliferative and antimicrobial potential of the compounds isolated from Daemonorops draco (Willd.) Blume. JOURNAL OF ETHNOPHARMACOLOGY 2021; 268:113668. [PMID: 33301918 DOI: 10.1016/j.jep.2020.113668] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
ETHNO-PHARMACOLOGICAL RELEVANCE Daemonorops draco (D. draco) commonly known as "Dragon's blood" is one of the most used plants by Momok, Anak Dalam and Talang Mamak tribes from Indonesia as a remedy for wound healing. AIM OF THE STUDY This study aimed to identify the extract, fractions and compounds responsible for the anti-inflammatory and pro-proliferative activities of the D. draco resin. Additionally, the antimicrobial activity against two bacteria and one yeast species was analysed. MATERIALS AND METHODS Bio-guided isolation of compounds with anti-inflammatory, pro-proliferative and antimicrobial activities from the D. draco resin was carried out by measuring: the inhibition of NF-κB and activation of Nrf2 in THP-1, HaCaT, NIH-3T3 cells; cell proliferation in NIH-3T3 and HaCaT cells; and the antimicrobial effect on E. coli, S. aureus and C. albicans. RESULTS Guided isolation by bioassay gave rise to the isolation and characterisation by nuclear magnetic resonance and mass spectrometry of three compounds: 1 (Bexarotene), 2 (Taspine) and 3 (2-hydroxy-1-naphthaldehyde isonicotinoyl hydrazone). All compounds showed NF-κB inhibitory activity with IC50 values of 0.10-0.13, 0.22-0.24 and 3.75-4.78 μM, respectively, while the positive control, Celastrol, had an IC50 of 7.96 μM. Likewise, all compounds showed an activating effect of Nrf2 with EC50 values of 5.34-5.43, 163.20-169.20 and 300.82-315.56 nM, respectively, while the positive control, CDDO-Me, had an EC50 of 0.11 nM. In addition, concerning the pro-proliferative activity, compound 1 (IC50 = 8.62-8.71 nM) showed a capacity of 100%, compound 2 (IC50 = 166-171 nM) showed a capacity of 75%, and compound 3 (IC50 = 469-486 nM) showed a capacity of 65%, while FSB 10% (positive control) had a pro-proliferative activity of 100% in the NIH3T3 cell lines (fibroblasts) and HaCaT (keratinocytes). Finally, all the compounds showed antimicrobial activity with MIC values of 0.12-0.16, 0.31-0.39 and 3.96-3.99 μM, respectively, in S. aureus, E. coli and C. albicans strains, while the positive control, Ofloxacin, had a MIC of 27.65 μM. CONCLUSION This study managed to isolate, for the first time, three compounds (Bexarotene, Taspine and 2-hydroxy-1-naphthaldehyde isonicotinoyl hydrazone) from the resin of D. draco, with anti-inflammatory, and pro-proliferative as well as antimicrobial activities.
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Affiliation(s)
- L Apaza Ticona
- Department of Organic Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain; Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Universidad Complutense de Madrid, Plza. Ramón y Cajal S/n, 28040, Madrid, Spain.
| | - Á Rumbero Sánchez
- Department of Organic Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - J Sánchez Sánchez-Corral
- Department of Organic Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - P Iglesias Moreno
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, Universidad Complutense de Madrid, Plza. Ramón y Cajal S/n, 28040, Madrid, Spain
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Texari L, Spann NJ, Troutman TD, Sakai M, Seidman JS, Heinz S. An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells. STAR Protoc 2021; 2:100358. [PMID: 33718886 PMCID: PMC7921621 DOI: 10.1016/j.xpro.2021.100358] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Integrative analysis of next-generation sequencing data can help understand disease mechanisms. Specifically, ChIP-seq can illuminate where transcription regulators bind to regulate transcription. A major obstacle to performing this assay on primary cells is the low numbers obtained from tissues. The extensively validated ChIP-seq protocol presented here uses small volumes and single-pot on-bead library preparation to generate diverse high-quality ChIP-seq data. This protocol allows for medium-to-high-throughput ChIP-seq of low-abundance cells and can also be applied to other mammalian cells. For complete details on the use and execution of this protocol, please refer to Brigidi et al. (2019), Carlin et al. (2018), Heinz et al. (2018), Nott et al. (2019), Sakai et al. (2019), and Seidman et al. (2020).
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Affiliation(s)
- Lorane Texari
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathanael J. Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ty D. Troutman
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason S. Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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Abstract
The circadian clock protein REVERBα is proposed to be a key regulator of liver metabolism. We now show that REVERBα action is critically dependent on metabolic state. Using transgenic mouse models, we show that the true role of REVERBα is to buffer against aberrant responses to metabolic perturbation, rather than confer rhythmic regulation to programs of lipid synthesis and storage, as has been thought previously. Thus, in the case of liver metabolism, the clock does not so much drive rhythmic processes, as provide protection against mistimed feeding cues. Understanding how the clock is coupled to metabolism is critical for understanding metabolic disease and the impacts of circadian disruptors such as shift work and 24-h lifestyles. The nuclear receptor REVERBα is a core component of the circadian clock and proposed to be a dominant regulator of hepatic lipid metabolism. Using antibody-independent ChIP-sequencing of REVERBα in mouse liver, we reveal a high-confidence cistrome and define direct target genes. REVERBα-binding sites are highly enriched for consensus RORE or RevDR2 motifs and overlap with corepressor complex binding. We find no evidence for transcription factor tethering and DNA-binding domain-independent action. Moreover, hepatocyte-specific deletion of Reverbα drives only modest physiological and transcriptional dysregulation, with derepressed target gene enrichment limited to circadian processes. Thus, contrary to previous reports, hepatic REVERBα does not repress lipogenesis under basal conditions. REVERBα control of a more extensive transcriptional program is only revealed under conditions of metabolic perturbation (including mistimed feeding, which is a feature of the global Reverbα−/− mouse). Repressive action of REVERBα in the liver therefore serves to buffer against metabolic challenge, rather than drive basal rhythmicity in metabolic activity.
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35
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A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation. Proc Natl Acad Sci U S A 2020; 117:14365-14375. [PMID: 32513690 DOI: 10.1073/pnas.2005924117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Proper resolution of inflammation is vital for repair and restoration of homeostasis after tissue damage, and its dysregulation underlies various noncommunicable diseases, such as cardiovascular and metabolic diseases. Macrophages play diverse roles throughout initial inflammation, its resolution, and tissue repair. Differential metabolic reprogramming is reportedly required for induction and support of the various macrophage activation states. Here we show that a long noncoding RNA (lncRNA), lncFAO, contributes to inflammation resolution and tissue repair in mice by promoting fatty acid oxidation (FAO) in macrophages. lncFAO is induced late after lipopolysaccharide (LPS) stimulation of cultured macrophages and in Ly6Chi monocyte-derived macrophages in damaged tissue during the resolution and reparative phases. We found that lncFAO directly interacts with the HADHB subunit of mitochondrial trifunctional protein and activates FAO. lncFAO deletion impairs resolution of inflammation related to endotoxic shock and delays resolution of inflammation and tissue repair in a skin wound. These results demonstrate that by tuning mitochondrial metabolism, lncFAO acts as a node of immunometabolic control in macrophages during the resolution and repair phases of inflammation.
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36
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Amir M, Campbell S, Kamenecka TM, Solt LA. Pharmacological modulation and genetic deletion of REV-ERBα and REV-ERBβ regulates dendritic cell development. Biochem Biophys Res Commun 2020; 527:1000-1007. [PMID: 32439175 DOI: 10.1016/j.bbrc.2020.05.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022]
Abstract
The nuclear receptors REV-ERBα and REV-ERBβ have been demonstrated to play key roles in the regulation of numerous physiological functions, such as metabolism and the circadian rhythm. Recent studies have established the REV-ERBs' roles in immunity, including macrophage and T cell responses. In contrast, their roles in dendritic cells have not been well defined. Dendritic cells are potent antigen presenting cells, connecting microbial sensing and innate immunity to adaptive immune responses. We demonstrate that both REV-ERBα and REV-ERBβ expression is upregulated during the course of bone marrow derived dendritic cell (BMDC) differentiation. BMDCs from REV-ERBα and REV-ERBβ deficient mice showed enhanced expression of maturation markers like CD86, MHCII, and proinflammatory cytokines. Conversely, treatment of BMDCs with a REV-ERB-specific agonist, SR9009, inhibited the expression of maturation markers and proinflammatory cytokines. Our study suggests the REV-ERBs act as negative regulators of dendritic cell development and activation. These results indicate that pharmacological modulation of REV-ERB activity could be an attractive strategy to modulate DC activation status and for DC-based therapies.
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Affiliation(s)
- Mohammed Amir
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Sean Campbell
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.
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Seidman JS, Troutman TD, Sakai M, Gola A, Spann NJ, Bennett H, Bruni CM, Ouyang Z, Li RZ, Sun X, Vu BT, Pasillas MP, Ego KM, Gosselin D, Link VM, Chong LW, Evans RM, Thompson BM, McDonald JG, Hosseini M, Witztum JL, Germain RN, Glass CK. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity 2020; 52:1057-1074.e7. [PMID: 32362324 DOI: 10.1016/j.immuni.2020.04.001] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023]
Abstract
Tissue-resident and recruited macrophages contribute to both host defense and pathology. Multiple macrophage phenotypes are represented in diseased tissues, but we lack deep understanding of mechanisms controlling diversification. Here, we investigate origins and epigenetic trajectories of hepatic macrophages during diet-induced non-alcoholic steatohepatitis (NASH). The NASH diet induced significant changes in Kupffer cell enhancers and gene expression, resulting in partial loss of Kupffer cell identity, induction of Trem2 and Cd9 expression, and cell death. Kupffer cell loss was compensated by gain of adjacent monocyte-derived macrophages that exhibited convergent epigenomes, transcriptomes, and functions. NASH-induced changes in Kupffer cell enhancers were driven by AP-1 and EGR that reprogrammed LXR functions required for Kupffer cell identity and survival to instead drive a scar-associated macrophage phenotype. These findings reveal mechanisms by which disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct gene expression programs and corresponding functions.
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Affiliation(s)
- Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Anita Gola
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 201892, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cassi M Bruni
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaoli Sun
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - BaoChau T Vu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kaori M Ego
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David Gosselin
- Department of Molecular Medicine, Université Laval, Quebec City, QC, Canada
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Ling-Wa Chong
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bonne M Thompson
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mojgan Hosseini
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Joseph L Witztum
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 201892, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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38
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Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
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39
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Kuznetsova T, Prange KHM, Glass CK, de Winther MPJ. Transcriptional and epigenetic regulation of macrophages in atherosclerosis. Nat Rev Cardiol 2020; 17:216-228. [PMID: 31578516 PMCID: PMC7770754 DOI: 10.1038/s41569-019-0265-3] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2019] [Indexed: 12/11/2022]
Abstract
Monocytes and macrophages provide defence against pathogens and danger signals. These cells respond to stimulation in a fast and stimulus-specific manner by utilizing complex cascaded activation by lineage-determining and signal-dependent transcription factors. The complexity of the functional response is determined by interactions between triggered transcription factors and depends on the microenvironment and interdependent signalling cascades. Dysregulation of macrophage phenotypes is a major driver of various diseases such as atherosclerosis, rheumatoid arthritis and type 2 diabetes mellitus. Furthermore, exposure of monocytes, which are macrophage precursor cells, to certain stimuli can lead to a hypo-inflammatory tolerized phenotype or a hyper-inflammatory trained phenotype in a macrophage. In atherosclerosis, macrophages and monocytes are exposed to inflammatory cytokines, oxidized lipids, cholesterol crystals and other factors. All these stimuli induce not only a specific transcriptional response but also interact extensively, leading to transcriptional and epigenetic heterogeneity of macrophages in atherosclerotic plaques. Targeting the epigenetic landscape of plaque macrophages can be a powerful therapeutic tool to modulate pro-atherogenic phenotypes and reduce the rate of plaque formation. In this Review, we discuss the emerging role of transcription factors and epigenetic remodelling in macrophages in the context of atherosclerosis and inflammation, and provide a comprehensive overview of epigenetic enzymes and transcription factors that are involved in macrophage activation.
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Affiliation(s)
- Tatyana Kuznetsova
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Koen H M Prange
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Menno P J de Winther
- Experimental Vascular Biology, Department of Medical Biochemistry, Amsterdam University Medical Centers - location AMC, University of Amsterdam, Amsterdam, Netherlands.
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University, Munich, Germany.
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40
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Huang SP, Guan X, Kai GY, Xu YZ, Xu Y, Wang HJ, Pang T, Zhang LY, Liu Y. Broussonin E suppresses LPS-induced inflammatory response in macrophages via inhibiting MAPK pathway and enhancing JAK2-STAT3 pathway. Chin J Nat Med 2020; 17:372-380. [PMID: 31171272 DOI: 10.1016/s1875-5364(19)30043-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Indexed: 02/07/2023]
Abstract
Macrophages play an important role in inflammation, and excessive and chronic activation of macrophages leads to systemic inflammatory diseases, such as atherosclerosis and rheumatoid arthritis. In this paper, we explored the anti-inflammatory effect of broussonin E, a novel phenolic compound isolated from the barks ofBroussonetia kanzinoki, and its underlying molecular mechanisms. We discovered that Broussonin E could suppress the LPS-induced pro-inflammatory production in RAW264.7 cells, involving TNF-α, IL-1β, IL-6, COX-2 and iNOS. And broussonin E enhanced the expressions of anti-inflammatory mediators such as IL-10, CD206 and arginase-1 (Arg-1) in LPS-stimulated RAW264.7 cells. Further, we demonstrated that broussonin E inhibited the LPS-stimulated phosphorylation of ERK and p38 MAPK. Moreover, we found that broussonin E could activate janus kinase (JAK) 2, signal transducer and activator of transcription (STAT) 3. Downregulated pro-inflammatory cytokines and upregulated anti-inflammatory factors by broussonin E were abolished by using the inhibitor of JAK2-STAT3 pathway, WP1066. Taken together, our results showed that broussonin E could suppress inflammation by modulating macrophages activation statevia inhibiting the ERK and p38 MAPK and enhancing JAK2-STAT3 signaling pathway, and can be further developed as a promising drug for the treatment of inflammation-related diseases such as atherosclerosis.
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Affiliation(s)
- Shao-Peng Huang
- School of Basic Medicine, Center for Drug Screening and Pharmacodynamics Evaluation, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006,China
| | - Xin Guan
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, China; Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Guo-Yin Kai
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Ya-Zhou Xu
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yuan Xu
- School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hao-Jie Wang
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Tao Pang
- Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lu-Yong Zhang
- School of Basic Medicine, Center for Drug Screening and Pharmacodynamics Evaluation, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006,China; Jiangsu Key Laboratory of Drug Screening, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Ying Liu
- School of Basic Medicine, Center for Drug Screening and Pharmacodynamics Evaluation, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006,China.
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41
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Amir M, Chaudhari S, Wang R, Campbell S, Mosure SA, Chopp LB, Lu Q, Shang J, Pelletier OB, He Y, Doebelin C, Cameron MD, Kojetin DJ, Kamenecka TM, Solt LA. REV-ERBα Regulates T H17 Cell Development and Autoimmunity. Cell Rep 2019; 25:3733-3749.e8. [PMID: 30590045 PMCID: PMC6400287 DOI: 10.1016/j.celrep.2018.11.101] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 11/19/2022] Open
Abstract
RORγt is well recognized as the lineage-defining transcription factor for T helper 17 (TH17) cell development. However, the cell-intrinsic mechanisms that negatively regulate TH17 cell development and autoimmunity remain poorly understood. Here, we demonstrate that the transcriptional repressor REV-ERBα is exclusively expressed in TH17 cells, competes with RORγt for their shared DNA consensus sequence, and negatively regulates TH17 cell development via repression of genes traditionally characterized as RORγt dependent, including Il17a. Deletion of REV-ERBα enhanced TH17-mediated pro-inflammatory cytokine expression, exacerbating experimental autoimmune encephalomyelitis (EAE) and colitis. Treatment with REV-ERB-specific synthetic ligands, which have similar phenotypic properties as RORγ modulators, suppressed TH17 cell development, was effective in colitis intervention studies, and significantly decreased the onset, severity, and relapse rate in several models of EAE without affecting thymic cellularity. Our results establish that REV-ERBα negatively regulates pro-inflammatory TH17 responses in vivo and identifies the REV-ERBs as potential targets for the treatment of TH17-mediated autoimmune diseases.
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Affiliation(s)
- Mohammed Amir
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Sweena Chaudhari
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Ran Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Sean Campbell
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Sarah A Mosure
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA; Scripps Research, Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, California 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Laura B Chopp
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Qun Lu
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Oliver B Pelletier
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Christelle Doebelin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Michael D Cameron
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA.
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42
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Hiebert P, Werner S. Regulation of Wound Healing by the NRF2 Transcription Factor-More Than Cytoprotection. Int J Mol Sci 2019; 20:ijms20163856. [PMID: 31398789 PMCID: PMC6720615 DOI: 10.3390/ijms20163856] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/31/2022] Open
Abstract
The nuclear factor-erythroid 2-related factor 2 (NRF2) transcription factor plays a central role in mediating the cellular stress response. Due to their antioxidant properties, compounds activating NRF2 have received much attention as potential medications for disease prevention, or even for therapy. Accumulating evidence suggests that activation of the NRF2 pathway also has a major impact on wound healing and may be beneficial in the treatment of chronic wounds, which remain a considerable health and economic burden. While NRF2 activation indeed shows promise, important considerations need to be made in light of corresponding evidence that also points towards pro-tumorigenic effects of NRF2. In this review, we discuss the evidence to date, highlighting recent advances using gain- and loss-of-function animal models and how these data fit with observations in humans.
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Affiliation(s)
- Paul Hiebert
- Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zürich, 8093 Zurich, Switzerland.
| | - Sabine Werner
- Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zürich, 8093 Zurich, Switzerland.
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43
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Sulli G, Lam MTY, Panda S. Interplay between Circadian Clock and Cancer: New Frontiers for Cancer Treatment. Trends Cancer 2019; 5:475-494. [PMID: 31421905 DOI: 10.1016/j.trecan.2019.07.002] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/07/2019] [Accepted: 07/08/2019] [Indexed: 12/23/2022]
Abstract
Circadian clocks constitute the evolutionary molecular machinery that dictates the temporal regulation of physiology to maintain homeostasis. Disruption of the circadian rhythm plays a key role in tumorigenesis and facilitates the establishment of cancer hallmarks. Conversely, oncogenic processes directly weaken circadian rhythms. Pharmacological modulation of core clock genes is a new approach in cancer therapy. The integration of circadian biology into cancer research offers new options for making cancer treatment more effective, encompassing the prevention, diagnosis, and treatment of this devastating disease. This review highlights the role of the circadian clock in tumorigenesis and cancer hallmarks, and discusses how pharmacological modulation of circadian clock genes can lead to new therapeutic options.
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Affiliation(s)
- Gabriele Sulli
- The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Medicine, Division of Regenerative Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Scintillon Institute, San Diego, CA 92121, USA.
| | - Michael Tun Yin Lam
- The Salk Institute for Biological Studies, La Jolla, CA, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, 9300 Campus Point Drive, La Jolla, CA 92037, USA
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Burgermeister E, Battaglin F, Eladly F, Wu W, Herweck F, Schulte N, Betge J, Härtel N, Kather JN, Weis CA, Gaiser T, Marx A, Weiss C, Hofheinz R, Miller IS, Loupakis F, Lenz HJ, Byrne AT, Ebert MP. Aryl hydrocarbon receptor nuclear translocator-like (ARNTL/BMAL1) is associated with bevacizumab resistance in colorectal cancer via regulation of vascular endothelial growth factor A. EBioMedicine 2019; 45:139-154. [PMID: 31300350 PMCID: PMC6642438 DOI: 10.1016/j.ebiom.2019.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The identification of new biomarkers and the development of novel, targetable contexts of vulnerability are of urgent clinical need in drug-resistant metastatic colorectal cancer (mCRC). Aryl-Hydrocarbon-Receptor-Nuclear-Translocator-Like (ARNTL/BMAL1) is a circadian clock-regulated transcription factor promoting expression of genes involved in angiogenesis and tumour progression. We hypothesised that BMAL1 increases expression of the vascular endothelial growth factor A VEGFA gene and, thereby, confers resistance to anti-angiogenic therapy with bevacizumab (Beva), a clinically used antibody for neutralization of VEGFA. METHODS PCR and immunohistochemistry were employed to assess BMAL1 expression in mice (C57BL/6 J Apcmin/+; BALB/c nu/nu xenografts) and CRC patients under combination chemotherapy with Beva. BMAL1 single nucleotide gene polymorphisms (SNPs) were analysed by DNA-microarray in clinical samples. BMAL1 functions were studied in human CRC cell lines using colorimetric growth, DNA-binding and reporter assays. FINDINGS In murine CRCs, high BMAL1 expression correlated with poor preclinical response to Beva treatment. In CRC patients' tumours (n = 74), high BMAL1 expression was associated with clinical non-response to combination chemotherapy with Beva (*p = .0061) and reduced progression-free survival (PFS) [*p = .0223, Hazard Ratio (HR) = 1.69]. BMAL1 SNPs also correlated with shorter PFS (rs7396943, rs7938307, rs2279287) and overall survival (OS) [rs11022780, *p = .014, HR = 1.61]. Mechanistically, Nuclear-Receptor-Subfamily-1-Group-D-Member-1 (NR1D1/REVERBA) bound a - 672 bp Retinoic-Acid-Receptor-Related-Orphan-Receptor-Alpha-responsive-element (RORE) adjacent to a BMAL1 DNA-binding motif (E-box) in the VEGFA gene promoter, resulting in increased VEGFA synthesis and proliferation of human CRC cell lines. INTERPRETATION BMAL1 was associated with Beva resistance in CRC. Inhibition of REVERBA-BMAL1 signalling may prevent resistance to anti-angiogenic therapy. FUND: This work was in part supported by the European Commission Seventh Framework Programme (Contract No. 278981 [ANGIOPREDICT]).
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Affiliation(s)
- Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States; Unit of Medical Oncology 1, Clinical and Experimental Oncology Department, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Fagr Eladly
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Wen Wu
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Frank Herweck
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Nadine Schulte
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Johannes Betge
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Nicolai Härtel
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jakob N Kather
- Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Cleo-Aron Weis
- Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Timo Gaiser
- Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Alexander Marx
- Institute of Pathology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christel Weiss
- Department of Medical Statistics, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ralf Hofheinz
- Department of Medicine III, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ian S Miller
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Fotios Loupakis
- Unit of Medical Oncology 1, Clinical and Experimental Oncology Department, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States
| | - Annette T Byrne
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland; UCD School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Matthias P Ebert
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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45
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SR9009 has REV-ERB-independent effects on cell proliferation and metabolism. Proc Natl Acad Sci U S A 2019; 116:12147-12152. [PMID: 31127047 DOI: 10.1073/pnas.1904226116] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The nuclear receptors REV-ERBα and -β link circadian rhythms and metabolism. Like other nuclear receptors, REV-ERB activity can be regulated by ligands, including naturally occurring heme. A putative ligand, SR9009, has been reported to elicit a range of beneficial effects in healthy as well as diseased animal models and cell systems. However, the direct involvement of REV-ERBs in these effects of SR9009 has not been thoroughly assessed, as experiments were not performed in the complete absence of both proteins. Here, we report the generation of a mouse model for conditional genetic deletion of REV-ERBα and -β. We show that SR9009 can decrease cell viability, rewire cellular metabolism, and alter gene transcription in hepatocytes and embryonic stem cells lacking both REV-ERBα and -β. Thus, the effects of SR9009 cannot be used solely as surrogate for REV-ERB activity.
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Chen B, Huang S, Su Y, Wu YJ, Hanna A, Brickshawana A, Graff J, Frangogiannis NG. Macrophage Smad3 Protects the Infarcted Heart, Stimulating Phagocytosis and Regulating Inflammation. Circ Res 2019; 125:55-70. [PMID: 31092129 DOI: 10.1161/circresaha.119.315069] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RATIONALE TGF (transforming growth factor)-β is critically involved in myocardial injury, repair, and fibrosis, activating both Smad (small mothers against decapentaplegic)-dependent and non-Smad pathways. The in vivo role of TGF-β signaling in regulation of macrophage function is poorly understood. We hypothesized that in the infarcted myocardium, activation of TGF-β/Smad signaling in macrophages may regulate repair and remodeling. OBJECTIVE To investigate the role of macrophage-specific TGF-β Smad3 signaling in a mouse model of myocardial infarction and to dissect the mechanisms mediating Smad-dependent modulation of macrophage function. METHODS AND RESULTS TGF-βs markedly activated Smad3 in macrophages, without affecting Smad-independent pathways. Phagocytosis rapidly and directly activated macrophage Smad3, in the absence of active TGF-β release. MyS3KO (myeloid cell-specific Smad3 knockout) mice had no baseline defects but exhibited increased late mortality and accentuated dilative postmyocardial infarction remodeling. Adverse outcome in infarcted MyS3KO mice was associated with perturbations in phagocytic activity, defective transition of macrophages to an anti-inflammatory phenotype, scar expansion, and accentuated apoptosis of border zone cardiomyocytes. In vitro, Smad3 null macrophages exhibited reduced expression of genes associated with eat-me signals, such as Mfge8 (milk fat globule-epidermal growth factor factor 8), and reduced capacity to produce the anti-inflammatory mediators IL (interleukin)-10 and TGF-β1, and the angiogenic growth factor VEGF (vascular endothelial growth factor). Mfge8 partly rescued the phagocytic defect of Smad3 null macrophages, without affecting inflammatory activity. Impaired anti-inflammatory actions of Smad3 null macrophages were associated with marked attenuation of phagocytosis-induced PPAR (peroxisome proliferator-activated receptor) expression. MyS3KO mice had no significant alterations in microvascular density and interstitial fibrosis in remodeling myocardial segments. CONCLUSIONS We demonstrate that Smad3 critically regulates function of infarct macrophages, by mediating acquisition of a phagocytic phenotype and by contributing to anti-inflammatory transition. Smad3-dependent actions in macrophages protect the infarcted heart from adverse remodeling.
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Affiliation(s)
- Bijun Chen
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Shuaibo Huang
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Ya Su
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Yi-Jin Wu
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Anis Hanna
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Adipong Brickshawana
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
| | - Jonathan Graff
- Department of Developmental Biology, University of Texas Southwestern, Dallas (J.G.)
| | - Nikolaos G Frangogiannis
- From the Wilf Family Cardiovascular Research Institute, Department of Medicine (Cardiology), Albert Einstein College of Medicine, Bronx, NY (B.C., S.H., Y.S., Y-J.W., A.H., A.B., N.G.F.)
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Abstract
Circadian dysfunction is a common attribute of many neurodegenerative diseases, most of which are associated with neuroinflammation. Circadian rhythm dysfunction has been associated with inflammation in the periphery, but the role of the core clock in neuroinflammation remains poorly understood. Here we demonstrate that Rev-erbα, a nuclear receptor and circadian clock component, is a mediator of microglial activation and neuroinflammation. We observed time-of-day oscillation in microglial immunoreactivity in the hippocampus, which was disrupted in Rev-erbα-/- mice. Rev-erbα deletion caused spontaneous microglial activation in the hippocampus and increased expression of proinflammatory transcripts, as well as secondary astrogliosis. Transcriptomic analysis of hippocampus from Rev-erbα-/- mice revealed a predominant inflammatory phenotype and suggested dysregulated NF-κB signaling. Primary Rev-erbα-/- microglia exhibited proinflammatory phenotypes and increased basal NF-κB activation. Chromatin immunoprecipitation revealed that Rev-erbα physically interacts with the promoter regions of several NF-κB-related genes in primary microglia. Loss of Rev-erbα in primary astrocytes had no effect on basal activation but did potentiate the inflammatory response to lipopolysaccharide (LPS). In vivo, Rev-erbα-/- mice exhibited enhanced hippocampal neuroinflammatory responses to peripheral LPS injection, while pharmacologic activation of Rev-erbs with the small molecule agonist SR9009 suppressed LPS-induced hippocampal neuroinflammation. Rev-erbα deletion influenced neuronal health, as conditioned media from Rev-erbα-deficient primary glial cultures exacerbated oxidative damage in cultured neurons. Rev-erbα-/- mice also exhibited significantly altered cortical resting-state functional connectivity, similar to that observed in neurodegenerative models. Our results reveal Rev-erbα as a pharmacologically accessible link between the circadian clock and neuroinflammation.
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Martins R, Carlos AR, Braza F, Thompson JA, Bastos-Amador P, Ramos S, Soares MP. Disease Tolerance as an Inherent Component of Immunity. Annu Rev Immunol 2019; 37:405-437. [PMID: 30673535 DOI: 10.1146/annurev-immunol-042718-041739] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pathogenic organisms exert a negative impact on host health, revealed by the clinical signs of infectious diseases. Immunity limits the severity of infectious diseases through resistance mechanisms that sense and target pathogens for containment, killing, or expulsion. These resistance mechanisms are viewed as the prevailing function of immunity. Under pathophysiologic conditions, however, immunity arises in response to infections that carry health and fitness costs to the host. Therefore, additional defense mechanisms are required to limit these costs, before immunity becomes operational as well as thereafter to avoid immunopathology. These are tissue damage control mechanisms that adjust the metabolic output of host tissues to different forms of stress and damage associated with infection. Disease tolerance is the term used to define this defense strategy, which does not exert a direct impact on pathogens but is essential to limit the health and fitness costs of infection. Under this argument, we propose that disease tolerance is an inherent component of immunity.
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Affiliation(s)
- Rui Martins
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | | | - Faouzi Braza
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | | | | | - Susana Ramos
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
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Mahadik K, Yadav P, Bhatt B, Shah RA, Balaji KN. Deregulated AUF1 Assists BMP-EZH2-Mediated Delayed Wound Healing during Candida albicans Infection. THE JOURNAL OF IMMUNOLOGY 2018; 201:3617-3629. [PMID: 30429285 DOI: 10.4049/jimmunol.1800688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/16/2018] [Indexed: 11/19/2022]
Abstract
Tissue repair is a complex process that necessitates an interplay of cellular processes, now known to be dictated by epigenetics. Intriguingly, macrophages are testimony to a large repertoire of evolving functions in this process. We identified a role for BMP signaling in regulating macrophage responses to Candida albicans infection during wound repair in a murine model. In this study, the RNA binding protein, AU-rich element-binding factor 1, was posttranslationally destabilized to bring about ubiquitin ligase, NEDD4-directed activation of BMP signaling. Concomitantly, PI3K/PKCδ mobilized the rapid phosphorylation of BMP-responsive Smad1/5/8. Activated BMP pathway orchestrated the elevated recruitment of EZH2 at promoters of genes assisting timely wound closure. In vivo, the repressive H3K27 trimethylation was observed to persist, accompanied by a robust upregulation of BMP pathway upon infection with C. albicans, culminating in delayed wound healing. Altogether, we uncovered the signaling networks coordinated by fungal colonies that are now increasingly associated with the infected wound microbiome, resulting in altered wound fate.
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Affiliation(s)
- Kasturi Mahadik
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Preeti Yadav
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Bharat Bhatt
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Hwang J, Jiang A, Fikrig E. Rev-erb Agonist Inhibits Chikungunya and O'nyong'nyong Virus Replication. Open Forum Infect Dis 2018; 5:ofy315. [PMID: 30568983 PMCID: PMC6293476 DOI: 10.1093/ofid/ofy315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/16/2018] [Indexed: 01/29/2023] Open
Abstract
Chikungunya virus (CHIKV), an alphavirus spread by Aedes spp. mosquitos, causes severe inflammation and joint pain, progressing to a chronic arthralgic state in a subset of patients. Due to recent global epidemics of CHIKV and the potential for related viruses to cause outbreaks, multiple approaches to combat these pathogens are of interest. We report that SR9009, a synthetic agonist of nuclear receptors Rev-erb α/β, inhibits replication of multiple alphaviruses (CHIKV and O'nyong'nyong virus) mainly by suppressing structural protein synthesis, although viral RNA accumulation is relatively unimpeded. Furthermore, SR9009 reduces the inflammatory response in cultured murine macrophages exposed to alphavirus-infected cells.
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Affiliation(s)
- Jesse Hwang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Alfred Jiang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut.,Howard Hughes Medical Institute, Chevy Chase, Maryland
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