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Martino D, Schultz N, Kaur R, van Haren SD, Kresoje N, Hoch A, Diray-Arce J, Su JL, Levy O, Pichichero M. Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways. Clin Epigenetics 2024; 16:85. [PMID: 38961479 PMCID: PMC11223352 DOI: 10.1186/s13148-024-01703-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunizations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripheral blood mononuclear cells from respiratory infection allergy/asthma-prone (IAP) infants and non-infection allergy/asthma prone (NIAP) were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fisher's exact p-value = 0.02). RESULTS An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPL), a TLR agonist, partially reversed this signature at a subset of CpGs, suggesting the potential for epigenetic remodeling. CONCLUSIONS This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for future investigation.
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Affiliation(s)
- David Martino
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - Nikki Schultz
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ravinder Kaur
- Centre for Infectious Disease and Vaccine Immunology, Research Institute, Rochester General Hospital, 1425 Portland Avenue, Rochester, NY, 14621, USA
| | - Simon D van Haren
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Nina Kresoje
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Annmarie Hoch
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Jessica Lasky Su
- Channing Division of Network Medicine and Harvard Medical School, Boston, MA, 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
- Channing Division of Network Medicine and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Michael Pichichero
- Centre for Infectious Disease and Vaccine Immunology, Research Institute, Rochester General Hospital, 1425 Portland Avenue, Rochester, NY, 14621, USA
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Martino D, Schultz N, Kaur R, Haren SD, Kresoje N, Hoch A, Diray-Arce J, Lasky Su J, Levy O, Pichichero M. Respiratory Infection- and Asthma-prone, Low Vaccine Responder Children Demonstrate Distinct Mononuclear Cell DNA Methylation Pathways. RESEARCH SQUARE 2024:rs.3.rs-4160354. [PMID: 38645021 PMCID: PMC11030504 DOI: 10.21203/rs.3.rs-4160354/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunisations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripharal immune cells from respiratory infection allergy/asthma prone (IAP) infants were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fishers Exact p-value = 0.01). Results An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPLA), a TLR agonist, partially reversing this signature at a subset of CpGs, suggesting the potential for epigenetic remodelling. Conclusions This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for furture investigation.
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Zhu Z, Li Y, Freishtat RJ, Celedón JC, Espinola JA, Harmon B, Hahn A, Camargo CA, Liang L, Hasegawa K. Epigenome-wide association analysis of infant bronchiolitis severity: a multicenter prospective cohort study. Nat Commun 2023; 14:5495. [PMID: 37679381 PMCID: PMC10485022 DOI: 10.1038/s41467-023-41300-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
Bronchiolitis is the most common lower respiratory infection in infants, yet its pathobiology remains unclear. Here we present blood DNA methylation data from 625 infants hospitalized with bronchiolitis in a 17-center prospective study, and associate them with disease severity. We investigate differentially methylated CpGs (DMCs) for disease severity. We characterize the DMCs based on their association with cell and tissues types, biological pathways, and gene expression. Lastly, we also examine the relationships of severity-related DMCs with respiratory and immune traits in independent cohorts. We identify 33 DMCs associated with severity. These DMCs are differentially methylated in blood immune cells. These DMCs are also significantly enriched in multiple tissues (e.g., lung) and cells (e.g., small airway epithelial cells), and biological pathways (e.g., interleukin-1-mediated signaling). Additionally, these DMCs are associated with respiratory and immune traits (e.g., asthma, lung function, IgE levels). Our study suggests the role of DNA methylation in bronchiolitis severity.
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Affiliation(s)
- Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Yijun Li
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
- Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Infectious Diseases, Children's National Hospital, Washington, DC, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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4
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Pischedda S, Rivero-Calle I, Gómez-Carballa A, Cebey-López M, Barral-Arca R, Gómez-Rial J, Pardo-Seco J, Curras-Tuala MJ, Viz-Lasheras S, Bello X, Crujeiras AB, Diaz-Lagares A, González-López MT, Martinón-Torres F, Salas A. Role and Diagnostic Performance of Host Epigenome in Respiratory Morbidity after RSV Infection: The EPIRESVi Study. Front Immunol 2022; 13:875691. [PMID: 35619695 PMCID: PMC9128527 DOI: 10.3389/fimmu.2022.875691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) infection has been associated with the subsequent development of recurrent wheezing and asthma, although the mechanisms involved are still unknown. We investigate the role of epigenetics in the respiratory morbidity after infection by comparing methylation patterns from children who develop recurrent wheezing (RW-RSV), subsequent asthma (AS-RVS), and those experiencing complete recovery (CR-RSV). Methods Prospective, observational study of infants aged < 2 years with RSV respiratory infection admitted to hospital and followed-up after discharge for at least three years. According to their clinical course, patients were categorized into subgroups: RW-RSV (n = 36), AS-RSV (n = 9), and CR-RSV (n = 32). The DNA genome-wide methylation pattern was analyzed in whole blood samples, collected during the acute phase of the infection, using the Illumina Infinium Methylation EPIC BeadChip (850K CpG sites). Differences in methylation were determined through a linear regression model adjusted for age, gender and cell composition. Results Patients who developed respiratory sequelae showed a statistically significant higher proportion of NK and CD8T cells (inferred through a deconvolution approach) than those with complete recovery. We identified 5,097 significant differentially methylated positions (DMPs) when comparing RW-RSV and AS-RVS together against CR-RSV. Methylation profiles affect several genes involved in airway inflammation processes. The most significant DMPs were found to be hypomethylated in cases and therefore generally leading to overexpression of affected genes. The lead CpG position (cg24509398) falls at the gene body of EYA3 (P-value = 2.77×10-10), a tyrosine phosphatase connected with pulmonary vascular remodeling, a key process in the asthma pathology. Logistic regression analysis resulted in a diagnostic epigenetic signature of 3-DMPs (involving genes ZNF2698, LOC102723354 and RPL15/NKIRAS1) that allows to efficiently differentiate sequelae cases from CR-RSV patients (AUC = 1.00). Enrichment pathway analysis reveals the role of the cell cycle checkpoint (FDR P-value = 4.71×10-2), DNA damage (FDP-value = 2.53×10-2), and DNA integrity checkpoint (FDR P-value = 2.56×10-2) in differentiating sequelae from CR-RSV patients. Conclusions Epigenetic mechanisms might play a fundamental role in the long-term sequelae after RSV infection, contributing to explain the different phenotypes observed.
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Affiliation(s)
- Sara Pischedda
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain
| | - Jose Gómez-Rial
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - María-José Curras-Tuala
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto De Investigación Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro De Investigación Biomédica En Red Fisiopatología De La Obesidad Y Nutrición (Ciberobn), Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Epigenomics Unit, Translational Medical Oncology (Oncomet), Instituto De Investigación Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS/SERGAS), Santiago De Compostela, Spain.,Centro De Investigación Biomédica En Red Cancer (CIBERONC), Madrid, Spain
| | | | - Federico Martinón-Torres
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Antonio Salas
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Santiago de Compostela, Spain.,GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.,Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
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Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
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Differential Analysis and Putative Roles of Genes, Cytokines and Apoptotic Proteins in Blood Samples of Patients with Respiratory Viral Infections: A Single Center Study. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insights into the molecular pathogenesis of respiratory viral infections were investigated using serum and peripheral blood from patients with clinical syndromes. Signatures of expression of cytokines, genes and apoptotic proteins that discriminate symptomatic individuals from healthy individuals were determined among 21 patients. In symptomatic patients, significant upregulation of IL-1β, IL-2, IL-4, IL-6, IL-8, IL-12, IL-15, TNF-a and IFN-g (P<0.05) was noted, while IL-10 was significantly downregulated (P<0.05). This is accompanied by either up or down-regulation of various pro-apoptotic and anti-apoptotic markers, suggesting a protective role of immune responses against viral infection and the capacity of viruses to subvert host cell apoptosis. Gene expression analysis for both T and B cells were categorized according to their functional status of activation, proliferation, and differentiation. Of note, genes SH2D1A and TCL1A were upregulated only in rhinovirus samples, while PSMB7, CD4, CD8A, HLA-DMA, HLA-DRA and CD69 were upregulated in samples of Flu A and RSV but were not significant in samples of rhinovirus as compared to healthy individuals. These results demonstrated Flu A and RSV elicit different alterations in human peripheral blood gene expression as compared to rhinovirus. Overall, despite the small number of study subjects, the current study for the first time has recognized signature genes, cytokines and proteins that are used by some respiratory viruses that may serve as candidates for rapid diagnosis as well as targets for therapeutic interventions.
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7
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Decoding Susceptibility to Respiratory Viral Infections and Asthma Inception in Children. Int J Mol Sci 2020; 21:ijms21176372. [PMID: 32887352 PMCID: PMC7503410 DOI: 10.3390/ijms21176372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/19/2023] Open
Abstract
Human Respiratory Syncytial Virus and Human Rhinovirus are the most frequent cause of respiratory tract infections in infants and children and are major triggers of acute viral bronchiolitis, wheezing and asthma exacerbations. Here, we will discuss the application of the powerful tools of systems biology to decode the molecular mechanisms that determine risk for infection and subsequent asthma. An important conceptual advance is the understanding that the innate immune system is governed by a Bow-tie architecture, where diverse input signals converge onto a few core pathways (e.g., IRF7), which in turn generate diverse outputs that orchestrate effector and regulatory functions. Molecular profiling studies in children with severe exacerbations of asthma/wheeze have identified two major immunological phenotypes. The IRF7hi phenotype is characterised by robust upregulation of antiviral response networks, and the IRF7lo phenotype is characterised by upregulation of markers of TGFβ signalling and type 2 inflammation. Similar phenotypes have been identified in infants and children with severe viral bronchiolitis. Notably, genome-wide association studies supported by experimental validation have identified key pathways that increase susceptibility to HRV infection (ORMDL3 and CHDR3) and modulate TGFβ signalling (GSDMB, TGFBR1, and SMAD3). Moreover, functional deficiencies in the activation of type I and III interferon responses are already evident at birth in children at risk of developing febrile lower respiratory tract infections and persistent asthma/wheeze, suggesting that the trajectory to asthma begins at birth or in utero. Finally, exposure to microbes and their products reprograms innate immunity and provides protection from the development of allergies and asthma in children, and therefore microbial products are logical candidates for the primary prevention of asthma.
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8
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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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9
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Abstract
PURPOSE OF REVIEW Allergic diseases are prototypic examples for gene × environment-wide interactions. This review considers the current evidence for genetic and epigenetic mechanisms in allergic diseases and highlights barriers and facilitators for the implementation of these novel tools both for research and clinical practice. RECENT FINDINGS The value of whole-genome sequencing studies and the use of polygenic risk score analysis in homogeneous well characterized populations are currently being tested. Epigenetic mechanisms are known to play a crucial role in the pathogenesis of allergic disorders, especially through mediating the effects of the environmental factors, well recognized risk modifiers. There is emerging evidence for the immune-modulatory role of probiotics through epigenetic changes. Direct or indirect targeting of epigenetic mechanisms affect expression of the genes favouring the development of allergic diseases and can improve tissue biology. The ability to specifically edit the epigenome, especially using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes. SUMMARY Additional research in the role of genetic and epigenetic mechanisms in relation to allergic diseases' endotypes is needed. An international project characterizing the human epigenome in relation to allergic diseases is warranted.
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10
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Fonseca W, Lukacs NW, Ptaschinski C. Factors Affecting the Immunity to Respiratory Syncytial Virus: From Epigenetics to Microbiome. Front Immunol 2018. [PMID: 29515570 PMCID: PMC5825926 DOI: 10.3389/fimmu.2018.00226] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a common pathogen that infects virtually all children by 2 years of age and is the leading cause of hospitalization of infants worldwide. While most children experience mild symptoms, some children progress to severe lower respiratory tract infection. Those children with severe disease have a much higher risk of developing childhood wheezing later in life. Many risk factors are known to result in exacerbated disease, including premature birth and early age of RSV infection, when the immune system is relatively immature. The development of the immune system before and after birth may be altered by several extrinsic and intrinsic factors that could lead to severe disease predisposition in children who do not exhibit any currently known risk factors. Recently, the role of the microbiome and the resulting metabolite profile has been an area of intense study in the development of lung disease, including viral infection and asthma. This review explores both known risk factors that can lead to severe RSV-induced disease as well as emerging topics in the development of immunity to RSV and the long-term consequences of severe infection.
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Affiliation(s)
- Wendy Fonseca
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States.,University of Michigan, Mary H. Weiser Food Allergy Center, Ann Arbor, MI, United States
| | - Catherine Ptaschinski
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States.,University of Michigan, Mary H. Weiser Food Allergy Center, Ann Arbor, MI, United States
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