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Tepale-Segura A, Gajón JA, Muñoz-Cruz S, Castro-Escamilla O, Bonifaz LC. The cholera toxin B subunit induces trained immunity in dendritic cells and promotes CD8 T cell antitumor immunity. Front Immunol 2024; 15:1362289. [PMID: 38812523 PMCID: PMC11133619 DOI: 10.3389/fimmu.2024.1362289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Innate immune training is a metabolic, functional, and epigenetic long-term reprogramming of innate cells triggered by different stimuli. This imprinting also reaches hematopoietic precursors in the bone marrow to sustain a memory-like phenotype. Dendritic cells (DCs) can exhibit memory-like responses, enhanced upon subsequent exposure to a pathogen; however, whether this imprinting is lineage and stimulus-restricted is still being determined. Nevertheless, the functional consequences of DCs training on the adaptive and protective immune response against non-infectious diseases remain unresolved. Methods We evaluated the effect of the nontoxic cholera B subunit (CTB), LPS and LTA in the induction of trained immunity in murine DCs revealed by TNFa and LDH expression, through confocal microscopy. Additionally, we obtained bone marrow DCs (BMDCs) from mice treated with CTB, LPS, and LTA and evaluated training features in DCs and their antigen-presenting cell capability using multiparametric cytometry. Finally, we design an experimental melanoma mouse model to demonstrate protection induced by CTB-trained DCs in vivo. Results CTB-trained DCs exhibit increased expression of TNFa, and metabolic reprogramming indicated by LDH expression. Moreover, CTB training has an imprint on DC precursors, increasing the number and antigen-presenting function in BMDCs. We found that training by CTB stimulates the recruitment of DC precursors and DCs infiltration at the skin and lymph nodes. Interestingly, training-induced by CTB promotes a highly co-stimulatory phenotype in tumor-infiltrating DCs (CD86+) and a heightened functionality of exhausted CD8 T cells (Ki67+, GZMB+), which were associated with a protective response against melanoma challenge in vivo. Conclusion Our work indicates that CTB can induce innate immune training on DCs, which turns into an efficient adaptive immune response in the melanoma model and might be a potential immunotherapeutic approach for tumor growth control.
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Affiliation(s)
- Araceli Tepale-Segura
- Unidad de Investigación Médica en Inmunoquímica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Inmunología, Mexico City, Mexico
| | - Julián A. Gajón
- Unidad de Investigación Médica en Inmunoquímica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Posgrado en Ciencias Bioquímicas, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Samira Muñoz-Cruz
- Unidad de Investigación Médica en Inmunoquímica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Octavio Castro-Escamilla
- División de Investigación Clínica, Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Laura C. Bonifaz
- Unidad de Investigación Médica en Inmunoquímica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Coordinación de Investigación en Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Kloc M, Halasa M, Kubiak JZ, Ghobrial RM. Invertebrate Immunity, Natural Transplantation Immunity, Somatic and Germ Cell Parasitism, and Transposon Defense. Int J Mol Sci 2024; 25:1072. [PMID: 38256145 PMCID: PMC10815962 DOI: 10.3390/ijms25021072] [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: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
While the vertebrate immune system consists of innate and adaptive branches, invertebrates only have innate immunity. This feature makes them an ideal model system for studying the cellular and molecular mechanisms of innate immunity sensu stricto without reciprocal interferences from adaptive immunity. Although invertebrate immunity is evolutionarily older and a precursor of vertebrate immunity, it is far from simple. Despite lacking lymphocytes and functional immunoglobulin, the invertebrate immune system has many sophisticated mechanisms and features, such as long-term immune memory, which, for decades, have been exclusively attributed to adaptive immunity. In this review, we describe the cellular and molecular aspects of invertebrate immunity, including the epigenetic foundation of innate memory, the transgenerational inheritance of immunity, genetic immunity against invading transposons, the mechanisms of self-recognition, natural transplantation, and germ/somatic cell parasitism.
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Affiliation(s)
- Malgorzata Kloc
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Marta Halasa
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jacek Z. Kubiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine-National Research Institute (WIM-PIB), Szaserow 128, 04-141 Warsaw, Poland;
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
| | - Rafik M. Ghobrial
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
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Zhu J, Liu J, Yan C, Wang D, Pan W. Trained immunity: a cutting edge approach for designing novel vaccines against parasitic diseases? Front Immunol 2023; 14:1252554. [PMID: 37868995 PMCID: PMC10587610 DOI: 10.3389/fimmu.2023.1252554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
The preventive situation of parasitosis, a global public health burden especially for developing countries, is not looking that good. Similar to other infections, vaccines would be the best choice for preventing and controlling parasitic infection. However, ideal antigenic molecules for vaccine development have not been identified so far, resulting from the complicated life history and enormous genomes of the parasites. Furthermore, the suppression or down-regulation of anti-infectious immunity mediated by the parasites or their derived molecules can compromise the effect of parasitic vaccines. Comparing the early immune profiles of several parasites in the permissive and non-permissive hosts, a robust innate immune response is proposed to be a critical event to eliminate the parasites. Therefore, enhancing innate immunity may be essential for designing novel and effective parasitic vaccines. The newly emerging trained immunity (also termed innate immune memory) has been increasingly recognized to provide a novel perspective for vaccine development targeting innate immunity. This article reviews the current status of parasitic vaccines and anti-infectious immunity, as well as the conception, characteristics, and mechanisms of trained immunity and its research progress in Parasitology, highlighting the possible consideration of trained immunity in designing novel vaccines against parasitic diseases.
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Affiliation(s)
- Jinhang Zhu
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiaxi Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chao Yan
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Dahui Wang
- Liangshan College (Li Shui) China, Lishui University, Lishui, Zhejiang, China
| | - Wei Pan
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
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Yang C, Wu H, Chen J, Liao Y, Mkuye R, Deng Y, Du X. Integrated transcriptomic and metabolomic analysis reveals the response of pearl oyster (Pinctada fucata martensii) to long-term hypoxia. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106133. [PMID: 37586225 DOI: 10.1016/j.marenvres.2023.106133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
The frequency at which organisms are exposed to hypoxic conditions in aquatic environments is increasing due to coastal eutrophication and global warming. To reveal the effects of long-term hypoxic stress on metabolic changes of pearl oyster, commonly known as Pinctada (Pinctada fucata martensii), the present study performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites following 25 days hypoxia challenge. Transcriptome analysis detected 1108 differentially expressed genes (DEGs) between the control group and the hypoxia group. The gene ontology (GO) analysis of DEGs revealed that they are significantly enriched in functions such as "microtubule-based process", "histone (H3-K4, H3-K27, and H4-K20) trimethylation", "histone H4 acetylation", "kinesin complex", and "ATPase activity", and KEGG pathway functions, such as "DNA replication", "Apoptosis", and "MAPK signaling pathways". Metabolome analysis identified 68 significantly different metabolites from all identified metabolites, and associated with 25 metabolic pathways between the control and hypoxia groups. These pathways included aminoacyl-tRNA biosynthesis, arginine and proline metabolism, and phenylalanine metabolism. Our integrated analysis suggested that pearl oysters were subject to oxidative stress, apoptosis, immune inhibition, and neuronal excitability reduction under long-term hypoxic conditions. We also found a remarkable depression in a variety of biological functions under long-term hypoxia, including metabolic rates, biomineralization activities, and the repression of reorganization of the cytoskeleton and cell metabolism. These findings provide a basis for elucidating the mechanisms used by marine bivalves to cope with long-term hypoxic stress.
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Affiliation(s)
- Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hailing Wu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiayi Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yongshan Liao
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China
| | - Robert Mkuye
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China.
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
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Xia J, Liu Y, Ma Y, Yang F, Ruan Y, Xu JF, Pi J. Advances of Long Non-Coding RNAs as Potential Biomarkers for Tuberculosis: New Hope for Diagnosis? Pharmaceutics 2023; 15:2096. [PMID: 37631310 PMCID: PMC10458399 DOI: 10.3390/pharmaceutics15082096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Tuberculosis (TB), one of the top ten causes of death globally induced by the infection of Mycobacterium tuberculosis (Mtb), remains a grave public health issue worldwide. With almost one-third of the world's population getting infected by Mtb, between 5% and 10% of these infected individuals are predicted to develop active TB disease, which would not only result in severe tissue damage and necrosis, but also pose serious threats to human life. However, the exact molecular mechanisms underlying the pathogenesis and immunology of TB remain unclear, which significantly restricts the effective control of TB epidemics. Despite significant advances in current detection technologies and treatments for TB, there are still no appropriate solutions that are suitable for simultaneous, early, rapid, and accurate screening of TB. Various cellular events can perturb the development and progression of TB, which are always associated with several specific molecular signaling events controlled by dysregulated gene expression patterns. Long non-coding RNAs (lncRNAs), a kind of non-coding RNA (ncRNA) with a transcript of more than 200 nucleotides in length in eukaryotic cells, have been found to regulate the expression of protein-coding genes that are involved in some critical signaling events, such as inflammatory, pathological, and immunological responses. Increasing evidence has claimed that lncRNAs might directly influence the susceptibility to TB, as well as the development and progression of TB. Therefore, lncRNAs have been widely expected to serve as promising molecular biomarkers and therapeutic targets for TB. In this review, we summarized the functions of lncRNAs and their regulatory roles in the development and progression of TB. More importantly, we widely discussed the potential of lncRNAs to act as TB biomarkers, which would offer new possibilities in novel diagnostic strategy exploration and benefit the control of the TB epidemic.
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Affiliation(s)
- Jiaojiao Xia
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China
| | - Yilin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Yuhe Ma
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Fen Yang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Yongdui Ruan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
| | - Jun-Fa Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
| | - Jiang Pi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China; (J.X.); (Y.L.); (Y.M.); (F.Y.); (Y.R.)
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
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Agidigbi TS, Kwon HK, Knight JR, Zhao D, Lee FY, Oh I. Transcriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection. Front Cell Infect Microbiol 2023; 13:1198115. [PMID: 37434783 PMCID: PMC10332306 DOI: 10.3389/fcimb.2023.1198115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Infection in diabetic foot ulcers (DFUs) is one of the major complications associated with patients with diabetes. Staphylococcus aureus is the most common offending pathogen in patients with infected DFU. Previous studies have suggested the application of species-specific antibodies against S. aureus for diagnosis and monitoring treatment response. Early and accurate identification of the main pathogen is critical for management of DFU infection. Understanding the host immune response against species-specific infection may facilitate diagnosis and may suggest potential intervention options to promote healing infected DFUs. We sought to investigate evolving host transcriptome associated with surgical treatment of S. aureus- infected DFU. Methods This study compared the transcriptome profile of 21 patients with S. aureus- infected DFU who underwent initial foot salvage therapy with irrigation and debridement followed by intravenous antibiotic therapy. Blood samples were collected at the recruitment (0 weeks) and 8 weeks after therapy to isolate peripheral blood mononuclear cells (PBMCs). We analyzed the PBMC expression of transcriptomes at two different time points (0 versus 8 weeks). Subjects were further divided into two groups at 8 weeks: healed (n = 17, 80.95%) versus non-healed (n = 4, 19.05%) based on the wound healing status. DESeq2 differential gene analysis was performed. Results and discussion An increased expression of IGHG1, IGHG2, IGHG3, IGLV3-21, and IGLV6-57 was noted during active infection at 0 weeks compared with that at 8 weeks. Lysine- and arginine-rich histones (HIST1H2AJ, HIST1H2AL, HIST1H2BM, HIST1H3B, and HIST1H3G) were upregulated at the initial phase of active infection at 0 weeks. CD177 and RRM2 were also upregulated at the initial phase of active infection (0 weeks) compared with that at 8 weeks of follow-up. Genes of heat shock protein members (HSPA1A, HSPE1, and HSP90B1) were high in not healed patients compared with that in healed patients 8 weeks after therapy. The outcome of our study suggests that the identification of genes evolution based on a transcriptomic profiling could be a useful tool for diagnosing infection and assessing severity and host immune response to therapies.
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Affiliation(s)
- Taiwo Samuel Agidigbi
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Hyuk-Kwon Kwon
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
- Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - James R. Knight
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Dejian Zhao
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Francis Y. Lee
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Irvin Oh
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
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Maher AK, Burnham KL, Jones EM, Tan MMH, Saputil RC, Baillon L, Selck C, Giang N, Argüello R, Pillay C, Thorley E, Short CE, Quinlan R, Barclay WS, Cooper N, Taylor GP, Davenport EE, Dominguez-Villar M. Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19. Nat Commun 2022; 13:7947. [PMID: 36572683 PMCID: PMC9791976 DOI: 10.1038/s41467-022-35638-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/14/2022] [Indexed: 12/27/2022] Open
Abstract
Although alterations in myeloid cells have been observed in COVID-19, the specific underlying mechanisms are not completely understood. Here, we examine the function of classical CD14+ monocytes in patients with mild and moderate COVID-19 during the acute phase of infection and in healthy individuals. Monocytes from COVID-19 patients display altered expression of cell surface receptors and a dysfunctional metabolic profile that distinguish them from healthy monocytes. Secondary pathogen sensing ex vivo leads to defects in pro-inflammatory cytokine and type-I IFN production in moderate COVID-19 cases, together with defects in glycolysis. COVID-19 monocytes switch their gene expression profile from canonical innate immune to pro-thrombotic signatures and are functionally pro-thrombotic, both at baseline and following ex vivo stimulation with SARS-CoV-2. Transcriptionally, COVID-19 monocytes are characterized by enrichment of pathways involved in hemostasis, immunothrombosis, platelet aggregation and other accessory pathways to platelet activation and clot formation. These results identify a potential mechanism by which monocyte dysfunction may contribute to COVID-19 pathology.
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Affiliation(s)
- Allison K Maher
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma M Jones
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Michelle M H Tan
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Rocel C Saputil
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Claudia Selck
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Nicolas Giang
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Rafael Argüello
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Clio Pillay
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Emma Thorley
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Charlotte-Eve Short
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Rachael Quinlan
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Nichola Cooper
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Emma E Davenport
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Li X, Ye Y, Peng K, Zeng Z, Chen L, Zeng Y. Histones: The critical players in innate immunity. Front Immunol 2022; 13:1030610. [PMID: 36479112 PMCID: PMC9720293 DOI: 10.3389/fimmu.2022.1030610] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
The highly conserved histones in different species seem to represent a very ancient and universal innate host defense system against microorganisms in the biological world. Histones are the essential part of nuclear matter and act as a control switch for DNA transcription. However, histones are also found in the cytoplasm, cell membranes, and extracellular fluid, where they function as host defenses and promote inflammatory responses. In some cases, extracellular histones can act as damage-associated molecular patterns (DAMPs) and bind to pattern recognition receptors (PRRs), thereby triggering innate immune responses and causing initial organ damage. Histones and their fragments serve as antimicrobial peptides (AMPs) to directly eliminate bacteria, viruses, fungi, and parasites in vitro and in vivo. Histones are also involved in phagocytes-related innate immune response as components of neutrophil extracellular traps (NETs), neutrophil activators, and plasminogen receptors. In addition, as a considerable part of epigenetic regulation, histone modifications play a vital role in regulating the innate immune response and expression of corresponding defense genes. Here, we review the regulatory role of histones in innate immune response, which provides a new strategy for the development of antibiotics and the use of histones as therapeutic targets for inflammatory diseases, sepsis, autoimmune diseases, and COVID-19.
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Affiliation(s)
- Xia Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Youyuan Ye
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Kailan Peng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhuo Zeng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Li Chen
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yanhua Zeng
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China,Department of Dermatology and Venereology, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China,*Correspondence: Yanhua Zeng, ;
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Georgakilas GK, Galanopoulos AP, Tsinaris Z, Kyritsi M, Mouchtouri VA, Speletas M, Hadjichristodoulou C. Machine-Learning-Assisted Analysis of TCR Profiling Data Unveils Cross-Reactivity between SARS-CoV-2 and a Wide Spectrum of Pathogens and Other Diseases. BIOLOGY 2022; 11:1531. [PMID: 36290433 PMCID: PMC9598299 DOI: 10.3390/biology11101531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
Abstract
During the last two years, the emergence of SARS-CoV-2 has led to millions of deaths worldwide, with a devastating socio-economic impact on a global scale. The scientific community's focus has recently shifted towards the association of the T cell immunological repertoire with COVID-19 progression and severity, by utilising T cell receptor sequencing (TCR-Seq) assays. The Multiplexed Identification of T cell Receptor Antigen (MIRA) dataset, which is a subset of the immunoACCESS study, provides thousands of TCRs that can specifically recognise SARS-CoV-2 epitopes. Our study proposes a novel Machine Learning (ML)-assisted approach for analysing TCR-Seq data from the antigens' point of view, with the ability to unveil key antigens that can accurately distinguish between MIRA COVID-19-convalescent and healthy individuals based on differences in the triggered immune response. Some SARS-CoV-2 antigens were found to exhibit equal levels of recognition by MIRA TCRs in both convalescent and healthy cohorts, leading to the assumption of putative cross-reactivity between SARS-CoV-2 and other infectious agents. This hypothesis was tested by combining MIRA with other public TCR profiling repositories that host assays and sequencing data concerning a plethora of pathogens. Our study provides evidence regarding putative cross-reactivity between SARS-CoV-2 and a wide spectrum of pathogens and diseases, with M. tuberculosis and Influenza virus exhibiting the highest levels of cross-reactivity. These results can potentially shift the emphasis of immunological studies towards an increased application of TCR profiling assays that have the potential to uncover key mechanisms of cell-mediated immune response against pathogens and diseases.
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Affiliation(s)
- Georgios K. Georgakilas
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
- Laboratory of Genetics, Department of Biology, University of Patras, 26500 Patras, Greece
| | - Achilleas P. Galanopoulos
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece
| | - Zafeiris Tsinaris
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
| | - Maria Kyritsi
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
| | - Varvara A. Mouchtouri
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 41222 Larisa, Greece
| | - Matthaios Speletas
- Department of Immunology & Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece
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10
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Foolchand A, Mazaleni S, Ghazi T, Chuturgoon AA. A Review: Highlighting the Links between Epigenetics, COVID-19 Infection, and Vitamin D. Int J Mol Sci 2022; 23:ijms232012292. [PMID: 36293144 PMCID: PMC9603374 DOI: 10.3390/ijms232012292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
The highly transmittable and infectious COVID-19 remains a major threat worldwide, with the elderly and comorbid individuals being the most vulnerable. While vaccines are currently available, therapeutic drugs will help ease the viral outbreak and prevent serious health outcomes. Epigenetic modifications regulate gene expression through changes in chromatin structure and have been linked to viral pathophysiology. Since epigenetic modifications contribute to the life cycle of the virus and host immune responses to infection, epigenetic drugs are promising treatment targets to ameliorate COVID-19. Deficiency of the multifunctional secosteroid hormone vitamin D is a global health threat. Vitamin D and its receptor function to regulate genes involved in immunity, apoptosis, proliferation, differentiation, and inflammation. Amassed evidence also indicates the biological relations of vitamin D with reduced disease risk, while its receptor can be modulated by epigenetic mechanisms. The immunomodulatory effects of vitamin D suggest a role for vitamin D as a COVID-19 therapeutic agent. Therefore, this review highlights the epigenetic effects on COVID-19 and vitamin D while also proposing a role for vitamin D in COVID-19 infections.
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11
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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12
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Angulo M, Angulo C. Trained immunity against diseases in domestic animals. Acta Trop 2022; 229:106361. [PMID: 35149041 DOI: 10.1016/j.actatropica.2022.106361] [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: 01/04/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 11/15/2022]
Abstract
Trained immunity is a biological concept that has been demonstrated in different animal species, including human beings. Evidences indicate that innate immune cells can be trained and have a "memory". Under this concept, studies have shown that a first stimulus can potentiate immune responses upon a second one or protect upon homologous or heterologous pathogenic challenges. Research progress on trained innate immunity in mouse models and human beings has provided key information of this phenomenon. In domestic animals, this concept offers a heterologous protection against diseases. Recent studies in domestic animals have demonstrated that trained immunity is induced even by mucosal routes rather than only parenteral routes, as previously evidenced in mice and humans. This situation has led to a major breakthrough in the biotechnology field. Remarkably, the recent first proof-of-concept in calves and goats provides a reality beyond trained immunity as an affordable immunobiotechnological approach to control diseases. Currently, several responses to questions that have been deciphered in mouse and humans seem different in domestic animals; even these differences have been observed among animal species and breeds, which open new questions and challenges. The information of mechanistic studies in domestic animals based on the trained immunity paradigm has not been integrated before; therefore, it needs to be discussed and accurately presented. Moreover, prospects should be defined and biotechnological perspectives provided to promote research and development (R&D) to become a near reality in domestic animal, so this is the main objective of the review.
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Affiliation(s)
- Miriam Angulo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz B.C.S. 23090, México.
| | - Carlos Angulo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz B.C.S. 23090, México.
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13
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Identify a DNA Damage Repair Gene Signature for Predicting Prognosis and Immunotherapy Response in Cervical Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:8736575. [PMID: 35368888 PMCID: PMC8967547 DOI: 10.1155/2022/8736575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022]
Abstract
The DNA damage repair (DDR) genes are increasingly gaining attention as potential therapeutic targets in cancers. In this study, we identified the DDR genes associated with the tumor mutation burden (TMB) and prognosis of cervical squamous cell carcinoma (CESC) based on The Cancer Genome Atlas (TCGA) database. Through LASSO Cox regression, the prognostic signature involving five DDR genes (ACTR2, TEX12, UBE2V1, HSF1, and FBXO6) was established, and the risk score was identified as an independent risk factor for CESC. The nomogram consisting of the five genes accurately predicted the overall survival (OS) and the immunotherapeutic response of CESC patients. Finally, the loss of the copies of the transcription factor (TF) SP140 in CESC patients may decrease the expression of FBXO6, improve DNA repair function, and reduce the diversity of neoantigens, thereby lowering the response to immunotherapies. Therefore, the DDR gene signature is a novel prognostic model and a biomarker for immunotherapies in CESC patients.
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14
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Agwunobi DO, Wang N, Huang L, Zhang Y, Chang G, Wang K, Li M, Wang H, Liu J. Phosphoproteomic Analysis of Haemaphysalis longicornis Saliva Reveals the Influential Contributions of Phosphoproteins to Blood-Feeding Success. Front Cell Infect Microbiol 2022; 11:769026. [PMID: 35118006 PMCID: PMC8804221 DOI: 10.3389/fcimb.2021.769026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Tick saliva, an essential chemical secretion of the tick salivary gland, is indispensable for tick survival owing to the physiological influence it exerts on the host defence mechanisms via the instrumentality of its cocktail of pharmacologically active molecules (proteins and peptides). Much research about tick salivary proteome has been performed, but how most of the individual salivary proteins are utilized by ticks to facilitate blood acquisition and pathogen transmission is not yet fully understood. In addition, the phosphorylation of some proteins plays a decisive role in their function. However, due to the low phosphorylation level of protein, especially for a small amount of protein, it is more difficult to study phosphorylation. Maybe, for this reason, the scarcity of works on the phosphorylated tick salivary proteomes still abound. Here, we performed a phosphoproteomic analysis of Haemaphysalis longicornis tick saliva via TiO2 enrichment and the most advanced Thermo Fisher Orbitrap Exploris 480 mass spectrometer for identification. A total of 262 phosphorylated tick saliva proteins were identified and were subjected to functional annotation/enrichment analysis. Cellular and metabolic process terms accounted for the largest proportion of the saliva proteins, with the participation of these proteins in vital intracellular and extracellular transport-oriented processes such as vesicle-mediated transport, exocytic process, cell adhesion, and movement of cell/subcellular component. “Endocytosis”, “Protein processing in endoplasmic reticulum”, and “Purine metabolism” were the most significantly enriched pathways. The knockdown (RNAi) of Tudor domain-containing protein (TCP), actin-depolymerizing factors (ADF), programmed cell death protein (PD), and serine/threonine-protein kinase (SPK) resulted in the dissociation of collagen fibers and the pilosebaceous unit, increased inflammatory infiltrates/granulocytes (possibly heterophiles), and the depletion of the epithelium. Ticks injected with SPK dsRNA engorged normally but with a change in skin colour (possibly an autoimmune reaction) and the failure to produce eggs pointing to a possible role of SPK in reproduction and host immune modulation. Ticks injected with ADF dsRNA failed to acquire blood, underscoring the role of ADF in facilitating tick feeding. The results of this study showed the presence of phosphorylation in tick saliva and highlight the roles of salivary phosphoproteins in facilitating tick feeding.
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Affiliation(s)
- Desmond O. Agwunobi
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ningmei Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lei Huang
- Hebei Xiaowutai Mountain National Nature Reserve Management Center, Zhangjiakou, China
| | - Yefei Zhang
- Hebei Xiaowutai Mountain National Nature Reserve Management Center, Zhangjiakou, China
| | - Guomin Chang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Kuang Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Mengxue Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hui Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Jingze Liu, ; Hui Wang,
| | - Jingze Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Jingze Liu, ; Hui Wang,
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15
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Song D, Jiang Y, Zhao Q, Li J, Zhao Y. lncRNA-NEAT1 Sponges miR-128 to Promote Inflammatory Reaction and Phenotypic Transformation of Airway Smooth Muscle Cells. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7499911. [PMID: 35082915 PMCID: PMC8786537 DOI: 10.1155/2022/7499911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Pediatric asthma is still a health threat to the children. Long noncoding RNA-NEAT1 (lncRNA-NEAT1) was reported to be positively correlated with the severity of asthma. We aimed to study the effects and mechanism of lncRNA-NEAT1on inflammatory reaction and phenotypic transformation of airway smooth muscle cells (ASMCs) in the bronchial asthma. METHOD The degree of lncRNA-NEAT1 and miR-128 mRNA in children with bronchial asthma and healthy individuals was tested by qRT-PCR. After the inflammatory reaction and phenotypic transformation of PDGF-BB-induced ASMCs, the expression of lncRNA-NEAT1 or miR-128 in the AMSC was disturbed in the AMSC. Subsequently, the expression of lncRNA-NEAT1 and miR-128 was detected by the way of qRT-PCR, and western blot was applied to measure the expression of MMP-2, MMP-9, α-SMA, calponin, NF-κB, and so on in the cells. The content of TNF-α, IL-1β, IL-6, and IL-8 in the cell culture supernatant was checked by ELISA. MTT, Transwell, and flow cytometry were used to detect cell proliferation, migration, and apoptosis. Further, the targeting relations between lncRNA-NEAT1 and miR-128 were evaluated by the dual-luciferase reporter assay. RESULT In the sputum of children with bronchial asthma, lncRNA-NEAT1 was significantly upregulated while miR-128 was rapidly downregulated. Besides, lncRNA-NEAT1 and miR-128 were competitively combined and, for their expression, negatively correlated. CONCLUSION lncRNA-NEAT1 sponges miR-128 to boost PDGF-BB-induced inflammatory reaction and phenotypic transformation of ASMCs to aggravate the occurrence and development of childhood bronchial asthma.
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Affiliation(s)
- Danyang Song
- Department of Pediatric, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Yajing Jiang
- Department of Pediatric, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Qiuju Zhao
- Department of Pediatric, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Jinling Li
- Department of Pediatric, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
| | - Yuqi Zhao
- Department of Pediatric, Cangzhou Central Hospital, Cangzhou, Hebei 061000, China
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16
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Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 2022; 305:165-178. [PMID: 34816452 PMCID: PMC8766910 DOI: 10.1111/imr.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
In recent years, there has been significant progress toward understanding the transcriptional networks underlying mammalian immune responses, fueled by advances in regulatory genomic technologies. Epigenomic studies profiling immune cells have generated detailed genome-wide maps of regulatory elements that will be key to deciphering the regulatory networks underlying cellular immune responses and autoimmune disorders. Unbiased analyses of these genomic maps have uncovered endogenous retroviruses as an unexpected ally in the regulation of human immune systems. Despite their parasitic origins, studies are finding an increasing number of examples of retroviral sequences having been co-opted for beneficial immune function and regulation by the host cell. Here, we review how endogenous retroviruses have given rise to numerous regulatory elements that shape the epigenetic landscape of host immune responses. We will discuss the implications of these elements on the function, dysfunction, and evolution of innate immunity.
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17
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Wei Z, Luo L, Hu S, Tian R, Liu Z. KDM2B overexpression prevents myocardial ischemia‑reperfusion injury in rats through regulating inflammatory response via the TLR4/NF‑κB p65 axis. Exp Ther Med 2021; 23:154. [PMID: 35069835 PMCID: PMC8753960 DOI: 10.3892/etm.2021.11077] [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: 08/13/2021] [Accepted: 10/19/2021] [Indexed: 11/05/2022] Open
Abstract
Histone modifier lysine-specific demethylase 2B (KDM2B) has been previously reported to activate the inflammatory response by transcription initiation of the IL-6 gene. However, the effects of KDM2B on the inflammatory response during myocardial ischemia-reperfusion (I/R) injury and corresponding mechanisms remain poorly understood. The present study aimed to investigate the role and mechanism of KDM2B in myocardial I/R injury. Therefore, a myocardial I/R injury model was established in rats through coronary artery ligation. Adeno-associated virus-encoding KDM2B and small interfering RNA-KDM2B were designed to determine the effects of KDM2B on myocardial I/R injury using H&E staining and a TUNEL assay in the myocardial tissues. Reverse transcription-quantitative PCR and western blotting were performed to detect the mRNA and protein expression levels of KDM2B, toll-like receptor 4 (TLR4), NF-κB p65 and NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3). ELISA was used to detect the levels of TNF-α, IL-6 and IL-1β in the peripheral blood samples. Pathological analysis demonstrated that the cells in the model group were disordered, with a large area of necrosis and neutrophil infiltration. Knocking down KDM2B expression significantly upregulated the mRNA and protein expression levels of TLR4, NLRP3, NF-κB p65 and the ratio of phosphorylated (p)-p65 to p65. KDM2B knockdown also significantly increased the levels of IL-1β, IL-6 and TNF-α in the peripheral blood, which aggravated myocardial injury and promoted the apoptosis of myocardial cells. However, overexpression of KDM2B downregulated the mRNA and protein expression levels of TLR4, NLRP3, NF-κB P65, the ratio of p-p65 to p65 whilst reducing the levels of IL-1β, IL-6 and TNF-α in the peripheral blood, which markedly improved myocardial injury and significantly inhibited the apoptosis of cells in myocardial tissue. In conclusion, the results indicated that overexpression of KDM2B may prevent myocardial I/R injury in rats by reducing the inflammatory response through regulation of the TLR4/NF-κB p65 axis.
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Affiliation(s)
- Zijie Wei
- Department of Cardiac Intensive Care, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Lihua Luo
- Department of Nephrology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Shuo Hu
- Department of Cardiac Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Rongcheng Tian
- Department of Emergency, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Ziyou Liu
- Department of Cardiac Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
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18
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Sethumadhavan DV, Jabeena CA, Govindaraju G, Soman A, Rajavelu A. The severity of SARS-CoV-2 infection is dictated by host factors? Epigenetic perspectives. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100079. [PMID: 34725650 PMCID: PMC8550886 DOI: 10.1016/j.crmicr.2021.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/02/2021] [Accepted: 10/24/2021] [Indexed: 12/15/2022] Open
Abstract
The emergence of COVID-19, caused by SARS-CoV-2 poses a significant threat to humans as it is highly contagious with increasing mortality. There exists a high degree of heterogeneity in the mortality rates of COVID-19 across the globe. There are multiple speculations on the varying degree of mortality. Still, all the clinical reports have indicated that preexisting chronic diseases like hypertension, diabetes, chronic obstructive pulmonary disease (COPD), kidney disorders, and cardiovascular diseases are associated with the increased risk for high mortality in SARS-CoV-2 infected patients. It is worth noting that host factors, mainly epigenetic factors could play a significant role in deciding the outcome of COVID-19 diseases. Over the recent years, it is evident that chronic diseases are developed due to altered epigenome that includes a selective loss/gain of DNA and histone methylation on the chromatin of the cells. Since, there is a high positive correlation between chronic diseases and elevated mortality due to SARS-CoV-2, in this review; we discuss the overall picture of the aberrant epigenome map in varying chronic ailments and its implications in COVID-19 disease severity and high mortality.
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Affiliation(s)
- Devadathan Valiyamangalath Sethumadhavan
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - C A Jabeena
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gayathri Govindaraju
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aparna Soman
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India
| | - Arumugam Rajavelu
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695014, Kerala, India.,Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600 036, India
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19
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Dixon CR, Malik P, de las Heras JI, Saiz-Ros N, de Lima Alves F, Tingey M, Gaunt E, Richardson AC, Kelly DA, Goldberg MW, Towers GJ, Yang W, Rappsilber J, Digard P, Schirmer EC. STING nuclear partners contribute to innate immune signaling responses. iScience 2021; 24:103055. [PMID: 34541469 PMCID: PMC8436130 DOI: 10.1016/j.isci.2021.103055] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/19/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
STimulator of INterferon Genes (STING) is an adaptor for cytoplasmic DNA sensing by cGAMP/cGAS that helps trigger innate immune responses (IIRs). Although STING is mostly localized in the ER, we find a separate inner nuclear membrane pool of STING that increases mobility and redistributes to the outer nuclear membrane upon IIR stimulation by transfected dsDNA or dsRNA mimic poly(I:C). Immunoprecipitation of STING from isolated nuclear envelopes coupled with mass spectrometry revealed a distinct nuclear envelope-STING proteome consisting of known nuclear membrane proteins and enriched in DNA- and RNA-binding proteins. Seventeen of these nuclear envelope STING partners are known to bind direct interactors of IRF3/7 transcription factors, and testing a subset of these revealed STING partners SYNCRIP, MEN1, DDX5, snRNP70, RPS27a, and AATF as novel modulators of dsDNA-triggered IIRs. Moreover, we find that SYNCRIP is a novel antagonist of the RNA virus, influenza A, potentially shedding light on reports of STING inhibition of RNA viruses.
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Affiliation(s)
- Charles R. Dixon
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Poonam Malik
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Jose I. de las Heras
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Natalia Saiz-Ros
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Flavia de Lima Alves
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia 19121, USA
| | - Eleanor Gaunt
- Division of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | - David A. Kelly
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Martin W. Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK
| | - Greg J. Towers
- Department of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia 19121, USA
| | - Juri Rappsilber
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
- Department of Bioanalytics, Institute of Biotechnology, Technische Universitat Berlin, 13355 Berlin, Germany
| | - Paul Digard
- Division of Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Eric C. Schirmer
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Swann 5.22, Mayfield Road, Edinburgh EH9 3BF, UK
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20
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Ren X, Wang R, Yu XT, Cai B, Guo F. Regulation of histone H3 lysine 9 methylation in inflammation. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1931477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xin Ren
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Rong Wang
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Xiao-ting Yu
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Bo Cai
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Fei Guo
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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21
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Differential effects of chronic immunosuppression on behavioral, epigenetic, and Alzheimer's disease-associated markers in 3xTg-AD mice. ALZHEIMERS RESEARCH & THERAPY 2021; 13:30. [PMID: 33472690 PMCID: PMC7818784 DOI: 10.1186/s13195-020-00745-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Circulating autoantibodies and sex-dependent discrepancy in prevalence are unexplained phenomena of Alzheimer's disease (AD). Using the 3xTg-AD mouse model, we reported that adult males show early manifestations of systemic autoimmunity, increased emotional reactivity, enhanced expression of the histone variant macroH2A1 in the cerebral cortex, and loss of plaque/tangle pathology. Conversely, adult females display less severe autoimmunity and retain their AD-like phenotype. This study examines the link between immunity and other traits of the current 3xTg-AD model. METHODS Young 3xTg-AD and wild-type mice drank a sucrose-laced 0.4 mg/ml solution of the immunosuppressant cyclophosphamide on weekends for 5 months. After behavioral phenotyping at 2 and 6 months of age, we assessed organ mass, serologic markers of autoimmunity, molecular markers of early AD pathology, and expression of genes associated with neurodegeneration. RESULTS Chronic immunosuppression prevented hematocrit drop and reduced soluble Aβ in 3xTg-AD males while normalizing the expression of histone variant macroH2A1 in 3xTg-AD females. This treatment also reduced hepatosplenomegaly, lowered autoantibody levels, and increased the effector T cell population while decreasing the proportion of regulatory T cells in both sexes. Exposure to cyclophosphamide, however, neither prevented reduced brain mass and BDNF expression nor normalized increased tau and anxiety-related behaviors. CONCLUSION The results suggest that systemic autoimmunity increases soluble Aβ production and affects transcriptional regulation of macroH2A1 in a sex-related manner. Despite the complexity of multisystem interactions, 3xTg-AD mice can be a useful in vivo model for exploring the regulatory role of autoimmunity in the etiology of AD-like neurodegenerative disorders.
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22
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Vashishtha VM. Are BCG-induced non-specific effects adequate to provide protection against COVID-19? Hum Vaccin Immunother 2021; 17:88-91. [PMID: 32762516 DOI: 10.1080/21645515.2020.1794219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The world is experiencing a pandemic of Coronavirus Disease (COVID-19) caused by type-2 Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Vaccination is the only option to prevent future surges of the disease. Efforts for developing an effective vaccine are underway, but the timeline for the widespread availability of safe and effective vaccines is unknown. Some ecological reports have linked regional universal use of the Bacillus Calmette-Guerin (BCG) vaccine with reduced morbidity and mortality of COVID-19. BCG protects from non-tuberculous diseases through 'non-specific' effects mediated by the modulation of innate immunity. This commentary provides details of the immunological mechanism of BCG-induced 'trained innate immunity' responsible for its nonspecific protective effects. A probable role of the BCG vaccine in the current pandemic is also examined.
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Affiliation(s)
- Vipin M Vashishtha
- Director and Consultant Pediatrician, Department of Pediatrics, Mangla Hospital & Research Center , Bijnor, Uttar Pradesh, India
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23
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Hanford HE, Von Dwingelo J, Abu Kwaik Y. Bacterial nucleomodulins: A coevolutionary adaptation to the eukaryotic command center. PLoS Pathog 2021; 17:e1009184. [PMID: 33476322 PMCID: PMC7819608 DOI: 10.1371/journal.ppat.1009184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Through long-term interactions with their hosts, bacterial pathogens have evolved unique arsenals of effector proteins that interact with specific host targets and reprogram the host cell into a permissive niche for pathogen proliferation. The targeting of effector proteins into the host cell nucleus for modulation of nuclear processes is an emerging theme among bacterial pathogens. These unique pathogen effector proteins have been termed in recent years as "nucleomodulins." The first nucleomodulins were discovered in the phytopathogens Agrobacterium and Xanthomonas, where their nucleomodulins functioned as eukaryotic transcription factors or integrated themselves into host cell DNA to promote tumor induction, respectively. Numerous nucleomodulins were recently identified in mammalian pathogens. Bacterial nucleomodulins are an emerging family of pathogen effector proteins that evolved to target specific components of the host cell command center through various mechanisms. These mechanisms include: chromatin dynamics, histone modification, DNA methylation, RNA splicing, DNA replication, cell cycle, and cell signaling pathways. Nucleomodulins may induce short- or long-term epigenetic modifications of the host cell. In this extensive review, we discuss the current knowledge of nucleomodulins from plant and mammalian pathogens. While many nucleomodulins are already identified, continued research is instrumental in understanding their mechanisms of action and the role they play during the progression of pathogenesis. The continued study of nucleomodulins will enhance our knowledge of their effects on nuclear chromatin dynamics, protein homeostasis, transcriptional landscapes, and the overall host cell epigenome.
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Affiliation(s)
- Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
- Center for Predicative Medicine, College of Medicine, University of Louisville, Kentucky, United States of America
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24
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Jawhara S. How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections. Gut Pathog 2020; 12:47. [PMID: 33062058 PMCID: PMC7549427 DOI: 10.1186/s13099-020-00385-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/03/2020] [Indexed: 02/08/2023] Open
Abstract
The emergence of the novel coronavirus SARS-CoV-2, which causes severe respiratory tract infections in humans (COVID-19), has become a global health concern. One of the most worrying features of COVID-19 is a phenomenon known as the "cytokine storm", which is a rapid overreaction of the immune system. Additionally, coagulation abnormalities, thrombocytopenia and digestive symptoms, including anorexia, vomiting, and diarrhea, are often observed in critically ill patients with COVID-19. Baker's yeast β-glucan, a natural immunomodulatory component derived from Saccharomyces cerevisiae, primes the immune system to respond better to any microbial infection. Our previous studies have shown that oral administration of yeast β-glucans decreased the diarrhoea, modulated cytokine expression, and reduced the intestinal inflammation. Additionally, we showed that β-glucan fractions decreased coagulation in plasma and reduced the activation of platelets. During the period of home confinement facing individuals during the COVID-19 pandemic, our immune defence could be weakened by different factors, including stress, anxiety and poor nutrition, while a healthy diet rich in vitamins C and D can reinforce the immune defence and reduce the risk of microbial infections. Additionally, β-glucan can be used to strengthen the immune defence in healthy individuals prior to any possible viral infections. This short review focuses on the role of baker's yeast β-glucan, with a healthy diet rich in natural vitamins C and D, in addition to a healthy gut microbiota can provide synergistic immune system support, helping the body to naturally defend prior to respiratory virus infections, until stronger options such as vaccines are available.
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Affiliation(s)
- Samir Jawhara
- grid.503422.20000 0001 2242 6780CNRS, UMR 8576, UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, INSERM U1285, Université Lille, 1 Place Verdun, 59000 Lille, France ,grid.503422.20000 0001 2242 6780University of Lille, 59000 Lille, France
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25
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Sandall CF, Ziehr BK, MacDonald JA. ATP-Binding and Hydrolysis in Inflammasome Activation. Molecules 2020; 25:molecules25194572. [PMID: 33036374 PMCID: PMC7583971 DOI: 10.3390/molecules25194572] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
The prototypical model for NOD-like receptor (NLR) inflammasome assembly includes nucleotide-dependent activation of the NLR downstream of pathogen- or danger-associated molecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomeric platforms that lie upstream of inflammatory responses associated with innate immunity. As members of the STAND ATPases, the NLRs are generally thought to share a similar model of ATP-dependent activation and effect. However, recent observations have challenged this paradigm to reveal novel and complex biochemical processes to discern NLRs from other STAND proteins. In this review, we highlight past findings that identify the regulatory importance of conserved ATP-binding and hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explore recent breakthroughs that generate connections between NLR protein structure and function. Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectives on the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations of NLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctions in nucleotide-binding domain topology with occupancy of ATP or ADP that are in turn disseminated on to the global protein structure. Ultimately, studies continue to reveal how the ATP-binding and hydrolysis properties of NACHT domains in different NLRs integrate with signaling modules and binding partners to control innate immune responses at the molecular level.
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26
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Ehtesham NZ, Samal J, Ahmad F, Arish M, Naz F, Alam A, Agrawal U, Hasnain SE. Will bacille Calmette-Guerin immunization arrest the COVID-19 pandemic? Indian J Med Res 2020; 152:16-20. [PMID: 32859863 PMCID: PMC7853263 DOI: 10.4103/ijmr.ijmr_1563_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Nasreen Zafar Ehtesham
- Inflammation Biology & Cell Signaling Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Jasmine Samal
- Inflammation Biology & Cell Signaling Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Faraz Ahmad
- Inflammation Biology & Cell Signaling Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Mohd Arish
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062, India
| | - Farha Naz
- Inflammation Biology & Cell Signaling Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Anwar Alam
- Inflammation Biology & Cell Signaling Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Usha Agrawal
- Tumor Biology Laboratory, ICMR-National Institute of Pathology, New Delhi 110 029, India
| | - Seyed Ehtesham Hasnain
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062; Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad 500 046, Telangana, India
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27
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Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
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28
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Management of epigenomic networks entailed in coronavirus infections and COVID-19. Clin Epigenetics 2020; 12:118. [PMID: 32758273 PMCID: PMC7404079 DOI: 10.1186/s13148-020-00912-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) are highly diverse single-stranded RNA viruses owing to their susceptibility to numerous genomic mutations and recombination. Such viruses involve human and animal pathogens including the etiologic agents of acute respiratory tract illnesses: severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the highly morbific SARS-CoV-2. Coronavirus disease 2019 (COVID-19), an emerging disease with a quick rise in infected cases and deaths, was recently identified causing a worldwide pandemic. COVID-19 disease outcomes were found to increase in elderly and patients with a compromised immune system. Evidences indicated that the main culprit behind COVID-19 deaths is the cytokine storm, which is illustrated by an uncontrolled over-production of soluble markers of inflammation. The regulation process of coronavirus pathogenesis through molecular mechanism comprise virus-host interactions linked to viral entry, replication and transcription, escape, and immune system control. Recognizing coronavirus infections and COVID-19 through epigenetics lens will lead to potential alteration in gene expression thus limiting coronavirus infections. Focusing on epigenetic therapies reaching clinical trials, clinically approved epigenetic-targeted agents, and combination therapy of antivirals and epigenetic drugs is currently considered an effective and valuable approach for viral replication and inflammatory overdrive control.
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29
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van Tuijl J, Joosten LAB, Netea MG, Bekkering S, Riksen NP. Immunometabolism orchestrates training of innate immunity in atherosclerosis. Cardiovasc Res 2020; 115:1416-1424. [PMID: 31050710 PMCID: PMC6910162 DOI: 10.1093/cvr/cvz107] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
Atherosclerosis is characterized by a persistent, low-grade inflammation of the arterial wall. Monocytes and monocyte-derived macrophages play a pivotal role in the various stages of atherosclerosis. In the past few years, metabolic reprogramming has been identified as an important controller of myeloid cell activation status. In addition, metabolic and epigenetic reprogramming are key regulatory mechanisms of trained immunity, which denotes the non-specific innate immune memory that can develop after brief stimulation of monocytes with microbial or non-microbial stimuli. In this review, we build the case that metabolic reprogramming of monocytes and macrophages, and trained immunity in particular, contribute to the pathophysiology of atherosclerosis. We discuss the specific metabolic adaptations, including changes in glycolysis, oxidative phosphorylation, and cholesterol metabolism, that have been reported in atherogenic milieus in vitro and in vivo. In addition, we will focus on the role of these metabolic pathways in the development of trained immunity.
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Affiliation(s)
- Julia van Tuijl
- Department of Internal Medicine, Radboud University Medical Center Nijmegen, Geert Grooteplein Zuid 8, GA, HB Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center Nijmegen, Geert Grooteplein Zuid 8, GA, HB Nijmegen, The Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Str. Pasteur 6, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center Nijmegen, Geert Grooteplein Zuid 8, GA, HB Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Sciences Institute (LIMES), University of Bonn, Carl-Troll-Straβe 31, Bonn, Germany
| | - Siroon Bekkering
- Department of Internal Medicine, Radboud University Medical Center Nijmegen, Geert Grooteplein Zuid 8, GA, HB Nijmegen, The Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center Nijmegen, Geert Grooteplein Zuid 8, GA, HB Nijmegen, The Netherlands
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30
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The Speckled Protein (SP) Family: Immunity's Chromatin Readers. Trends Immunol 2020; 41:572-585. [PMID: 32386862 DOI: 10.1016/j.it.2020.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 01/25/2023]
Abstract
Chromatin 'readers' are central interpreters of the epigenome that facilitate cell-specific transcriptional programs and are therapeutic targets in cancer and inflammation. The Speckled Protein (SP) family of chromatin 'readers' in humans consists of SP100, SP110, SP140, and SP140L. SPs possess functional domains (SAND, PHD, bromodomain) that dock to DNA or post-translationally modified histones and a caspase activation and recruitment domain (CARD) to promote multimerization. Mutations within immune expressed SPs associate with numerous immunological diseases including Crohn's disease, multiple sclerosis, chronic lymphocytic leukemia, veno-occlusive disease with immunodeficiency, as well as Mycobacterium tuberculosis infection, underscoring their importance in immune regulation. In this review, we posit that SPs are central chromatin regulators of gene silencing that establish immune cell identity and function.
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31
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Subuddhi A, Kumar M, Majumder D, Sarkar A, Ghosh Z, Vasudevan M, Kundu M, Basu J. Unraveling the role of H3K4 trimethylation and lncRNA HOTAIR in SATB1 and DUSP4-dependent survival of virulent Mycobacterium tuberculosis in macrophages. Tuberculosis (Edinb) 2019; 120:101897. [PMID: 32090865 DOI: 10.1016/j.tube.2019.101897] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/15/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022]
Abstract
The modification of chromatin influences host transcriptional programs during bacterial infection, at times skewing the balance in favor of pathogen survival. To test the role of chromatin modifications during Mycobacterium tuberculosis infection, we analysed genome-wide deposition of H3K4me3 marks in macrophages infected with either avirulent M. tuberculosis H37Ra or virulent H37Rv, by chromatin immunoprecipitation, followed by sequencing. We validated differences in association of H3K4me3 at the loci of special AT-rich sequence binding protein 1 (SATB1) and dual specificity MAP kinase phosphatase 4 (DUSP4) between H37Rv and H37Ra-infected macrophages, and demonstrated their role in regulating bacterial survival in macrophages as well as the expression of chemokines. SATB1 repressed gp91phox (an NADPH oxidase subunit) thereby regulating reactive oxygen species (ROS) generation during infection. Long non-coding RNA HOX transcript antisense RNA (HOTAIR) was upregulated in H37Ra-, but downregulated in H37Rv-infected macrophages. HOTAIR overexpression correlated with deposition of repressive H3K27me3 marks around the TSSs of DUSP4 and SATB1, suggesting that its downregulation favors the transcription of SATB1 and DUSP4. In summary, we have delineated histone modification- and lncRNA-dependent mechanisms regulating gene expression patterns facilitating survival of virulent M. tuberculosis. Our observations raise the possibility of harnessing histone-modifying enzymes to develop host-directed therapies for tuberculosis.
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Affiliation(s)
| | - Manish Kumar
- Department of Chemistry, Bose Institute, Kolkata, 700009, India
| | | | - Arijita Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata, 700054, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, 700054, India
| | | | | | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, 700009, India.
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32
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Ramirez-Prado JS, Latrasse D, Rodriguez-Granados NY, Huang Y, Manza-Mianza D, Brik-Chaouche R, Jaouannet M, Citerne S, Bendahmane A, Hirt H, Raynaud C, Benhamed M. The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1118-1131. [PMID: 31437321 DOI: 10.1111/tpj.14502] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.
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Affiliation(s)
- Juan Sebastian Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Maelle Jaouannet
- CNRS, INRA, Université Nice Sophia Antipolis, UMR 1355-7254, Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Heribert Hirt
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Cecile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
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Fiege JK, Stone IA, Dumm RE, Waring BM, Fife BT, Agudo J, Brown BD, Heaton NS, Langlois RA. Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance. PLoS Pathog 2019; 15:e1008077. [PMID: 31557273 PMCID: PMC6782110 DOI: 10.1371/journal.ppat.1008077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 10/08/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023] Open
Abstract
Influenza A virus (IAV) is a seasonal pathogen with the potential to cause devastating pandemics. IAV infects multiple epithelial cell subsets in the respiratory tract, eliciting damage to the lungs. Clearance of IAV is primarily dependent on CD8+ T cells, which must balance control of the infection with immunopathology. Using a virus expressing Cre recombinase to permanently label infected cells in a Cre-inducible reporter mouse, we previously discovered infected club cells that survive both lytic virus replication and CD8+ T cell-mediated clearance. In this study, we demonstrate that ciliated epithelial cells, type I and type II alveolar cells can also become survivor cells. Survivor cells are stable in the lung long-term and demonstrate enhanced proliferation compared to uninfected cells. When we investigated how survivor cells evade CD8+ T cell killing we observed that survivor cells upregulated the inhibitory ligand PD-L1, but survivor cells did not use PD-L1 to evade CD8+ T cell killing. Instead our data suggest that survivor cells are not inherently resistant to CD8+ T cell killing, but instead no longer present IAV antigen and cannot be detected by CD8+ T cells. Finally, we evaluate the failure of CD8+ T cells to kill these previously infected cells. This work demonstrates that additional cell types can survive IAV infection and that these cells robustly proliferate and are stable long term. By sparing previously infected cells, the adaptive immune system may be minimizing pathology associated with IAV infection.
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Affiliation(s)
- Jessica K. Fiege
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Ian A. Stone
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Rebekah E. Dumm
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Barbara M. Waring
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Brian T. Fife
- University of Minnesota, Department of Medicine and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Judith Agudo
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Brian D. Brown
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Nicholas S. Heaton
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Ryan A. Langlois
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
- * E-mail:
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Sun R, Hedl M, Abraham C. Twist1 and Twist2 Induce Human Macrophage Memory upon Chronic Innate Receptor Treatment by HDAC-Mediated Deacetylation of Cytokine Promoters. THE JOURNAL OF IMMUNOLOGY 2019; 202:3297-3308. [PMID: 31028123 DOI: 10.4049/jimmunol.1800757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
Intestinal tissues are continuously exposed to microbial products that stimulate pattern-recognition receptors (PRRs). Ongoing PRR stimulation can confer epigenetic changes in macrophages, which can then regulate subsequent immune outcomes and adaptation to the local environment. Mechanisms leading to these changes are incompletely understood. We found that short-term stimulation of the PRR NOD2 in primary human monocyte-derived macrophages resulted in increased H3 and H4 acetylation of cytokine promoters, consistent with the increased cytokine secretion observed. However, with prolonged NOD2 stimulation, both the acetylation and cytokine secretion were dramatically decreased. Chronic NOD2 stimulation upregulated the transcription factors Twist1 and Twist2, which bound to the promoters of the histone deacetylases HDAC1 and HDAC3 and induced HDAC1 and HDAC3 expression. HDAC1 and HDAC3 then mediated histone deacetylation at cytokine promoters and, in turn, cytokine downregulation under these conditions. Similar regulation was observed upon chronic stimulation of multiple PRRs. Consistent with the chronic microbial exposure in the intestinal environment, TWIST1, TWIST2, HDAC1, and HDAC3 were upregulated in human intestinal relative to peripheral macrophages. Importantly, complementing HDAC1 and HDAC3 in Twist1/Twist2-deficient monocyte-derived macrophages restored the reduced histone acetylation on cytokine promoters and the decreased cytokine secretion with chronic NOD2 stimulation. Taken together, we identify mechanisms wherein Twist1 and Twist2 promote chromatin modifications, resulting in macrophage instruction and adaptation to conditions in the intestinal microenvironment.
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Affiliation(s)
- Rui Sun
- Department of Internal Medicine, Yale University, New Haven, CT 06510
| | - Matija Hedl
- Department of Internal Medicine, Yale University, New Haven, CT 06510
| | - Clara Abraham
- Department of Internal Medicine, Yale University, New Haven, CT 06510
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Hamada A, Torre C, Drancourt M, Ghigo E. Trained Immunity Carried by Non-immune Cells. Front Microbiol 2019; 9:3225. [PMID: 30692968 PMCID: PMC6340064 DOI: 10.3389/fmicb.2018.03225] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
“Trained immunity” is a term proposed by Netea to describe the ability of an organism to develop an exacerbated immunological response to protect against a second infection independent of the adaptative immunity. This immunological memory can last from 1 week to several months and is only described in innate immune cells such as monocytes, macrophages, and natural killer cells. Paradoxically, the lifespan of these cells in the blood is shorter than the duration of trained immunity. This observation suggested that trained immunity could be carried by long lifespan cells such as stem cells and non-immune cells like fibroblasts. It is now evident that in addition to performing their putative function in the development and maintenance of tissue homeostasis, non-immune cells also play an important role in the response to pathogens by producing anti-microbial factors, with long-term inflammation suggesting that non-immune cells can be trained to confer long-lasting immunological memory. This review provides a summary of the current relevant knowledge about the cells which possess immunological memory and discusses the possibility that non-immune cells may carry immunological memory and mechanisms that might be involved.
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Affiliation(s)
- Attoumani Hamada
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Cédric Torre
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Eric Ghigo
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
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Long C, Lai Y, Li J, Huang J, Zou C. LPS promotes HBO1 stability via USP25 to modulate inflammatory gene transcription in THP-1 cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:773-782. [PMID: 30745998 DOI: 10.1016/j.bbagrm.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The histone acetyltransferase HBO1 (Histone acetyltransferase binding to origin recognition complex 1, Myst2/Kat7) participates in a range of life processes including DNA replication and tumorigenesis. Recent studies revealed that HBO1 is involved in gene transcriptional activation. However, the molecular behavior of HBO1 in inflammation is yet to be studied. Here we report that endotoxin lipopolysaccharide (LPS) elevates HBO1 protein level via up-regulating UPS25 (ubiquitin specific peptidase 25) and alters inflammatory gene transcription in THP-1 monocytes and in human primary macrophages. LPS protects HBO1 from ubiquitin proteasomal degradation without significantly altering its transcription. By immunoprecipitation, we identified that HBO1 associates with a deubiquitinating enzyme USP25 in THP-1 cells. LPS increases protein level of USP25 resulting in accumulation of HBO1 by suppression of HBO1 ubiquitination. Stabilized-HBO1 modulates inflammatory gene transcription in THP-1 cells. These findings indicate that USP25 promotes stability of HBO1 in bacterial infection thereby enhances HBO1-mediated inflammatory gene transcription.
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Affiliation(s)
- Chen Long
- Department of Minimally Invasive Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China 410011.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Yandong Lai
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Jin Li
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Jiangsheng Huang
- Department of Minimally Invasive Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China 410011
| | - Chunbin Zou
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
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Kapadia M, Mian MF, Michalski B, Azam AB, Ma D, Salwierz P, Christopher A, Rosa E, Zovkic IB, Forsythe P, Fahnestock M, Sakic B. Sex-Dependent Differences in Spontaneous Autoimmunity in Adult 3xTg-AD Mice. J Alzheimers Dis 2018; 63:1191-1205. [DOI: 10.3233/jad-170779] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Minesh Kapadia
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - M. Firoz Mian
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bernadeta Michalski
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Amber B. Azam
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Donglai Ma
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Patrick Salwierz
- Biochemistry and Bachelor of Health Sciences Undergraduate programs, McMaster University, Hamilton, ON, Canada
| | - Adam Christopher
- Biochemistry and Bachelor of Health Sciences Undergraduate programs, McMaster University, Hamilton, ON, Canada
| | - Elyse Rosa
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Iva B. Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Paul Forsythe
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Margaret Fahnestock
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Boris Sakic
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
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Li Y, Lei X, Guo W, Wu S, Duan Y, Yang X, Yang X. Transgenerational endotoxin tolerance-like effect caused by paternal dietary Astragalus polysaccharides in broilers' jejunum. Int J Biol Macromol 2018; 111:769-779. [DOI: 10.1016/j.ijbiomac.2018.01.095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/05/2018] [Accepted: 01/14/2018] [Indexed: 02/08/2023]
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Mourits VP, Wijkmans JC, Joosten LA, Netea MG. Trained immunity as a novel therapeutic strategy. Curr Opin Pharmacol 2018; 41:52-58. [PMID: 29702467 DOI: 10.1016/j.coph.2018.04.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/12/2018] [Indexed: 01/13/2023]
Abstract
Recent studies have shown that upon certain vaccinations or infections human innate immune cells can undergo extensive metabolic and epigenetic reprogramming, which results in enhanced immune responses upon heterologous re-infection, a process termed trained immunity. Trained immunity has also been shown to be inappropriately activated in inflammatory diseases. This provides the potential for identifying novel therapeutic targets: potentiation of trained immunity could protect from secondary infections and reverse immunotolerant states, while inhibition of trained immunity might reduce excessive immune activation in chronic inflammatory conditions. By targeting specific mechanisms of trained immunity on either immunologic, metabolic or epigenetic level, novel therapeutic approaches could be developed.
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Affiliation(s)
- Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Leo Ab Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
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40
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Infectious Agents as Stimuli of Trained Innate Immunity. Int J Mol Sci 2018; 19:ijms19020456. [PMID: 29401667 PMCID: PMC5855678 DOI: 10.3390/ijms19020456] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
The discoveries made over the past few years have modified the current immunological paradigm. It turns out that innate immunity cells can mount some kind of immunological memory, similar to that observed in the acquired immunity and corresponding to the defense mechanisms of lower organisms, which increases their resistance to reinfection. This phenomenon is termed trained innate immunity. It is based on epigenetic changes in innate immune cells (monocytes/macrophages, NK cells) after their stimulation with various infectious or non-infectious agents. Many infectious stimuli, including bacterial or fungal cells and their components (LPS, β-glucan, chitin) as well as viruses or even parasites are considered potent inducers of innate immune memory. Epigenetic cell reprogramming occurring at the heart of the phenomenon may provide a useful basis for designing novel prophylactic and therapeutic strategies to prevent and protect against multiple diseases. In this article, we present the current state of art on trained innate immunity occurring as a result of infectious agent induction. Additionally, we discuss the mechanisms of cell reprogramming and the implications for immune response stimulation/manipulation.
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Ramirez-Prado JS, Piquerez SJM, Bendahmane A, Hirt H, Raynaud C, Benhamed M. Modify the Histone to Win the Battle: Chromatin Dynamics in Plant-Pathogen Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:355. [PMID: 29616066 PMCID: PMC5868138 DOI: 10.3389/fpls.2018.00355] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/02/2018] [Indexed: 05/02/2023]
Abstract
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses. Herein, we review the state of the art in the epigenomic aspects of plant immunity, focusing on chromatin modifications, chromatin modifiers, and their physiological consequences. In addition, we explore the exciting field of understanding how plant pathogens have adapted to manipulate the plant epigenomic regulation in order to weaken their immune system and thrive in their host, as well as how histone modifications in eukaryotic pathogens are involved in the regulation of their virulence.
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Affiliation(s)
- Juan S. Ramirez-Prado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Sophie J. M. Piquerez
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Abdelhafid Bendahmane
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Heribert Hirt
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Cécile Raynaud
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Moussa Benhamed
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
- *Correspondence: Moussa Benhamed,
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Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL. Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol 2017; 2:eaag3160. [PMID: 28783698 PMCID: PMC5549562 DOI: 10.1126/sciimmunol.aag3160] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022]
Abstract
Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with immune-restricted expression, and single-nucleotide polymorphisms (SNPs) within SP140 associate with Crohn's disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unclear. We show that SP140 is critical for transcriptional programs that uphold the macrophage state. SP140 preferentially occupies promoters of silenced, lineage-inappropriate genes bearing the histone modification H3K27me3, such as the HOXA cluster in human macrophages, and ensures their repression. Depletion of SP140 in mouse or human macrophages resulted in severely compromised microbe-induced activation. We reveal that peripheral blood mononuclear cells (PBMCs) or B cells from individuals carrying CD-associated SNPs within SP140 have defective SP140 messenger RNA splicing and diminished SP140 protein levels. Moreover, CD patients carrying SP140 SNPs displayed suppressed innate immune gene signatures in a mixed population of PBMCs that stratified them from other CD patients. Hematopoietic-specific knockdown of Sp140 in mice resulted in exacerbated dextran sulfate sodium (DSS)-induced colitis, and low SP140 levels in human CD intestinal biopsies correlated with relatively lower intestinal innate cytokine levels and improved response to anti-tumor necrosis factor (TNF) therapy. Thus, the epigenetic reader SP140 is a key regulator of macrophage transcriptional programs for cellular state, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by ineffective innate immunity, normally critical for intestinal homeostasis.
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Affiliation(s)
- Stuti Mehta
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - D Alexander Cronkite
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Megha Basavappa
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tahnee L Saunders
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hajera Amatullah
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sara A Morrison
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Pierre Tonnerre
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James C Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Sreehaas Digumarthi
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shannan J Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan C Mullen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Terry K Means
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kate L Jeffrey
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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Abstract
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus–host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype. Epigenetic modifications, such as histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, function as important regulators that remodel host chromatin, altering host expression patterns and networks in a highly flexible manner. For most of the past two and a half decades, research has focused on the molecular mechanisms by which RNA viruses antagonize the signaling and sensing components that regulate induction of the host innate immune and antiviral defense programs upon infection. More recently, a growing body of evidence supports the hypothesis that viruses, even lytic RNA viruses that replicate in the cytoplasm, have developed intricate, highly evolved, and well-coordinated processes that are designed to regulate the host epigenome, and control host innate immune antiviral defense processes, thereby promoting robust virus replication and pathogenesis. In this article, we discuss the strategies that are used to evaluate the mechanisms by which viruses regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus infections as a model. By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host’s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection.
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Marks DL, Olson RL, Fernandez-Zapico ME. Epigenetic control of the tumor microenvironment. Epigenomics 2016; 8:1671-1687. [PMID: 27700179 DOI: 10.2217/epi-2016-0110] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Stromal cells of the tumor microenvironment have been shown to play important roles in both supporting and limiting cancer growth. The altered phenotype of tumor-associated stromal cells (fibroblasts, immune cells, endothelial cells etc.) is proposed to be mainly due to epigenetic dysregulation of gene expression; however, only limited studies have probed the roles of epigenetic mechanisms in the regulation of stromal cell function. We review recent studies demonstrating how specific epigenetic mechanisms (DNA methylation and histone post-translational modification-based gene expression regulation, and miRNA-mediated translational regulation) drive aspects of stromal cell phenotype, and discuss the implications of these findings for treatment of malignancies. We also summarize the effects of epigenetic mechanism-targeted drugs on stromal cells and discuss the consideration of the microenvironment response in attempts to use these drugs for cancer treatment.
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Affiliation(s)
- David L Marks
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Rachel Lo Olson
- Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,University of Minnesota Rochester, Rochester, MN 55904, USA
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A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming. Nat Microbiol 2016; 1:16174. [PMID: 27694949 PMCID: PMC5066596 DOI: 10.1038/nmicrobiol.2016.174] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 08/17/2016] [Indexed: 12/20/2022]
Abstract
The mechanisms by which pathogens evade elimination without affecting host fitness are not well understood. For the pathogen Pseudomonas aeruginosa, this evasion appears to be triggered by excretion of the quorum sensing (QS) molecule 2-aminoacetophenone (2-AA), which dampens host immune responses and modulates host metabolism, thereby enabling the bacteria to persist at a high burden level. Here, we examined how 2-AA trains host tissues to become tolerant to a high bacterial burden, without compromising host fitness. We found that 2-AA regulates histone deacetylase1 (HDAC1) expression and activity, resulting in hypoacetylation of lysine 18 of histone H3 (H3K18) at pro-inflammatory cytokine loci. Specifically, 2-AA induced reprogramming of immune cells occurs via alterations in histone acetylation of immune cytokines in vivo and in vitro. This host epigenetic reprograming, which was maintained for up to 7 days, dampened host responses to subsequent exposure to 2-AA or other pathogen-associated molecules. The process was found to involve a distinct molecular mechanism of host chromatin regulation. Inhibition of HDAC1 prevented the immunomodulatory effects of 2-AA. These observations provide the first mechanistic example of a QS molecule regulating a host epigenome to enable tolerance of infection. These insights have enormous potential for developing preventive treatments against bacterial infections.
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46
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Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics 2016; 11:750-760. [PMID: 27672717 PMCID: PMC5094631 DOI: 10.1080/15592294.2016.1221569] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the NLR family, CARD domain containing gene 5 (NLRC5), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = −6.03, Pnominal = 4.96 × 10−9; cg16411857: t = −7.63, Pnominal = 3.07 × 10−13). Hypomethylation of these 2 CpGs was replicated in an independent sample (GSE67705: cg07839457: t = −4.44, Pnominal = 1.61 × 10−5; cg16411857: t = −5.90; P = 1.99 × 10−8). Methylation of these 2 CpGs in NLRC5 was negatively correlated with viral load in the 2 HIV-infected samples (cg07839457: P = 1.8 × 10−4; cg16411857: P = 0.03 in the VACS; and cg07839457: P = 0.04; cg164111857: P = 0.01 in GSE53840). Our findings demonstrate that differential DNA methylation is associated with HIV infection and suggest the involvement of a novel host gene, NLRC5, in HIV pathogenesis.
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Affiliation(s)
- Xinyu Zhang
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Amy C Justice
- c Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System , West Haven , CT , USA
| | - Ying Hu
- d Center for Biomedical Informatics & Information Technology, National Cancer Institute , Bethesda , MD , USA
| | - Zuoheng Wang
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Hongyu Zhao
- f Department of Biostatistics , Yale School of Public Health , New Haven , CT , USA
| | - Guilin Wang
- g Yale Center of Genomic Analysis, West Campus , Orange , CT , USA
| | - Eric O Johnson
- h Fellow Program and Behavioral Health and Criminal Justice Division, RTI International , Research Triangle Park, NC , USA
| | - Brinda Emu
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Richard E Sutton
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - John H Krystal
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Ke Xu
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
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47
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Angrisano T, Pero R, Brancaccio M, Coretti L, Florio E, Pezone A, Calabrò V, Falco G, Keller S, Lembo F, Avvedimento VE, Chiariotti L. Cyclical DNA Methylation and Histone Changes Are Induced by LPS to Activate COX-2 in Human Intestinal Epithelial Cells. PLoS One 2016; 11:e0156671. [PMID: 27253528 PMCID: PMC4890762 DOI: 10.1371/journal.pone.0156671] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 05/18/2016] [Indexed: 01/26/2023] Open
Abstract
Bacterial lipopolysaccharide (LPS) induces release of inflammatory mediators both in immune and epithelial cells. We investigated whether changes of epigenetic marks, including selected histone modification and DNA methylation, may drive or accompany the activation of COX-2 gene in HT-29 human intestinal epithelial cells upon exposure to LPS. Here we describe cyclical histone acetylation (H3), methylation (H3K4, H3K9, H3K27) and DNA methylation changes occurring at COX-2 gene promoter overtime after LPS stimulation. Histone K27 methylation changes are carried out by the H3 demethylase JMJD3 and are essential for COX-2 induction by LPS. The changes of the histone code are associated with cyclical methylation signatures at the promoter and gene body of COX-2 gene.
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Affiliation(s)
- Tiziana Angrisano
- Dipartimento di Biologia, Università degli Studi di Napoli “Federico II”, Monte Sant'Angelo via Cintia 21, 80126 Naples, Italy
- * E-mail: (TA); (LC)
| | - Raffaela Pero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
| | - Mariarita Brancaccio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
| | - Lorena Coretti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
| | - Ermanno Florio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
| | - Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
| | - Viola Calabrò
- Dipartimento di Biologia, Università degli Studi di Napoli “Federico II”, Monte Sant'Angelo via Cintia 21, 80126 Naples, Italy
| | - Geppino Falco
- Dipartimento di Biologia, Università degli Studi di Napoli “Federico II”, Monte Sant'Angelo via Cintia 21, 80126 Naples, Italy
| | - Simona Keller
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
| | - Francesca Lembo
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, via D. Montesano 47, 80131 Naples, Italy
| | | | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, via S. Pansini, 5, 80131 Naples, Italy
- Istituto di Endocrinologia ed Oncologia Sperimentale C.N.R., via S. Pansini, 5, 80131 Naples, Italy
- * E-mail: (TA); (LC)
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48
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North JR, Takenaka S, Rozek A, Kielczewska A, Opal S, Morici LA, Finlay BB, Schaber CJ, Straube R, Donini O. A novel approach for emerging and antibiotic resistant infections: Innate defense regulators as an agnostic therapy. J Biotechnol 2016; 226:24-34. [PMID: 27015977 DOI: 10.1016/j.jbiotec.2016.03.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 03/15/2016] [Accepted: 03/21/2016] [Indexed: 01/08/2023]
Abstract
Innate Defense Regulators (IDRs) are short synthetic peptides that target the host innate immune system via an intracellular adaptor protein which functions at key signaling nodes. In this work, further details of the mechanism of action of IDRs have been discovered. The studies reported here show that the lead clinical IDR, SGX94, has broad-spectrum activity against Gram-negative and Gram-positive bacterial infections caused by intracellular or extracellular bacteria and also complements the actions of standard of care antibiotics. Based on in vivo and primary cell culture studies, this activity is shown to result from the primary action of SGX94 on tissue-resident cells and subsequent secondary signaling to activate myeloid-derived cells, resulting in enhanced bacterial clearance and increased survival. Data from non-clinical and clinical studies also show that SGX94 treatment modulates pro-inflammatory and anti-inflammatory cytokine levels, thereby mitigating the deleterious inflammatory consequences of innate immune activation. Since they act through host pathways to provide both broad-spectrum anti-infective capability as well as control of inflammation, IDRs are unlikely to be impacted by resistance mechanisms and offer potential clinical advantages in the fight against emerging and antibiotic resistant bacterial infections.
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Affiliation(s)
- John R North
- Inimex Pharmaceuticals Inc., 8540 Baxter Place, Burnaby, BC V5A 4T8, Canada
| | - Shunsuke Takenaka
- Inimex Pharmaceuticals Inc., 8540 Baxter Place, Burnaby, BC V5A 4T8, Canada
| | - Annett Rozek
- Inimex Pharmaceuticals Inc., 8540 Baxter Place, Burnaby, BC V5A 4T8, Canada
| | | | - Steven Opal
- The Warren Alpert Medical School of Brown University, Pawtucket, RI 02912, United States
| | - Lisa A Morici
- Tulane University School of Medicine, 1430 Tulane Avenue #8010, New Orleans, LA 70112, United States
| | - B Brett Finlay
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Richard Straube
- Soligenix Inc., 29 Emmons Drive, Suite C-10, Princeton, NJ, 08540, United States
| | - Oreola Donini
- Inimex Pharmaceuticals Inc., 8540 Baxter Place, Burnaby, BC V5A 4T8, Canada; Soligenix Inc., 29 Emmons Drive, Suite C-10, Princeton, NJ, 08540, United States.
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49
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Scully EP, Lockhart A, Garcia-Beltran W, Palmer CD, Musante C, Rosenberg E, Allen TM, Chang JJ, Bosch RJ, Altfeld M. Innate immune reconstitution with suppression of HIV-1. JCI Insight 2016; 1:e85433. [PMID: 27158667 DOI: 10.1172/jci.insight.85433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Progressive HIV-1 infection leads to both profound immune suppression and pathologic inflammation in the majority of infected individuals. While adaptive immune dysfunction, as evidenced by CD4+ T cell depletion and exhaustion, has been extensively studied, less is known about the functional capacity of innate immune cell populations in the context of HIV-1 infection. Given the broad susceptibility to opportunistic infections and the dysregulated inflammation observed in progressive disease, we hypothesized that there would be significant changes in the innate cellular responses. Using a cohort of patients with multiple samplings before and after antiretroviral therapy (ART) initiation, we demonstrated increased responses to innate immune stimuli following viral suppression, as measured by the production of inflammatory cytokines. Plasma viral load itself had the strongest association with this change in innate functional capacity. We further identified epigenetic modifications in the TNFA promoter locus in monocytes that are associated with viremia, suggesting a molecular mechanism for the observed changes in innate immune function following initiation of ART. These data indicate that suppression of HIV-1 viremia is associated with changes in innate cellular function that may in part determine the restoration of protective immune responses.
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Affiliation(s)
- Eileen P Scully
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ainsley Lockhart
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Wilfredo Garcia-Beltran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Christine D Palmer
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Chelsey Musante
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Todd M Allen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - J Judy Chang
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Ronald J Bosch
- Harvard School of Public Health, Boston, Massachusetts, USA
| | - Marcus Altfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA; Heinrich-Pette-Institut, Hamburg, Germany
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50
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Jones W, Bianchi K. Aerobic glycolysis: beyond proliferation. Front Immunol 2015; 6:227. [PMID: 26029212 PMCID: PMC4432802 DOI: 10.3389/fimmu.2015.00227] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/28/2015] [Indexed: 11/13/2022] Open
Abstract
Aerobic glycolysis has been generally associated with cancer cell proliferation, but fascinating and novel data show that it is also coupled to a series of further cellular functions. In this Mini Review, we will discuss some recent findings to illustrate newly defined roles for this process, in particular in non-malignant cells, supporting the idea that metabolism can be considered as an integral part of cellular signaling. Consequently, metabolism should be regarded as a plastic and highly dynamic determinant of a wide range of cellular specific functions.
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Affiliation(s)
- William Jones
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Katiuscia Bianchi
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London , London , UK
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