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Jiang G, Zou Y, Zhao D, Yu J. Optimising vaccine immunogenicity in ageing populations: key strategies. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(24)00497-3. [PMID: 39326424 DOI: 10.1016/s1473-3099(24)00497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/17/2024] [Accepted: 07/25/2024] [Indexed: 09/28/2024]
Abstract
Vaccination has been shown to be the most effective means of preventing infectious diseases, although older people commonly have a suboptimal immune response to vaccines and thus impaired protection against subsequent adverse outcomes. This Review provides an overview of the existing mechanistic insights into compromised vaccine response for respiratory infectious diseases in older people, defined as aged 65 years and older, including immunosenescence, epigenetic regulation, trained immunity, and gut microbiota. We further summarise the latest proven or potential strategies to strengthen weakened immunogenicity. Insights from these analyses will be conducive to the development of the next generation of vaccines.
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Affiliation(s)
- Guangzhen Jiang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yushu Zou
- Department of Biomedical Informatics, School of Basic Medical Sciences and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences and State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China.
| | - Jingyou Yu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China.
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2
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Kwiatkowska KM, Anticoli S, Salvioli S, Calzari L, Gentilini D, Albano C, Di Prinzio RR, Zaffina S, Carsetti R, Ruggieri A, Garagnani P. B Cells Isolated from Individuals Who Do Not Respond to the HBV Vaccine Are Characterized by Higher DNA Methylation-Estimated Aging Compared to Responders. Vaccines (Basel) 2024; 12:880. [PMID: 39204006 PMCID: PMC11360008 DOI: 10.3390/vaccines12080880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 09/03/2024] Open
Abstract
Healthcare workers (HCWs) are a high-risk group for hepatitis B virus (HBV) infection. Notably, about 5-10% of the general population does not respond to the HBV vaccination. In this study, we aimed to investigate DNA methylation (DNAm) in order to estimate the biological age of B cells from HCW of both sexes, either responder (R) or non-responder (NR), to HBV vaccination. We used genome-wide DNA methylation data to calculate a set of biomarkers in B cells collected from 41 Rs and 30 NRs between 22 and 62 years old. Unresponsiveness to HBV vaccination was associated with accelerated epigenetic aging (DNAmAge, AltumAge, DunedinPoAm) and was accompanied by epigenetic drift. Female non-responders had higher estimates of telomere length and lower CRP inflammation risk score when compared to responders. Overall, epigenetic differences between responders and non-responders were more evident in females than males. In this study we demonstrated that several methylation DNAm-based clocks and biomarkers are associated with an increased risk of non-response to HBV vaccination, particularly in females. Based on these results, we propose that accelerated epigenetic age could contribute to vaccine unresponsiveness. These insights may help improve the evaluation of the effectiveness of vaccination strategies, especially among HCWs and vulnerable patients.
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Affiliation(s)
| | - Simona Anticoli
- Istituto Superiore di Sanità, Center for Gender Specific Medicine, 00161 Rome, Italy; (S.A.); (A.R.)
| | - Stefano Salvioli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
- IRCCS Azienda Ospedaliero, Universitaria di Bologna, 40138 Bologna, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy; (L.C.)
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy; (L.C.)
- Department of Brain and Behavioral Sciences, Università di Pavia, 27100 Pavia, Italy
| | - Christian Albano
- Immunology Research Area, B Cell Unit, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy (R.C.)
| | - Reparata Rosa Di Prinzio
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy (S.Z.)
| | - Salvatore Zaffina
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy (S.Z.)
| | - Rita Carsetti
- Immunology Research Area, B Cell Unit, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy (R.C.)
| | - Anna Ruggieri
- Istituto Superiore di Sanità, Center for Gender Specific Medicine, 00161 Rome, Italy; (S.A.); (A.R.)
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
- IRCCS Azienda Ospedaliero, Universitaria di Bologna, 40138 Bologna, Italy
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3
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Fu H, Pickering H, Rubbi L, Ross TM, Reed EF, Pellegrini M. Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation. Sci Rep 2024; 14:1455. [PMID: 38228690 PMCID: PMC10791625 DOI: 10.1038/s41598-024-51665-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024] Open
Abstract
Influenza virus infection alters the promoter DNA methylation of key immune response-related genes, including type-1 interferons and proinflammatory cytokines. However, less is known about the effect of the influenza vaccine on the epigenome. We utilized a targeted DNA methylation approach to study the longitudinal effects (day 0 pre-vaccination and day 28 post-vaccination) on influenza vaccination responses in peripheral blood mononuclear cells. We found that baseline, pre-vaccination methylation profiles are associated with pre-existing, protective serological immunity. Additionally, we identified 481 sites that were differentially methylated between baseline and day 28 post-vaccination. These were enriched for genes involved in the regulation of the RIG-I signaling pathway, an important regulator of viral responses. Our results suggest that DNA methylation changes to components of the RIG-I pathway are associated with vaccine effectiveness. Therefore, immunization strategies that target this pathway may improve serological responses to influenza vaccination.
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Affiliation(s)
- Hongxiang Fu
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Ted M Ross
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
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4
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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5
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Batista-Roche JL, Gómez-Gil B, Lund G, Berlanga-Robles CA, García-Gasca A. Global m6A RNA Methylation in SARS-CoV-2 Positive Nasopharyngeal Samples in a Mexican Population: A First Approximation Study. EPIGENOMES 2022; 6:epigenomes6030016. [PMID: 35893012 PMCID: PMC9326742 DOI: 10.3390/epigenomes6030016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/11/2022] [Accepted: 06/20/2022] [Indexed: 02/05/2023] Open
Abstract
The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causal agent of COVID-19 (Coronavirus Disease-19). Both mutation and/or recombination events in the SARS-CoV-2 genome have resulted in variants that differ in transmissibility and severity. Furthermore, RNA methylation of the N6 position of adenosine (m6A) is known to be altered in cells infected with SARS-CoV-2. However, it is not known whether this epitranscriptomic modification differs across individuals dependent on the presence of infection with distinct SARS-CoV-2 variants, the viral load, or the vaccination status. To address this issue, we selected RNAs (n = 60) from SARS-CoV-2 sequenced nasopharyngeal samples (n = 404) of 30- to 60-year-old outpatients or hospitalized individuals from the city of Mazatlán (Mexico) between February 2021 and March 2022. Control samples were non-infected individuals (n = 10). SARS-CoV-2 was determined with real-time PCR, viral variants were determined with sequencing, and global m6A levels were determined by using a competitive immunoassay method. We identified variants of concern (VOC; alpha, gamma, delta, omicron), the variant of interest (VOI; epsilon), and the lineage B.1.1.519. Global m6A methylation differed significantly across viral variants (p = 3.2 × 10−7). In particular, we found that m6A levels were significantly lower in the VOC delta- and omicron-positive individuals compared to non-infected individuals (p = 2.541236 × 10−2 and 1.134411 × 10−4, respectively). However, we uncovered no significant correlation between global m6A levels and viral nucleocapsid (N) gene expression or age. Furthermore, individuals with complete vaccination schemes showed significantly lower m6A levels than unvaccinated individuals (p = 2.6 × 10−4), and differences in methylation levels across variants in unvaccinated individuals were significant (p = 3.068 × 10−3). These preliminary results suggest that SARS-CoV-2 variants show differences in global m6A levels.
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Affiliation(s)
- Jorge Luis Batista-Roche
- Molecular and Cellular Biology, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
| | - Bruno Gómez-Gil
- Microbial Genomics, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
| | - Gertrud Lund
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato 36821, Mexico;
| | | | - Alejandra García-Gasca
- Molecular and Cellular Biology, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
- Correspondence: ; Tel.: +52-669-989-8700
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6
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Pang APS, Higgins-Chen AT, Comite F, Raica I, Arboleda C, Went H, Mendez T, Schotsaert M, Dwaraka V, Smith R, Levine ME, Ndhlovu LC, Corley MJ. Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination. Front Genet 2022; 13:819749. [PMID: 35719387 PMCID: PMC9203887 DOI: 10.3389/fgene.2022.819749] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/25/2022] [Indexed: 01/01/2023] Open
Abstract
The host epigenetic landscape rapidly changes during SARS-CoV-2 infection, and evidence suggest that severe COVID-19 is associated with durable scars to the epigenome. Specifically, aberrant DNA methylation changes in immune cells and alterations to epigenetic clocks in blood relate to severe COVID-19. However, a longitudinal assessment of DNA methylation states and epigenetic clocks in blood from healthy individuals prior to and following test-confirmed non-hospitalized COVID-19 has not been performed. Moreover, the impact of mRNA COVID-19 vaccines upon the host epigenome remains understudied. Here, we first examined DNA methylation states in the blood of 21 participants prior to and following test-confirmed COVID-19 diagnosis at a median time frame of 8.35 weeks; 756 CpGs were identified as differentially methylated following COVID-19 diagnosis in blood at an FDR adjusted p-value < 0.05. These CpGs were enriched in the gene body, and the northern and southern shelf regions of genes involved in metabolic pathways. Integrative analysis revealed overlap among genes identified in transcriptional SARS-CoV-2 infection datasets. Principal component-based epigenetic clock estimates of PhenoAge and GrimAge significantly increased in people over 50 following infection by an average of 2.1 and 0.84 years. In contrast, PCPhenoAge significantly decreased in people fewer than 50 following infection by an average of 2.06 years. This observed divergence in epigenetic clocks following COVID-19 was related to age and immune cell-type compositional changes in CD4+ T cells, B cells, granulocytes, plasmablasts, exhausted T cells, and naïve T cells. Complementary longitudinal epigenetic clock analyses of 36 participants prior to and following Pfizer and Moderna mRNA-based COVID-19 vaccination revealed that vaccination significantly reduced principal component-based Horvath epigenetic clock estimates in people over 50 by an average of 3.91 years for those who received Moderna. This reduction in epigenetic clock estimates was significantly related to chronological age and immune cell-type compositional changes in B cells and plasmablasts pre- and post-vaccination. These findings suggest the potential utility of epigenetic clocks as a biomarker of COVID-19 vaccine responses. Future research will need to unravel the significance and durability of short-term changes in epigenetic age related to COVID-19 exposure and mRNA vaccination.
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Affiliation(s)
- Alina P. S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Albert T. Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Florence Comite
- Comite Center for Precision Medicine & Health, New York, NY, United States
- Lenox Hill Hospital/Northwell, New York, NY, United States
| | - Ioana Raica
- Comite Center for Precision Medicine & Health, New York, NY, United States
| | | | | | | | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ryan Smith
- TruDiagnostic, Lexington, KY, United States
| | - Morgan E. Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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7
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de Mol J, Kuiper J, Tsiantoulas D, Foks AC. The Dynamics of B Cell Aging in Health and Disease. Front Immunol 2021; 12:733566. [PMID: 34675924 PMCID: PMC8524000 DOI: 10.3389/fimmu.2021.733566] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
Aging is considered to be an important risk factor for several inflammatory diseases. B cells play a major role in chronic inflammatory diseases by antibody secretion, antigen presentation and T cell regulation. Different B cell subsets have been implicated in infections and multiple autoimmune diseases. Since aging decreases B cell numbers, affects B cell subsets and impairs antibody responses, the aged B cell is expected to have major impacts on the development and progression of these diseases. In this review, we summarize the role of B cells in health and disease settings, such as atherosclerotic disease. Furthermore, we provide an overview of age-related changes in B cell development and function with respect to their impact in chronic inflammatory diseases.
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Affiliation(s)
- Jill de Mol
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Johan Kuiper
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | | | - Amanda C. Foks
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
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Abstract
Innate and adaptive immune responses decline with age, leading to greater susceptibility to infectious diseases and reduced responses to vaccines. Diseases are more severe in old than in young individuals and have a greater impact on health outcomes such as morbidity, disability, and mortality. Aging is characterized by increased low-grade chronic inflammation, so-called inflammaging, that represents a link between changes in immune cells and a number of diseases and syndromes typical of old age. In this review we summarize current knowledge on age-associated changes in immune cells with special emphasis on B cells, which are more inflammatory and less responsive to infections and vaccines in the elderly. We highlight recent findings on factors and pathways contributing to inflammaging and how these lead to dysfunctional immune responses. We summarize recent published studies showing that adipose tissue, which increases in size with aging, contributes to inflammaging and dysregulated B cell function.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA; .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.,Miami Integrative Metabolomics Research Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Alain Diaz
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Maria Romero
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Denisse Garcia
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA; .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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9
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Keshavarz M, Sabbaghi A, Koushki K, Miri SM, Sarshari B, Vahdat K, Ghaemi A. Epigenetic reprogramming mechanisms of immunity during influenza A virus infection. Microbes Infect 2021; 23:104831. [PMID: 33878459 DOI: 10.1016/j.micinf.2021.104831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
This paper reviews epigenetic mechanisms by which influenza viruses affect cellular gene activity to control their life cycles, aiming to provide new insights into the complexity of functional interactions between viral and cellular factors, as well as to introduce novel targets for therapeutic intervention and vaccine development against influenza infections.
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Affiliation(s)
- Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ailar Sabbaghi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Khadijeh Koushki
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Miri
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrang Sarshari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Katayoun Vahdat
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
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10
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Li PH, Zhang R, Cheng LQ, Liu JJ, Chen HZ. Metabolic regulation of immune cells in proinflammatory microenvironments and diseases during ageing. Ageing Res Rev 2020; 64:101165. [PMID: 32898718 DOI: 10.1016/j.arr.2020.101165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023]
Abstract
The process of ageing includes molecular changes within cells and interactions between cells, eventually resulting in age-related diseases. Although various cells (immune cells, parenchymal cells, fibroblasts and endothelial cells) in tissues secrete proinflammatory signals in age-related diseases, immune cells are the major contributors to inflammation. Many studies have emphasized the role of metabolic dysregulation in parenchymal cells in age-related inflammatory diseases. However, few studies have discussed metabolic modifications in immune cells during ageing. In this review, we introduce the metabolic dysregulation of major nutrients (glucose, lipids, and amino acids) within immune cells during ageing, which leads to dysfunctional NAD + metabolism that increases immune cell senescence and leads to the acquisition of the corresponding senescence-associated secretory phenotype (SASP). We then focus on senescent immune cell interactions with parenchymal cells and the extracellular matrix and their involvement in angiogenesis, which lead to proinflammatory microenvironments in tissues and inflammatory diseases at the systemic level. Elucidating the roles of metabolic modifications in immune cells during ageing will provide new insights into the mechanisms of ageing and therapeutic directions for age-related inflammatory diseases.
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Affiliation(s)
- Pei-Heng Li
- Department of Internal Medicine, Peking Union Medical college Hospital, Beijing, China; State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ran Zhang
- Buck Institute for Research on Ageing, Novato, United States
| | - Li-Qin Cheng
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Jin-Jing Liu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Beijing, China.
| | - Hou-Zao Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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11
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Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock RE, Koff WC, Kollmann TR, Sadarangani M, Lee AHY. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front Immunol 2020; 11:578801. [PMID: 33329547 PMCID: PMC7734088 DOI: 10.3389/fimmu.2020.578801] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Vaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts. Methods We applied cutting edge multi-omics approaches to extensively characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final HBV antibody titres. Results Using both an unsupervised molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Biological associations were unravelled, with signalling pathways such as JAK-STAT and interleukin signalling, Toll-like receptor cascades, interferon signalling, and Th17 cell differentiation emerging as important pre-vaccination modulators of response. Conclusion This study provides further evidence that baseline cellular and molecular characteristics of an individual's immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.
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Affiliation(s)
- Casey P. Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rachel D. Edgar
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Queenie Chan
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Kim-Anh Le Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, CA, United States
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Robert E.W. Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | | | - Tobias R. Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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12
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Frasca D, Blomberg BB. Aging induces B cell defects and decreased antibody responses to influenza infection and vaccination. IMMUNITY & AGEING 2020; 17:37. [PMID: 33292323 PMCID: PMC7674578 DOI: 10.1186/s12979-020-00210-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Background Aging is characterized by a progressive decline in the capacity of the immune system to fight influenza virus infection and to respond to vaccination. Among the several factors involved, in addition to increased frailty and high-risk conditions, the age-associated decrease in cellular and humoral immune responses plays a relevant role. This is in large part due to inflammaging, the chronic low-grade inflammatory status of the elderly, associated with intrinsic inflammation of the immune cells and decreased immune function. Results Aging is usually associated with reduced influenza virus-specific and influenza vaccine-specific antibody responses but some elderly individuals with higher pre-exposure antibody titers, due to a previous infection or vaccination, have less probability to get infected. Examples of this exception are the elderly individuals infected during the 2009 pandemic season who made antibodies with broader epitope recognition and higher avidity than those made by younger individuals. Several studies have allowed the identification of B cell intrinsic defects accounting for sub-optimal antibody responses of elderly individuals. These defects include 1) reduced class switch recombination, responsible for the generation of a secondary response of class switched antibodies, 2) reduced de novo somatic hypermutation of the antibody variable region, 3) reduced binding and neutralization capacity, as well as binding specificity, of the secreted antibodies, 4) increased epigenetic modifications that are associated with lower antibody responses, 5) increased frequencies of inflammatory B cell subsets, and 6) shorter telomeres. Conclusions Although influenza vaccination represents the most effective way to prevent influenza infection, vaccines with greater immunogenicity are needed to improve the response of elderly individuals. Recent advances in technology have made possible a broad approach to better understand the age-associated changes in immune cells, needed to design tailored vaccines and effective therapeutic strategies that will be able to improve the immune response of vulnerable individuals.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA.
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, RMSB 3146A, 1600 NW 10th Ave, Miami, FL, 33136, USA
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13
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Ciabattini A, Garagnani P, Santoro F, Rappuoli R, Franceschi C, Medaglini D. Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population. Semin Immunopathol 2020; 42:619-634. [PMID: 33159214 PMCID: PMC7646713 DOI: 10.1007/s00281-020-00821-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the vaccination of older people. The development of a vaccine against SARS-CoV-2 tailored for the elderly population faces the challenge of the poor immune responsiveness of the older population due to immunosenescence, comorbidities, and pharmacological treatments. Moreover, it is likely that the inflammaging phenotype associated with age could both influence vaccination efficacy and exacerbate the risk of COVID-19-related "cytokine storm syndrome" with an overlap between the factors which impact vaccination effectiveness and those that boost virulence and worsen the prognosis of SARS-CoV-2 infection. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. In the ongoing effort in vaccine development, different SARS-CoV-2 vaccine candidates have been developed, tested in pre-clinical and clinical studies and are undergoing clinical testing, but only a small fraction of these are currently being tested in the older fraction of the population. Recent advances in systems biology integrating clinical, immunologic, and omics data can help to identify stable and robust markers of vaccine response and move towards a better understanding of SARS-CoV-2 vaccine responses in the elderly.
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Affiliation(s)
- Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paolo Garagnani
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute at Huddinge University Hospital, SE-171 77, Stockholm, Sweden
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40139, Bologna, Italy
- Interdepartmental Centre 'L. Galvan' (CIG), University of Bologna, Via G. Petroni 26, 40139, Bologna, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rino Rappuoli
- GSK, Siena, Italy
- vAMRes Lab, Toscana Life Sciences, Siena, Italy
- Faculty of Medicine, Imperial College, London, UK
| | | | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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14
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Hernandez Puente CV, Hsu PC, Rogers LJ, Jousheghany F, Siegel E, Kadlubar SA, Beck JT, Makhoul I, Hutchins LF, Kieber-Emmons T, Monzavi-Karbassi B. Association of DNA-Methylation Profiles With Immune Responses Elicited in Breast Cancer Patients Immunized With a Carbohydrate-Mimicking Peptide: A Pilot Study. Front Oncol 2020; 10:879. [PMID: 32582547 PMCID: PMC7290046 DOI: 10.3389/fonc.2020.00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/04/2020] [Indexed: 02/04/2023] Open
Abstract
Immune response to a given antigen, particularly in cancer patients, is complex and is controlled by various genetic and environmental factors. Identifying biomarkers that can predict robust response to immunization is an urgent need in clinical cancer vaccine development. Given the involvement of DNA methylation in the development of lymphocytes, tumorigenicity and tumor progression, we aimed to analyze pre-vaccination DNA methylation profiles of peripheral blood mononuclear cells (PBMCs) from breast cancer subjects vaccinated with a novel peptide-based vaccine referred to as P10s-PADRE. This pilot study was performed to evaluate whether signatures of differentially methylated (DM) loci can be developed as potential predictive biomarkers for prescreening subjects with cancer who will most likely generate an immune response to the vaccine. Genomic DNA was isolated from PBMCs of eight vaccinated subjects, and their DNA methylation profiles were determined using Infinium® MethylationEPIC BeadChip array from Illumina. A linear regression model was applied to identify loci that were differentially methylated with respect to anti-peptide antibody titers and with IFN-γ production. The data were summarized using unsupervised-learning methods: hierarchical clustering and principal-component analysis. Pathways and networks involved were predicted by Ingenuity Pathway Analysis. We observed that the profile of DM loci separated subjects in regards to the levels of immune responses. Canonical pathways and networks related to metabolic and immunological functions were found to be involved. The data suggest that it is feasible to correlate methylation signatures in pre-treatment PBMCs with immune responses post-treatment in cancer patients going through standard-of-care chemotherapy. Larger and prospective studies that focus on DM loci in PBMCs is warranted to develop pre-screening biomarkers before BC vaccination. Clinical Trial Registration:www.ClinicalTrials.gov, Identifier: NCT02229084.
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Affiliation(s)
- Cinthia Violeta Hernandez Puente
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,UnivLyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Ping-Ching Hsu
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Lora J Rogers
- Division of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Fariba Jousheghany
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Eric Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Susan A Kadlubar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Issam Makhoul
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Hematology Oncology, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Laura F Hutchins
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Division of Hematology Oncology, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Thomas Kieber-Emmons
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Behjatolah Monzavi-Karbassi
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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15
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Bannister S, Messina NL, Novakovic B, Curtis N. The emerging role of epigenetics in the immune response to vaccination and infection: a systematic review. Epigenetics 2020; 15:555-593. [PMID: 31914857 PMCID: PMC7574386 DOI: 10.1080/15592294.2020.1712814] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
Extensive research has highlighted the role of infection-induced epigenetic events in the development of cancer. More recently, attention has focused on the ability of non-carcinogenic infections, as well as vaccines, to modify the human epigenome and modulate the immune response. This review explores this rapidly evolving area of investigation and outlines the many and varied ways in which vaccination and natural infection can influence the human epigenome from modulation of the innate and adaptive immune response, to biological ageing and modification of disease risk. The implications of these epigenetic changes on immune regulation and their potential application to the diagnosis and treatment of chronic infection and vaccine development are also discussed.
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Affiliation(s)
- Samantha Bannister
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
- Infectious Diseases Unit, Royal Children’s Hospital Melbourne, Parkville, Australia
| | - Nicole L. Messina
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
| | - Boris Novakovic
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Epigenetics Research Group, Murdoch Children’s Research Institute, Parkville, Australia
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
- Infectious Diseases Unit, Royal Children’s Hospital Melbourne, Parkville, Australia
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16
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Nishioka K, Daidoji T, Nakaya T. Demethylation around the transcriptional start site of the IFN-β gene induces IFN-β production and protection against influenza virus infection. Biochem Biophys Res Commun 2019; 520:269-276. [PMID: 31594636 DOI: 10.1016/j.bbrc.2019.09.136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/29/2019] [Indexed: 01/10/2023]
Abstract
Seasonal influenza is related to lifestyle-associated risk factors and it has been suggested that the epigenetic state of the individual plays an important role in the severity of infection. It is well known that epigenetics stringently regulate gene expression in each tissue and that aberrant epigenetic states can influence disease development. Despite some studies, limited information is available on changes in epigenetic states before and after influenza virus infection; in particular, it is unknown whether the epigenetic state at specific sites affects subsequent infection. Here, we analyzed CpG methylation states in clones derived from human primary small airway epithelial cells with the same genetic background but different viral replication rates. Our study revealed that demethylating CpGs downstream of the IFN-β transcription start site using a CRISPR/dCas9 system suppressed viral replication during subsequent influenza virus infection. Thus, our observations suggest that epigenome editing might provide adequate protection against the influenza virus.
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Affiliation(s)
- Keisuke Nishioka
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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