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Caldwell BA, Li L. Epigenetic regulation of innate immune dynamics during inflammation. J Leukoc Biol 2024; 115:589-606. [PMID: 38301269 PMCID: PMC10980576 DOI: 10.1093/jleuko/qiae026] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.
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Affiliation(s)
- Blake A. Caldwell
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
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2
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Li YY, Yuan MM, Li YY, Li S, Wang JD, Wang YF, Li Q, Li J, Chen RR, Peng JM, Du B. Cell-free DNA methylation reveals cell-specific tissue injury and correlates with disease severity and patient outcomes in COVID-19. Clin Epigenetics 2024; 16:37. [PMID: 38429730 PMCID: PMC10908074 DOI: 10.1186/s13148-024-01645-7] [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: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The recently identified methylation patterns specific to cell type allows the tracing of cell death dynamics at the cellular level in health and diseases. This study used COVID-19 as a disease model to investigate the efficacy of cell-specific cell-free DNA (cfDNA) methylation markers in reflecting or predicting disease severity or outcome. METHODS Whole genome methylation sequencing of cfDNA was performed for 20 healthy individuals, 20 cases with non-hospitalized COVID-19 and 12 cases with severe COVID-19 admitted to intensive care unit (ICU). Differentially methylated regions (DMRs) and gene ontology pathway enrichment analyses were performed to explore the locus-specific methylation difference between cohorts. The proportion of cfDNA derived from lung and immune cells to a given sample (i.e. tissue fraction) at cell-type resolution was estimated using a novel algorithm, which reflects lung injuries and immune response in COVID-19 patients and was further used to evaluate clinical severity and patient outcome. RESULTS COVID‑19 patients had globally reduced cfDNA methylation level compared with healthy controls. Compared with non-hospitalized COVID-19 patients, the cfDNA methylation pattern was significantly altered in severe patients with the identification of 11,156 DMRs, which were mainly enriched in pathways related to immune response. Markedly elevated levels of cfDNA derived from lung and more specifically alveolar epithelial cells, bronchial epithelial cells, and lung endothelial cells were observed in COVID-19 patients compared with healthy controls. Compared with non-hospitalized patients or healthy controls, severe COVID-19 had significantly higher cfDNA derived from B cells, T cells and granulocytes and lower cfDNA from natural killer cells. Moreover, cfDNA derived from alveolar epithelial cells had the optimal performance to differentiate COVID-19 with different severities, lung injury levels, SOFA scores and in-hospital deaths, with the area under the receiver operating characteristic curve of 0.958, 0.941, 0.919 and 0.955, respectively. CONCLUSION Severe COVID-19 has a distinct cfDNA methylation signature compared with non-hospitalized COVID-19 and healthy controls. Cell type-specific cfDNA methylation signature enables the tracing of COVID-19 related cell deaths in lung and immune cells at cell-type resolution, which is correlated with clinical severities and outcomes, and has extensive application prospects to evaluate tissue injuries in diseases with multi-organ dysfunction.
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Affiliation(s)
- Yuan-Yuan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Ming-Ming Yuan
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Yuan-Yuan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Shan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China
| | - Jing-Dong Wang
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Yu-Fei Wang
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Qian Li
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Jun Li
- Geneplus-Shenzhen, Building B, First Branch, Zhongcheng Life Science Park, Zhongxing Road, Kengzi Street, Pingshan District, Shenzhen, 518000, China
| | - Rong-Rong Chen
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China
| | - Jin-Min Peng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.
| | - Bin Du
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.
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3
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Krause C, Bergmann E, Schmidt SV. Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection. Mol Biol Rep 2024; 51:342. [PMID: 38400997 PMCID: PMC10894183 DOI: 10.1007/s11033-024-09266-2] [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: 11/29/2023] [Accepted: 01/18/2024] [Indexed: 02/26/2024]
Abstract
Myeloid cells play a vital role in innate immune responses as they recognize and phagocytose pathogens like viruses, present antigens, produce cytokines, recruit other immune cells to combat infections, and contribute to the attenuation of immune responses to restore homeostasis. Signal integration by pathogen recognition receptors enables myeloid cells to adapt their functions by a network of transcription factors and chromatin remodelers. This review provides a brief overview of the subtypes of myeloid cells and the main epigenetic regulation mechanisms. Special focus is placed on the epigenomic alterations in viral nucleic acids of HIV and SARS-CoV-2 along with the epigenetic changes in the host's myeloid cell compartment. These changes are important as they lead to immune suppression and promote the progression of the disease. Finally, we highlight some promising examples of 'epidrugs' that modulate the epigenome of immune cells and could be used as therapeutics for viral infections.
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Affiliation(s)
- Carolyn Krause
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
- Department of Microbiology and Immunology, the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Eva Bergmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany
| | - Susanne Viktoria Schmidt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127, Bonn, Germany.
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4
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García-delaTorre P, Rivero-Segura NA, Sánchez-García S, Becerril-Rojas K, Sandoval-Rodriguez FE, Castro-Morales D, Cruz-Lopez M, Vazquez-Moreno M, Rincón-Heredia R, Ramirez-Garcia P, Gomez-Verjan JC. GrimAge is elevated in older adults with mild COVID-19 an exploratory analysis. GeroScience 2024:10.1007/s11357-024-01095-2. [PMID: 38358578 DOI: 10.1007/s11357-024-01095-2] [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: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 has been contained; however, the side effects associated with its infection continue to be a challenge for public health, particularly for older adults. On the other hand, epigenetic status contributes to the inter-individual health status and is associated with COVID-19 severity. Nevertheless, current studies focus only on severe COVID-19. Considering that most of the worldwide population developed mild COVID-19 infection. In the present exploratory study, we aim to analyze the association of mild COVID-19 with epigenetic ages (HorvathAge, HannumAge, GrimAge, PhenoAge, SkinAge, and DNAmTL) and clinical variables obtained from a Mexican cohort of older adults. We found that all epigenetic ages significantly differ from the chronological age, but only GrimAge is elevated. Additionally, both the intrinsic epigenetic age acceleration (IEAA) and the extrinsic epigenetic age acceleration (EEAA) are accelerated in all patients. Moreover, we found that immunological estimators and DNA damage were associated with PhenoAge, SkinBloodHorvathAge, and HorvathAge, suggesting that the effects of mild COVID-19 on the epigenetic clocks are mainly associated with inflammation and immunology changes. In conclusion, our results show that the effects of mild COVID-19 on the epigenetic clock are mainly associated with the immune system and an increase in GrimAge, IEAA, and EEAA.
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Affiliation(s)
- Paola García-delaTorre
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | | | - Sergio Sánchez-García
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | | | | | - Diana Castro-Morales
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Miguel Cruz-Lopez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Ruth Rincón-Heredia
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Perla Ramirez-Garcia
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico.
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Naik N, Patel M, Sen R. Developmental Impacts of Epigenetics and Metabolism in COVID-19. J Dev Biol 2024; 12:9. [PMID: 38390960 PMCID: PMC10885083 DOI: 10.3390/jdb12010009] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Developmental biology is intricately regulated by epigenetics and metabolism but the mechanisms are not completely understood. The situation becomes even more complicated during diseases where all three phenomena are dysregulated. A salient example is COVID-19, where the death toll exceeded 6.96 million in 4 years, while the virus continues to mutate into different variants and infect people. Early evidence during the pandemic showed that the host's immune and inflammatory responses to COVID-19 (like the cytokine storm) impacted the host's metabolism, causing damage to the host's organs and overall physiology. The involvement of angiotensin-converting enzyme 2 (ACE2), the pivotal host receptor for the SARS-CoV-2 virus, was identified and linked to epigenetic abnormalities along with other contributing factors. Recently, studies have revealed stronger connections between epigenetics and metabolism in COVID-19 that impact development and accelerate aging. Patients manifest systemic toxicity, immune dysfunction and multi-organ failure. Single-cell multiomics and other state-of-the-art high-throughput studies are only just beginning to demonstrate the extent of dysregulation and damage. As epigenetics and metabolism directly impact development, there is a crucial need for research implementing cutting-edge technology, next-generation sequencing, bioinformatics analysis, the identification of biomarkers and clinical trials to help with prevention and therapeutic interventions against similar threats in the future.
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Affiliation(s)
- Noopur Naik
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Mansi Patel
- Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Rwik Sen
- Active Motif, Inc., Carlsbad, CA 92008, USA
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Lefkowitz RB, Miller CM, Martinez-Caballero JD, Ramos I. Epigenetic Control of Innate Immunity: Consequences of Acute Respiratory Virus Infection. Viruses 2024; 16:197. [PMID: 38399974 PMCID: PMC10893272 DOI: 10.3390/v16020197] [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: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by acute respiratory viruses induce a systemic innate immune response, which can be measured by the increased levels of expression of inflammatory genes in immune cells. There is growing evidence that these acute viral infections, alongside transient transcriptomic responses, induce epigenetic remodeling as part of the immune response, such as DNA methylation and histone modifications, which might persist after the infection is cleared. In this article, we first review the primary mechanisms of epigenetic remodeling in the context of innate immunity and inflammation, which are crucial for the regulation of the immune response to viral infections. Next, we delve into the existing knowledge concerning the impact of respiratory virus infections on the epigenome, focusing on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Influenza A Virus (IAV), and Respiratory Syncytial Virus (RSV). Finally, we offer perspectives on the potential consequences of virus-induced epigenetic remodeling and open questions in the field that are currently under investigation.
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Affiliation(s)
- Rivka Bella Lefkowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan David Martinez-Caballero
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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7
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McClain MT, Zhbannikov I, Satterwhite LL, Henao R, Giroux NS, Ding S, Burke TW, Tsalik EL, Nix C, Balcazar JP, Petzold EA, Shen X, Woods CW. Epigenetic and transcriptional responses in circulating leukocytes are associated with future decompensation during SARS-CoV-2 infection. iScience 2024; 27:108288. [PMID: 38179063 PMCID: PMC10765013 DOI: 10.1016/j.isci.2023.108288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/03/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission. We performed combined single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) at admission and compared subjects who improved from their moderate disease with those who later clinically decompensated and required invasive mechanical ventilation or died. Chromatin accessibility and transcriptomic immune profiles were markedly altered between the two groups, with strong signals in CD4+ T cells, inflammatory T cells, dendritic cells, and NK cells. Multiomic signature scores at admission were tightly associated with future clinical deterioration (auROC 1.0). Epigenetic and transcriptional changes in PBMCs reveal early, broad immune dysregulation before typical clinical signs of decompensation are apparent and thus may act as biomarkers to predict future severity in COVID-19.
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Affiliation(s)
- Micah T. McClain
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705, USA
| | - Ilya Zhbannikov
- Department of Medicine, Clinical Research Unit, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa L. Satterwhite
- Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Ricardo Henao
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas S. Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas W. Burke
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Christina Nix
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Jorge Prado Balcazar
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Elizabeth A. Petzold
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Terasaki Institute for Biological Innovation, Los Angeles, CA 90024, USA
| | - Christopher W. Woods
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710, USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705, USA
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8
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Cardoso GC, Ganzella FADO, Miniskiskosky G, da Cunha RS, Ramos EADS. Digital methylation-specific PCR: New applications for liquid biopsy. Biomol Concepts 2024; 15:bmc-2022-0041. [PMID: 38345545 DOI: 10.1515/bmc-2022-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
Epigenetic analysis is a fundamental part of understanding pathophysiological processes with potential applications in diagnosis, prognosis, and assessment of disease susceptibility. Epigenetic changes have been widely studied in chronic obstructive pulmonary disease (COPD), but currently, there is no molecular marker used to improve the treatment of patients. Furthermore, this progressive disease is a risk factor for the development of more severe COVID-19. Methylation-specific polymerase chain reaction (MSP-PCR) plays an important role in the analysis of DNA methylation profiles, and it is one of the most widely used techniques. In this context, the combination of MSP-PCR with emerging PCR technologies, such as digital PCR (dPCR), results in more accurate analyses of the DNA methylation profile of the genes under study. In this study, we propose the application of the MSP-dPCR technique to evaluate the methylation profile of the ADAM33 gene from saliva samples and lung tissue biopsies of patients with COPD and COVID-19. MSP-dPCR generated a measurable prediction of gene methylation rate, with the potential application of this combined technology for diagnostic and prognostic purposes. It has also proven to be a powerful tool for liquid biopsy applications.
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Affiliation(s)
- Gabriela Casani Cardoso
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | | | - Guilherme Miniskiskosky
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Regiane Stafim da Cunha
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
| | - Edneia Amancio de Souza Ramos
- Human Pathology Experimental Laboratory, Basic Pathology Department, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
- Post-Graduate Program of Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba, 81531-980, Paraná, Brazil
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Fernández-de-las-Peñas C, Raveendran AV, Giordano R, Arendt-Nielsen L. Long COVID or Post-COVID-19 Condition: Past, Present and Future Research Directions. Microorganisms 2023; 11:2959. [PMID: 38138102 PMCID: PMC10745830 DOI: 10.3390/microorganisms11122959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The presence of symptoms after an acute SARS-CoV-2 infection (long-COVID) has become a worldwide healthcare emergency but remains underestimated and undertreated due to a lack of recognition of the condition and knowledge of the underlying mechanisms. In fact, the prevalence of post-COVID symptoms ranges from 50% during the first months after the infection up to 20% two-years after. This perspective review aimed to map the existing literature on post-COVID symptoms and to identify gaps in the literature to guide the global effort toward an improved understanding of long-COVID and suggest future research directions. There is a plethora of symptomatology that can be due to COVID-19; however, today, there is no clear classification and definition of this condition, termed long-COVID or post-COVID-19 condition. The heterogeneity in the symptomatology has led to the presence of groups/clusters of patients, which could exhibit different risk factors and different mechanisms. Viral persistence, long-lasting inflammation, immune dysregulation, autoimmune reactions, reactivation of latent infections, endothelial dysfunction and alteration in gut microbiota have been proposed as potential mechanisms explaining the complexity of long-COVID. In such an equation, viral biology (e.g., re-infections, SARS-CoV-2 variants), host biology (e.g., genetics, epigenetics) and external factors (e.g., vaccination) should be also considered. These various factors will be discussed in the current perspective review and future directions suggested.
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Affiliation(s)
- César Fernández-de-las-Peñas
- Department of Physical Therapy, Occupational Therapy, Physical Medicine and Rehabilitation, Universidad Rey Juan Carlos, 28922 Madrid, Spain
- Center for Neuroplasticity and Pain (CNAP), Center for Sensory-Motor Interaction (SMI), Department of Health Science and Technology, Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark; (R.G.); (L.A.-N.)
| | | | - Rocco Giordano
- Center for Neuroplasticity and Pain (CNAP), Center for Sensory-Motor Interaction (SMI), Department of Health Science and Technology, Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark; (R.G.); (L.A.-N.)
| | - Lars Arendt-Nielsen
- Center for Neuroplasticity and Pain (CNAP), Center for Sensory-Motor Interaction (SMI), Department of Health Science and Technology, Faculty of Medicine, Aalborg University, DK-9220 Aalborg, Denmark; (R.G.); (L.A.-N.)
- Department of Medical Gastroenterology, Mech-Sense, Aalborg University Hospital, DK-9000 Aalborg, Denmark
- Steno Diabetes Center North Denmark, Clinical Institute, Aalborg University Hospital, DK-9000 Aalborg, Denmark
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10
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Castaldo M, Ebbesen BD, Fernández-DE-Las-Peñas C, Arendt-Nielsen L, Giordano R. COVID-19 and musculoskeletal pain: an overview of the current knowledge. Minerva Anestesiol 2023; 89:1134-1142. [PMID: 38019176 DOI: 10.23736/s0375-9393.23.17471-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has provoked billions of infections worldwide. Several meta-analyses have observed that up to 50% of individuals who had survived to a SARS-CoV-2 acute infection suffer from post-COVID symptoms lasting for weeks or months and up to one year after infection. The prevalence of post-COVID pain ranges between 10% to 20% when assessed with other overall post-COVID symptoms and can reach up to 50% to 60% when investigated specifically. The most common musculoskeletal manifestations of post-COVID-19 condition include fatigue, myalgia, arthralgia or back pain. Despite pain of musculoskeletal origin is one of the most prevalent post-COVID pain symptoms, the exact pathophysiological mechanisms of musculoskeletal post-COVID pain are not completely understood. Studies have reported the complexity of post-COVID pain including immune, biological, and psychological factors, and more recently, they have suggested that genetic and epigenetic factors may also play a potential role, highlighting the need for further investigation into these mechanisms. Its management is still controversial, as no specific guideline for treating musculoskeletal post-COVID pain has been proposed with only general consideration about the relevance of multidisciplinary and multimodal treatment approaches. In this paper we will highlight the clinical features, the mechanism, and the management possibilities of musculoskeletal post-COVID pain.
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Affiliation(s)
- Matteo Castaldo
- School of Medicine, Center for Neuroplasticity and Pain, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark -
| | - Brian D Ebbesen
- School of Medicine, Center for Neuroplasticity and Pain, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Gastroenterology and Hepatology, Mech-Sense, Aalborg University Hospital, Aalborg, Denmark
| | - César Fernández-DE-Las-Peñas
- School of Medicine, Center for Neuroplasticity and Pain, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Physical Therapy, Occupational Therapy, Physical Medicine and Rehabilitation, Universidad Rey Juan Carlos (URJC), Alcorcón, Spain
| | - Lars Arendt-Nielsen
- School of Medicine, Center for Neuroplasticity and Pain, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Gastroenterology and Hepatology, Mech-Sense, Aalborg University Hospital, Aalborg, Denmark
- Steno Diabetes Center North Denmark, Clinical Institute, Aalborg University Hospital, Aalborg, Denmark
| | - Rocco Giordano
- School of Medicine, Center for Neuroplasticity and Pain, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Oral and Maxillofacial Surgery, Aalborg University Hospital, Aalborg, Denmark
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11
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Bejaoui Y, Humaira Amanullah F, Saad M, Taleb S, Bradic M, Megarbane A, Ait Hssain A, Abi Khalil C, El Hajj N. Epigenetic age acceleration in surviving versus deceased COVID-19 patients with acute respiratory distress syndrome following hospitalization. Clin Epigenetics 2023; 15:186. [PMID: 38017502 PMCID: PMC10685564 DOI: 10.1186/s13148-023-01597-4] [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: 08/03/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Aging has been reported as a major risk factor for severe symptoms and higher mortality rates in COVID-19 patients. Molecular hallmarks such as epigenetic alterations and telomere attenuation reflect the biological process of aging. Epigenetic clocks have been shown to be valuable tools for measuring biological age in various tissues and samples. As such, these epigenetic clocks can determine accelerated biological aging and time-to-mortality across various tissues. Previous reports have shown accelerated biological aging and telomere attrition acceleration following SARS-CoV-2 infection. However, the effect of accelerated epigenetic aging on outcome (death/recovery) in COVID-19 patients with acute respiratory distress syndrome (ARDS) has not been well investigated. RESULTS In this study, we measured DNA methylation age and telomere attrition in 87 severe COVID-19 cases with ARDS under mechanical ventilation. Furthermore, we compared dynamic changes in epigenetic aging across multiple time points until recovery or death. Epigenetic age was measured using the Horvath, Hannum, DNAm skin and blood, GrimAge, and PhenoAge clocks, whereas telomere length was calculated using the surrogate marker DNAmTL. Our analysis revealed significant accelerated epigenetic aging but no telomere attrition acceleration in severe COVID-19 cases. In addition, we observed epigenetic age deceleration at inclusion versus end of follow-up in recovered but not in deceased COVID-19 cases using certain clocks. When comparing dynamic changes in epigenetic age acceleration (EAA), we detected higher EAA using both the Horvath and PhenoAge clocks in deceased versus recovered patients. The DNAmTL measurements revealed telomere attrition acceleration in deceased COVID-19 patients between inclusion and end of follow-up and a significant change in dynamic telomere attrition acceleration when comparing patients who recovered versus those who died. CONCLUSIONS EAA and telomere attrition acceleration were associated with treatment outcomes in hospitalized COVID-19 patients with ARDS. A better understanding of the long-term effects of EAA in COVID-19 patients and how they might contribute to long COVID symptoms in recovered individuals is urgently needed.
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Affiliation(s)
- Yosra Bejaoui
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Education City, Doha, Qatar
| | - Fathima Humaira Amanullah
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Education City, Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Sara Taleb
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Education City, Doha, Qatar
- Proteomics Core Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Martina Bradic
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andre Megarbane
- Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American Univeristy, Beirut, Lebanon
| | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad Medical Corporation, Doha, Qatar
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA.
- Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar.
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, USA.
| | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Education City, Doha, Qatar.
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
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12
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Wang C, Liu T, Wang Z, Li W, Zhao Q, Mi Z, Xue X, Shi P, Sun Y, Zhang Y, Wang N, Bao F, Chen W, Liu H, Zhang F. IL-23/IL-23R Promote Macrophage Pyroptosis and T Helper 1/T Helper 17 Cell Differentiation in Mycobacterial Infection. J Invest Dermatol 2023; 143:2264-2274.e18. [PMID: 37187409 DOI: 10.1016/j.jid.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Pathogen-induced epigenetic modifications can reshape anti-infection immune processes and control the magnitude of host responses. DNA methylation profiling has identified crucial aberrant methylation changes associated with diseases, thus providing biological insights into the roles of epigenetic factors in mycobacterial infection. In this study, we performed a genome-wide methylation analysis of skin biopsies from patients with leprosy and healthy controls. T helper 17 differentiation pathway was found to be significantly associated with leprosy through functional enrichment analysis. As a key gene in this pathway, IL-23R was found to be critical to mycobacterial immunity in leprosy, according to integrated analysis with DNA methylation, RNA sequencing, and GWASs. Functional analysis revealed that IL-23/IL-23R-enhanced bacterial clearance by activating caspase-1/GSDMD-mediated pyroptosis in a manner dependent on NLRP3 through signal transducer and activator of transcription 3 signaling in macrophages. Moreover, IL23/IL-23R promoted T helper 1 and T helper 17 cell differentiation and proinflammatory cytokine secretion, thereby increasing host bactericidal activity. IL-23R knockout attenuated the effects and increased susceptibility to mycobacterial infection mentioned earlier. These findings illustrate the biological functions of IL-23/IL-23R in modulating intracellular bacterial clearance in macrophages and further support their regulatory effects in T helper cell differentiation. Our study highlights that IL-23/IL-23R might serve as potential targets for the prevention and treatment of leprosy and other mycobacterial infections.
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Affiliation(s)
- Chuan Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Tingting Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhenzhen Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Wenchao Li
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Qing Zhao
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Mi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaotong Xue
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Peidian Shi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yonghu Sun
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuan Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Na Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fangfang Bao
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Wenjie Chen
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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13
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Gupta MK, Peng H, Li Y, Xu CJ. The role of DNA methylation in personalized medicine for immune-related diseases. Pharmacol Ther 2023; 250:108508. [PMID: 37567513 DOI: 10.1016/j.pharmthera.2023.108508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Epigenetics functions as a bridge between host genetic & environmental factors, aiding in human health and diseases. Many immune-related diseases, including infectious and allergic diseases, have been linked to epigenetic mechanisms, particularly DNA methylation. In this review, we summarized an updated overview of DNA methylation and its importance in personalized medicine, and demonstrated that DNA methylation has excellent potential for disease prevention, diagnosis, and treatment in a personalized manner. The future implications and limitations of the DNA methylation study have also been well-discussed.
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Affiliation(s)
- Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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14
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Napoli C, Coscioni E, Trama U, Strozziero MG, Benincasa G. An evidence-based debate on epigenetics and immunosenescence in COVID-19. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100069. [PMID: 37781451 PMCID: PMC10539895 DOI: 10.1016/j.crimmu.2023.100069] [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: 07/19/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023] Open
Abstract
Immunosenescence contributes to the decline of immune function leading to a reduced ability to respond to severe coronavirus disease 2019 (COVID-19) in elderly patients. Clinical course of COVID-19 is widely heterogeneous and guided by the possible interplay between genetic background and epigenetic-sensitive mechanisms underlying the immunosenescence which could explain, at least in part, the higher percentage of disease severity in elderly individuals. The most convincing evidence regards the hypomethylation of the angiotensin-converting enzyme 2 (ACE2) promoter gene in lungs as well as the citrullination of histone H3 in neutrophils which have been associated with worsening of COVID-19 outcome in elderly patients. In contrast, centenarians who have showed milder symptoms have been associated to a younger "epigenetic age" based on DNA methylation profiles at specific genomic sites (epigenetic clock). Some large prospective studies showed that the acceleration of epigenetic aging as well as the shortening of telomeres were significantly associated with lymphopenia and poor outcome suggesting prognostic biomarkers in elderly COVID-19 patients. Furthermore, randomized clinical trials showed that statins, L-arginine, and resveratrol could mediate anti-inflammatory effects via indirect epigenetic interference and might improve COVID-19 outcome. Here, we discuss the epigenetic-sensitive events which might contribute to increase the risk of severity and mortality in older subjects and possible targeted therapies to counteract immunosenescence.
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Affiliation(s)
- Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Enrico Coscioni
- Division of Cardiac Surgery, AOU San Giovanni di Dio e Ruggid'Aragona, 84131, Salerno, Italy
| | - Ugo Trama
- Regional Pharmaceutical Unit, Campania Region, 80143 Naples, Italy
| | - Maria Grazia Strozziero
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
- IRCCS Synlab SDN Naples Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, Naples, Italy
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15
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Oh T, Kim G, Baek SH, Woo Y, Koo BS, Hwang EH, Shim K, An YJ, Kim Y, Won J, Lee Y, Lim KS, Park JH, Hong JJ. Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques. Commun Biol 2023; 6:879. [PMID: 37640792 PMCID: PMC10462721 DOI: 10.1038/s42003-023-05253-8] [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: 04/28/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Characterizing the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the molecular level is necessary to understand viral pathogenesis and identify clinically relevant biomarkers. However, in humans, the pulmonary host response during disease onset remains poorly understood. Herein, we utilized a spatial transcriptome atlas to identify pulmonary microstructure-specific COVID-19 gene signatures during the acute phase of lung infection in cynomolgus macaques. The innate immune response to virus-induced cell death was primarily active in the alveolar regions involving activated macrophage infiltration. Inflamed vascular regions exhibited prominent upregulation of interferon and complement pathway genes that mediate antiviral activity and tissue damage response. Furthermore, known biomarker genes were significantly expressed in specific microstructures, and some of them were universally expressed across all microstructures. These findings underscore the importance of identifying key drivers of disease progression and clinically applicable biomarkers by focusing on pulmonary microstructures appearing during SARS-CoV-2 infection.
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Affiliation(s)
- Taehwan Oh
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Green Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - YoungMin Woo
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Kyuyoung Shim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea
| | - You Jung An
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Yujin Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Jinyoung Won
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Kyung Seob Lim
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Jae-Hak Park
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea.
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16
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Schuetz A, Corley MJ, Sacdalan C, Phuang-Ngern Y, Nakpor T, Wansom T, Ehrenberg PK, Sriplienchan S, Thomas R, Ratnaratorn N, Sukhumvittaya S, Tragonlugsana N, Slike BM, Akapirat S, Pinyakorn S, Rerknimitr R, Pang AP, Kroon E, Teeratakulpisan N, Krebs SJ, Phanuphak N, Ndhlovu LC, Vasan S. Distinct mucosal and systemic immunological characteristics in transgender women potentially relating to HIV acquisition. JCI Insight 2023; 8:e169272. [PMID: 37432754 PMCID: PMC10543719 DOI: 10.1172/jci.insight.169272] [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: 02/02/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Transgender women (TGW) are disproportionally affected by HIV infection, with a global estimated prevalence of 19.9%, often attributed to behavioral risk factors, with less known about biological factors. We evaluated potential biological risk factors for HIV acquisition in TGW at the sites of viral entry by assessing immune parameters of the neovaginal surface and gut mucosa. The neovagina in TGW, compared with the vagina in cisgender women (CW), shows distinct cell composition and may pose a more inflammatory environment, evidenced by increased CD4+ T cell activation and higher levels of soluble markers of inflammation (C-reactive protein, soluble CD30). Increased inflammation may be driven by microbiome composition, as shown by a greater abundance of Prevotella and a higher Shannon Diversity Index. In addition, we have observed higher frequency of CD4+CCR5+ target cells and decreased DNA methylation of the CCR5 gene in the gut mucosa of TGW compared with CW and men who have sex with men, which was inversely correlated with testosterone levels. The rectal microbiome composition in TGW appears to favor a proinflammatory milieu as well as mucosal barrier disruption. Thus, it is possible that increased inflammation and higher frequencies of CCR5-expressing target cells at sites of mucosal viral entry may contribute to increased risk of HIV acquisition in TGW, with further validation in larger studies warranted.
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Affiliation(s)
- Alexandra Schuetz
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | - Tanyaporn Wansom
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Bonnie M. Slike
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Siriwat Akapirat
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Rungsun Rerknimitr
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alina P.S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Shelly J. Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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17
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Wrede D, Bordak M, Abraham Y, Mehedi M. Pulmonary Pathogen-Induced Epigenetic Modifications. EPIGENOMES 2023; 7:13. [PMID: 37489401 PMCID: PMC10366755 DOI: 10.3390/epigenomes7030013] [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: 05/23/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
Epigenetics generally involves genetic control by factors other than our own DNA sequence. Recent research has focused on delineating the mechanisms of two major epigenetic phenomena: DNA methylation and histone modification. As epigenetics involves many cellular processes, it is no surprise that it can also influence disease-associated gene expression. A direct link between respiratory infections, host cell epigenetic regulations, and chronic lung diseases is still unknown. Recent studies have revealed bacterium- or virus-induced epigenetic changes in the host cells. In this review, we focused on respiratory pathogens (viruses, bacteria, and fungi) induced epigenetic modulations (DNA methylation and histone modification) that may contribute to lung disease pathophysiology by promoting host defense or allowing pathogen persistence.
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Affiliation(s)
| | | | | | - Masfique Mehedi
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA; (D.W.); (M.B.); (Y.A.)
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18
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Mao W, Miller CM, Nair VD, Ge Y, Amper MAS, Cappuccio A, George M, Goforth CW, Guevara K, Marjanovic N, Nudelman G, Pincas H, Ramos I, Sealfon RSG, Soares‐Schanoski A, Vangeti S, Vasoya M, Weir DL, Zaslavsky E, Kim‐Schulze S, Gnjatic S, Merad M, Letizia AG, Troyanskaya OG, Sealfon SC, Chikina M. A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation. Mol Syst Biol 2023; 19:e11361. [PMID: 36919946 PMCID: PMC10167476 DOI: 10.15252/msb.202211361] [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: 09/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics in humans following an acute perturbation, such as infection. We characterized the temporal trajectory of blood epigenetic remodeling in 133 participants in a prospective study of young adults before, during, and after asymptomatic and mildly symptomatic SARS-CoV-2 infection. The differential methylation caused by asymptomatic or mildly symptomatic infections was indistinguishable. While differential gene expression largely returned to baseline levels after the virus became undetectable, some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease. We leveraged these responses to construct methylation-based machine learning models that distinguished samples from pre-, during-, and postinfection time periods, and quantitatively predicted the time since infection. The clinical trajectory in the young adults and in a diverse cohort with more severe outcomes was predicted by the similarity of methylation before or early after SARS-CoV-2 infection to the model-defined postinfection state. Unlike the phenomenon of trained immunity, the postacute SARS-CoV-2 epigenetic landscape we identify is antiprotective.
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Affiliation(s)
- Weiguang Mao
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
- Present address:
Center for Computational BiologyFlatiron Institute, Simons FoundationNew YorkNYUSA
| | - Clare M Miller
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Venugopalan D Nair
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Yongchao Ge
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mary Anne S Amper
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Antonio Cappuccio
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | | | - Kristy Guevara
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Nada Marjanovic
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - German Nudelman
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Hanna Pincas
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Irene Ramos
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Rachel S G Sealfon
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
| | - Alessandra Soares‐Schanoski
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Present address:
Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | - Sindhu Vangeti
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mital Vasoya
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Dawn L Weir
- Naval Medical Research CenterMDSilver SpringUSA
| | - Elena Zaslavsky
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Seunghee Kim‐Schulze
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Sacha Gnjatic
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
- Department of Computer SciencePrinceton UniversityNJPrincetonUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityNJPrincetonUSA
| | - Stuart C Sealfon
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
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19
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Motta CS, Torices S, da Rosa BG, Marcos AC, Alvarez-Rosa L, Siqueira M, Moreno-Rodriguez T, Matos ADR, Caetano BC, Martins JSCDC, Gladulich L, Loiola E, Bagshaw ORM, Stuart JA, Siqueira MM, Stipursky J, Toborek M, Adesse D. Human Brain Microvascular Endothelial Cells Exposure to SARS-CoV-2 Leads to Inflammatory Activation through NF-κB Non-Canonical Pathway and Mitochondrial Remodeling. Viruses 2023; 15:745. [PMID: 36992454 PMCID: PMC10056985 DOI: 10.3390/v15030745] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/15/2023] Open
Abstract
Neurological effects of COVID-19 and long-COVID-19, as well as neuroinvasion by SARS-CoV-2, still pose several questions and are of both clinical and scientific relevance. We described the cellular and molecular effects of the human brain microvascular endothelial cells (HBMECs) in vitro exposure by SARS-CoV-2 to understand the underlying mechanisms of viral transmigration through the blood-brain barrier. Despite the low to non-productive viral replication, SARS-CoV-2-exposed cultures displayed increased immunoreactivity for cleaved caspase-3, an indicator of apoptotic cell death, tight junction protein expression, and immunolocalization. Transcriptomic profiling of SARS-CoV-2-challenged cultures revealed endothelial activation via NF-κB non-canonical pathway, including RELB overexpression and mitochondrial dysfunction. Additionally, SARS-CoV-2 led to altered secretion of key angiogenic factors and to significant changes in mitochondrial dynamics, with increased mitofusin-2 expression and increased mitochondrial networks. Endothelial activation and remodeling can further contribute to neuroinflammatory processes and lead to further BBB permeability in COVID-19.
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Affiliation(s)
- Carolline Soares Motta
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Silvia Torices
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Barbara Gomes da Rosa
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Anne Caroline Marcos
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Liandra Alvarez-Rosa
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
- Laboratório Compartilhado, Instituto de Ciências Biomédicas, UFRJ, Rio de Janeiro 05508-000, Brazil
| | - Michele Siqueira
- Laboratório Compartilhado, Instituto de Ciências Biomédicas, UFRJ, Rio de Janeiro 05508-000, Brazil
| | - Thaidy Moreno-Rodriguez
- Urology Department, University of California San Francisco, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aline da Rocha Matos
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais (LVRE), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Braulia Costa Caetano
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais (LVRE), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Jessica Santa Cruz de Carvalho Martins
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais (LVRE), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Luis Gladulich
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Erick Loiola
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Olivia R. M. Bagshaw
- Faculty of Mathematics & Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Jeffrey A. Stuart
- Faculty of Mathematics & Science, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Marilda M. Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais (LVRE), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Joice Stipursky
- Laboratório Compartilhado, Instituto de Ciências Biomédicas, UFRJ, Rio de Janeiro 05508-000, Brazil
| | - Michal Toborek
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Adesse
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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20
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Cassiano LMG, Cavalcante-Silva V, Oliveira MS, Prado BVO, Cardoso CG, Salim ACM, Franco GR, D’Almeida V, Francisco SC, Coimbra RS. Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic markings. Front Immunol 2023; 14:1048790. [PMID: 36993968 PMCID: PMC10040807 DOI: 10.3389/fimmu.2023.1048790] [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: 09/21/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, that regulates the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic markings in leukocytes favorably regulates central components of COVID-19 physiopathology.
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Affiliation(s)
- Larissa M. G. Cassiano
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vanessa Cavalcante-Silva
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marina S. Oliveira
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
| | | | | | - Anna C. M. Salim
- Plataforma de Sequenciamento NGS (Next Generation Sequencing), Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
| | - Gloria R. Franco
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vânia D’Almeida
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Roney S. Coimbra
- Neurogenômica, Imunopatologia, Instituto René Rachou, Fiocruz, Belo Horizonte, Brazil
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21
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Calzari L, Zanotti L, Inglese E, Scaglione F, Cavagnola R, Ranucci F, Di Blasio AM, Stefanini G, Carlo G, Parati G, Gentilini D. Role of epigenetics in the clinical evolution of COVID-19 disease. Epigenome-wide association study identifies markers of severe outcome. Eur J Med Res 2023; 28:81. [PMID: 36800980 PMCID: PMC9936487 DOI: 10.1186/s40001-023-01032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND COVID-19 has a wide spectrum of clinical manifestations and given its impact on morbidity and mortality, there is an unmet medical need to discover endogenous cellular and molecular biomarkers that predict the expected clinical course of the disease. Recently, epigenetics and especially DNA methylation have been pointed out as a promising tool for outcome prediction in several diseases. METHODS AND RESULTS Using the Illumina Infinium Methylation EPIC BeadChip850K, we investigated genome-wide differences in DNA methylation in an Italian Cohort of patients with comorbidities and compared severe (n = 64) and mild (123) prognosis. Results showed that the epigenetic signature, already present at the time of Hospital admission, can significantly predict risk of severe outcomes. Further analyses provided evidence of an association between age acceleration and a severe prognosis after COVID-19 infection. The burden of Stochastic Epigenetic Mutation (SEMs) has been significantly increased in patients with poor prognosis. Results have been replicated in silico considering COVID-19 negative subjects and available previously published datasets. CONCLUSIONS Using original methylation data and taking advantage of already published datasets, we confirmed in the blood that epigenetics is actively involved in immune response after COVID-19 infection, allowing the identification of a specific signature able to discriminate the disease evolution. Furthermore, the study showed that epigenetic drift and age acceleration are associated with severe prognosis. All these findings prove that host epigenetics undergoes notable and specific rearrangements to respond to COVID-19 infection which can be used for a personalized, timely, and targeted management of COVID-19 patients during the first stages of hospitalization.
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Affiliation(s)
- Luciano Calzari
- grid.418224.90000 0004 1757 9530Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy
| | - Lucia Zanotti
- grid.418224.90000 0004 1757 9530Sleep Disorders Center & Department of Cardiovascular, Neural and Metabolic Sciences, IRCCS Istituto Auxologico Italiano, San Luca Hospital, Milan, Italy
| | - Elvira Inglese
- grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy ,Chemical-Clinical Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Francesco Scaglione
- Chemical-Clinical Analysis Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Rebecca Cavagnola
- grid.418224.90000 0004 1757 9530Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy ,grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Francesco Ranucci
- grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Anna Maria Di Blasio
- grid.418224.90000 0004 1757 9530Molecular Biology Laboratory, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy
| | - Giulio Stefanini
- grid.452490.eDepartment of Biomedical Sciences, Humanitas University, Pieve Emanuele-Milan, Italy ,grid.417728.f0000 0004 1756 8807IRCCS Humanitas Research Hospital, Rozzano-Milan, Italy
| | - Gaetano Carlo
- grid.511455.1Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Gianfranco Parati
- grid.418224.90000 0004 1757 9530Sleep Disorders Center & Department of Cardiovascular, Neural and Metabolic Sciences, IRCCS Istituto Auxologico Italiano, San Luca Hospital, Milan, Italy ,grid.7563.70000 0001 2174 1754Department of Medicine and Surgery, University of Milan‐Bicocca, Milan, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy. .,Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy.
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22
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Sharma SB, Melvin WJ, Audu CO, Bame M, Rhoads N, Wu W, Kanthi Y, Knight JS, Adili R, Holinstat MA, Wakefield TW, Henke PK, Moore BB, Gallagher KA, Obi AT. The histone methyltransferase MLL1/KMT2A in monocytes drives coronavirus-associated coagulopathy and inflammation. Blood 2023; 141:725-742. [PMID: 36493338 PMCID: PMC9743412 DOI: 10.1182/blood.2022015917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Coronavirus-associated coagulopathy (CAC) is a morbid and lethal sequela of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. CAC results from a perturbed balance between coagulation and fibrinolysis and occurs in conjunction with exaggerated activation of monocytes/macrophages (MO/Mφs), and the mechanisms that collectively govern this phenotype seen in CAC remain unclear. Here, using experimental models that use the murine betacoronavirus MHVA59, a well-established model of SARS-CoV-2 infection, we identify that the histone methyltransferase mixed lineage leukemia 1 (MLL1/KMT2A) is an important regulator of MO/Mφ expression of procoagulant and profibrinolytic factors such as tissue factor (F3; TF), urokinase (PLAU), and urokinase receptor (PLAUR) (herein, "coagulopathy-related factors") in noninfected and infected cells. We show that MLL1 concurrently promotes the expression of the proinflammatory cytokines while suppressing the expression of interferon alfa (IFN-α), a well-known inducer of TF and PLAUR. Using in vitro models, we identify MLL1-dependent NF-κB/RelA-mediated transcription of these coagulation-related factors and identify a context-dependent, MLL1-independent role for RelA in the expression of these factors in vivo. As functional correlates for these findings, we demonstrate that the inflammatory, procoagulant, and profibrinolytic phenotypes seen in vivo after coronavirus infection were MLL1-dependent despite blunted Ifna induction in MO/Mφs. Finally, in an analysis of SARS-CoV-2 positive human samples, we identify differential upregulation of MLL1 and coagulopathy-related factor expression and activity in CD14+ MO/Mφs relative to noninfected and healthy controls. We also observed elevated plasma PLAU and TF activity in COVID-positive samples. Collectively, these findings highlight an important role for MO/Mφ MLL1 in promoting CAC and inflammation.
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Affiliation(s)
- Sriganesh B. Sharma
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - William J. Melvin
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Christopher O. Audu
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Monica Bame
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | - Nicole Rhoads
- Department of Pharmacology, University of Michigan, Ann Arbor, MI
| | - Weisheng Wu
- Bioinformatics Core, Biomedical Research Core Facilities, University of Michigan, Ann Arbor, MI
| | - Yogendra Kanthi
- Laboratory of Vascular Thrombosis & Inflammation, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Jason S. Knight
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Reheman Adili
- Department of Pharmacology, University of Michigan, Ann Arbor, MI
| | - Michael A. Holinstat
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Department of Pharmacology, University of Michigan, Ann Arbor, MI
| | - Thomas W. Wakefield
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Peter K. Henke
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Bethany B. Moore
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | - Katherine A. Gallagher
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | - Andrea T. Obi
- Section of General Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
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23
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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24
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Teodori L, Osimani B, Isidoro C, Ramakrishna S. Mass versus personalized medicine against COVID-19 in the "system sciences" era. Cytometry A 2022; 101:995-999. [PMID: 35716116 DOI: 10.1002/cyto.a.24662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 01/27/2023]
Abstract
The importance of personalized/precision medicine for targeted therapies and improved outcomes both in terms of efficacy and safety in health care is by now grounded. We here discuss the current landscape of personalized medicine approaches against SARS-CoV-2. A schematic of the approach is illustrated in the figure in the text.
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Affiliation(s)
- Laura Teodori
- Laboratory of Diagnostics and Metrology, ENEA, Rome, Italy
| | - Barbara Osimani
- Department of Biomedical Sciences and Public Health, Marche Polytechnic University, Ancona, Italy
| | - Ciro Isidoro
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
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25
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Morselli M, Farrell C, Montoya D, Gören T, Sabırlı R, Türkçüer İ, Kurt Ö, Köseler A, Pellegrini M. DNA methylation profiles in pneumonia patients reflect changes in cell types and pneumonia severity. Epigenetics 2022; 17:1646-1660. [PMID: 35311624 PMCID: PMC9621067 DOI: 10.1080/15592294.2022.2051862] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Immune cell-type composition changes with age, potentially weakening the response to infectious diseases. Profiling epigenetics marks of immune cells can help us understand the relationship with disease severity. We therefore leveraged a targeted DNA methylation method to study the differences in a cohort of pneumonia patients (both COVID-19 positive and negative) and unaffected individuals from peripheral blood.This approach allowed us to predict the pneumonia diagnosis with high accuracy (AUC = 0.92), and the PCR positivity to the SARS-CoV-2 viral genome with moderate, albeit lower, accuracy (AUC = 0.77). We were also able to predict the severity of pneumonia (PORT score) with an R2 = 0.69. By estimating immune cellular frequency from DNA methylation data, patients under the age of 65 positive to the SARS-CoV-2 genome (as revealed by PCR) showed an increase in T cells, and specifically in CD8+ cells, compared to the negative control group. Conversely, we observed a decreased frequency of neutrophils in the positive compared to the negative group. No significant difference was found in patients over the age of 65. The results suggest that this DNA methylation-based approach can be used as a cost-effective and clinically useful biomarker platform for predicting pneumonias and their severity.
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Affiliation(s)
- Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Institute for Genomics and Proteomics; University of California Los Angeles, Los Angeles, CA, USA
- CONTACT Marco Morselli Department of Molecular, Cell, and Developmental Biology, Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
| | - Colin Farrell
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Dennis Montoya
- Department of Biochemistry and Molecular Medicine, University of California Davis Medical Center, Sacramento, CA, USA
| | - Tarık Gören
- Department of Emergency Medicine, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Ramazan Sabırlı
- Department of Emergency Medicine, Bakircay University School of Medicine, Cigli Training and Research Hospital, İzmir, Turkey
| | - İbrahim Türkçüer
- Department of Emergency Medicine, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Medical Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Institute for Genomics and Proteomics; University of California Los Angeles, Los Angeles, CA, USA
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26
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Biological Age Predictors: The Status Quo and Future Trends. Int J Mol Sci 2022; 23:ijms232315103. [PMID: 36499430 PMCID: PMC9739540 DOI: 10.3390/ijms232315103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
There is no single universal biomarker yet to estimate overall health status and longevity prospects. Moreover, a consensual approach to the very concept of aging and the means of its assessment are yet to be developed. Markers of aging could facilitate effective health control, more accurate life expectancy estimates, and improved health and quality of life. Clinicians routinely use several indicators that could be biomarkers of aging. Duly validated in a large cohort, models based on a combination of these markers could provide a highly accurate assessment of biological age and the pace of aging. Biological aging is a complex characteristic of chronological age (usually), health-to-age concordance, and medically estimated life expectancy. This study is a review of the most promising techniques that could soon be used in routine clinical practice. Two main selection criteria were applied: a sufficient sample size and reliability based on validation. The selected biological age calculators were grouped according to the type of biomarker used: (1) standard clinical and laboratory markers; (2) molecular markers; and (3) epigenetic markers. The most accurate were the calculators, which factored in a variety of biomarkers. Despite their demonstrated effectiveness, most of them require further improvement and cannot yet be considered for use in standard clinical practice. To illustrate their clinical application, we reviewed their use during the COVID-19 pandemic.
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27
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Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines. Genome Med 2022; 14:134. [PMID: 36443794 PMCID: PMC9706884 DOI: 10.1186/s13073-022-01137-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. METHODS In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14 + CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. RESULTS We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. CONCLUSION Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.
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28
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Bradic M, Taleb S, Thomas B, Chidiac O, Robay A, Hassan N, Malek J, Ait Hssain A, Abi Khalil C. DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome. J Transl Med 2022; 20:526. [PMID: 36371196 PMCID: PMC9652914 DOI: 10.1186/s12967-022-03737-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/30/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND COVID-19 infections could be complicated by acute respiratory distress syndrome (ARDS), increasing mortality risk. We sought to assess the methylome of peripheral blood mononuclear cells in COVID-19 with ARDS. METHODS We recruited 100 COVID-19 patients with ARDS under mechanical ventilation and 33 non-COVID-19 controls between April and July 2020. COVID-19 patients were followed at four time points for 60 days. DNA methylation and immune cell populations were measured at each time point. A multivariate cox proportional risk regression analysis was conducted to identify predictive signatures according to survival. RESULTS The comparison of COVID-19 to controls at inclusion revealed the presence of a 14.4% difference in promoter-associated CpGs in genes that control immune-related pathways such as interferon-gamma and interferon-alpha responses. On day 60, 24% of patients died. The inter-comparison of baseline DNA methylation to the last recorded time point in both COVID-19 groups or the intra-comparison between inclusion and the end of follow-up in every group showed that most changes occurred as the disease progressed, mainly in the AIM gene, which is associated with an intensified immune response in those who recovered. The multivariate Cox proportional risk regression analysis showed that higher methylation of the "Apoptotic execution Pathway" genes (ROC1, ZNF789, and H1F0) at inclusion increases mortality risk by over twofold. CONCLUSION We observed an epigenetic signature of immune-related genes in COVID-19 patients with ARDS. Further, Hypermethylation of the apoptotic execution pathway genes predicts the outcome. TRIAL REGISTRATION IMRPOVIE study, NCT04473131.
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Affiliation(s)
- Martina Bradic
- grid.5386.8000000041936877XDepartment of Genetic Medicine, Weill Cornell Medicine, New York, USA ,grid.51462.340000 0001 2171 9952Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah Taleb
- grid.452146.00000 0004 1789 3191Division of Genomics and Translational Biomedicine, College of Health and Life Sciences- HBKU, Doha, Qatar
| | - Binitha Thomas
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Omar Chidiac
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Amal Robay
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Nessiya Hassan
- grid.413548.f0000 0004 0571 546XNursery and midwifery research department, Hamad Medical Corporation., Doha, Qatar
| | - Joel Malek
- grid.416973.e0000 0004 0582 4340Genomics Core. Weill Cornell Medicine-Qatar., Doha, Qatar
| | - Ali Ait Hssain
- grid.413548.f0000 0004 0571 546XMedical Intensive Care Unit, Hamad Medical Corporation., Doha, Qatar
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA. .,Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar. .,Joan and Sanford I. Weill Department of Medicine., Weill Cornell Medicine, New York, USA.
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SARS-CoV-2-induced hypomethylation of the ferritin heavy chain (FTH1) gene underlies serum hyperferritinemia in severe COVID-19 patients. Biochem Biophys Res Commun 2022; 631:138-145. [PMID: 36183555 PMCID: PMC9509293 DOI: 10.1016/j.bbrc.2022.09.083] [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: 08/30/2022] [Revised: 09/02/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022]
Abstract
High serum ferritin (hyperferritinemia), a reliable hallmark of severe COVID-19 often associates with a moderate decrease in serum iron (hypoferremia) and a moderate increase in serum hepcidin. This suggests that hyperferritinemia in severe COVID-19 is reflective of inflammation rather than iron overload. To test this possibility, the expression status of ferritin heavy chain (FTH1), transferrin receptor 1 (TFRC), hepcidin (HAMP), and ferroportin (SLC40A1) genes and promoter methylation status of FTH1 and TFRC genes were examined in blood samples obtained from COVID-19 patients showing no, mild or severe symptoms and in healthy-donor monocytes stimulated with SARS-CoV-2-derived peptides. Severe COVID-19 samples showed a significant increase in FTH1 expression and hypomethylation relative to mild or asymptomatic COVID-19 samples. S-peptide treated monocytes also showed a significant increase in FTH1 expression and hypomethylation relative to that in controls; treatment with ECD or NP did not change FTH1 expression nor its methylation status. In silico and in vitro analysis showed a significant increase in the expression of the TET3 demethylase in S peptide-treated monocytes. Findings presented here suggest that S peptide-driven hypomethylation of the FTH1 gene promoter underlies hyperferritinemia in severe COVID-19 disease.
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Lee JH, Kanwar B, Khattak A, Balentine J, Nguyen NH, Kast RE, Lee CJ, Bourbeau J, Altschuler EL, Sergi CM, Nguyen TNM, Oh S, Sohn MG, Coleman M. COVID-19 Molecular Pathophysiology: Acetylation of Repurposing Drugs. Int J Mol Sci 2022; 23:13260. [PMID: 36362045 PMCID: PMC9656873 DOI: 10.3390/ijms232113260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 01/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated type 1 interferon (IFN-1) production, the pathophysiology of which involves sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) tetramerization and the cytosolic DNA sensor cyclic-GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. As a result, type I interferonopathies are exacerbated. Aspirin inhibits cGAS-mediated signaling through cGAS acetylation. Acetylation contributes to cGAS activity control and activates IFN-1 production and nuclear factor-κB (NF-κB) signaling via STING. Aspirin and dapsone inhibit the activation of both IFN-1 and NF-κB by targeting cGAS. We define these as anticatalytic mechanisms. It is necessary to alleviate the pathologic course and take the lag time of the odds of achieving viral clearance by day 7 to coordinate innate or adaptive immune cell reactions.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Badar Kanwar
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Asif Khattak
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Jenny Balentine
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Ngoc Huy Nguyen
- Department of Health, Phutho Province, Tran Phu Str., Viet Tri City 227, Vietnam
| | | | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC H4A 3S5, Canada
| | - Eric L. Altschuler
- Department of Physical Medicine and Rehabilitation, Metropolitan Hospital, New York, NY 10029, USA
| | - Consolato M. Sergi
- Division of Anatomical Pathology, Children’s Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | | | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul 03600, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul 17104, Korea
| | - Michael Coleman
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
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Bowler S, Papoutsoglou G, Karanikas A, Tsamardinos I, Corley MJ, Ndhlovu LC. A machine learning approach utilizing DNA methylation as an accurate classifier of COVID-19 disease severity. Sci Rep 2022; 12:17480. [PMID: 36261477 PMCID: PMC9580434 DOI: 10.1038/s41598-022-22201-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Since the onset of the COVID-19 pandemic, increasing cases with variable outcomes continue globally because of variants and despite vaccines and therapies. There is a need to identify at-risk individuals early that would benefit from timely medical interventions. DNA methylation provides an opportunity to identify an epigenetic signature of individuals at increased risk. We utilized machine learning to identify DNA methylation signatures of COVID-19 disease from data available through NCBI Gene Expression Omnibus. A training cohort of 460 individuals (164 COVID-19-infected and 296 non-infected) and an external validation dataset of 128 individuals (102 COVID-19-infected and 26 non-COVID-associated pneumonia) were reanalyzed. Data was processed using ChAMP and beta values were logit transformed. The JADBio AutoML platform was leveraged to identify a methylation signature associated with severe COVID-19 disease. We identified a random forest classification model from 4 unique methylation sites with the power to discern individuals with severe COVID-19 disease. The average area under the curve of receiver operator characteristic (AUC-ROC) of the model was 0.933 and the average area under the precision-recall curve (AUC-PRC) was 0.965. When applied to our external validation, this model produced an AUC-ROC of 0.898 and an AUC-PRC of 0.864. These results further our understanding of the utility of DNA methylation in COVID-19 disease pathology and serve as a platform to inform future COVID-19 related studies.
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Affiliation(s)
- Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA
| | - Georgios Papoutsoglou
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
| | - Aristides Karanikas
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
| | - Ioannis Tsamardinos
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
- Department of Computer Science, University of Crete, 70013, Heraklion, Greece
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA.
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Loi E, Moi L, Cabras P, Arduino G, Costanzo G, Del Giacco S, Erlich HA, Firinu D, Caddori A, Zavattari P. HLA-C dysregulation as a possible mechanism of immune evasion in SARS-CoV-2 and other RNA-virus infections. Front Immunol 2022; 13:1011829. [PMID: 36325330 PMCID: PMC9618630 DOI: 10.3389/fimmu.2022.1011829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
One of the mechanisms by which viruses can evade the host’s immune system is to modify the host’s DNA methylation pattern. This work aims to investigate the DNA methylation and gene expression profile of COVID-19 patients, divided into symptomatic and asymptomatic, and healthy controls, focusing on genes involved in the immune response. In this study, changes in the methylome of COVID-19 patients’ upper airways cells, the first barrier against respiratory infections and the first cells presenting viral antigens, are shown for the first time. Our results showed alterations in the methylation pattern of genes encoding proteins implicated in the response against pathogens, in particular the HLA-C gene, also important for the T-cell mediated memory response. HLA-C expression significantly decreases in COVID-19 patients, especially in those with a more severe prognosis and without other possibly confounding co-morbidities. Moreover, our bionformatic analysis revealed that the identified methylation alteration overlaps with enhancers regulating HLA-C expression, suggesting an additional mechanism exploited by SARS-CoV-2 to inhibit this fundamental player in the host’s immune response. HLA-C could therefore represent both a prognostic marker and an excellent therapeutic target, also suggesting a preventive intervention that conjugate a virus-specific antigenic stimulation with an adjuvant increasing the T-cell mediated memory response.
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Affiliation(s)
- Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Paola Cabras
- Department of Internal Medicine, Hospital SS. Trinità, Cagliari, Italy
| | - Giulia Arduino
- Department of Internal Medicine, Hospital SS. Trinità, Cagliari, Italy
| | - Giulia Costanzo
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefano Del Giacco
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Henry A. Erlich
- Department of Genetics and Genomics, Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Aldo Caddori
- Department of Internal Medicine, Hospital SS. Trinità, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
- *Correspondence: Patrizia Zavattari,
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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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Ahmadi Badi S, Malek A, Paolini A, Rouhollahi Masoumi M, Seyedi SA, Amanzadeh A, Masotti A, Khatami S, Siadat SD. Downregulation of ACE, AGTR1, and ACE2 genes mediating SARS-CoV-2 pathogenesis by gut microbiota members and their postbiotics on Caco-2 cells. Microb Pathog 2022; 173:105798. [PMID: 36174833 PMCID: PMC9511898 DOI: 10.1016/j.micpath.2022.105798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Coronavirus disease-2019 (COVID-19) is a complex infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can cause also gastrointestinal symptoms. There are various factors that determine the host susceptibility and severity of infection, including the renin-angiotensin system, the immune response, and the gut microbiota. In this regard, we aimed to investigate the gene expression of ACE, AGTR1, ACE2, and TMPRSS2, which mediate SARS-CoV-2 pathogenesis by Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, and Bacteroides fragilis on Caco-2 cells. Also, the enrichment analysis considering the studied genes was analyzed on raw data from the microarray analysis of COVID-19 patients. MATERIALS AND METHODS Caco-2 cells were treated with live, heat-inactivated form and cell free supernatants of A. muciniphila, F. prausnitzii, B. thetaiotaomicron and B. fragilis for overnight. After RNA extraction and cDNA synthesis, the expression of studied genes was assessed by RT-qPCR. DNA methylation of studied genes was analyzed by Partek® Genomics Suite® software on the GSE174818 dataset. We used GSE164805 and GSE166552 datasets from COVID-19 patients to perform enrichment analysis by considering the mentioned genes via GEO2R, DAVID. Finally, the related microRNAs to GO terms concerned on the studied genes were identified by miRPath. RESULTS The downregulation of ACE, AGTR1, and ACE2 genes by A. muciniphila, F. prausnitzii, B. thetaiotaomicron, and B. fragilis in live, heat-inactivated, and cell-free supernatants was reported for the first time. These genes had hypomethylated DNA status in COVID-19 patients' raw data. The highest fold enrichment in upregulated RAS pathways and immune responses belonged to ACE, AGTR1, and ACE2 by considering the protein-protein interaction network. The common miRNAs targeting the studied genes were reported as miR-124-3p and miR-26b-5p. In combination with our experimental data and bioinformatic analysis, we showed the potential of A. muciniphila, F. prausnitzii, B. thetaiotaomicron, and B. fragilis and postbiotics to reduce ACE, ATR1, and ACE2 expression, which are essential genes that drive upregulated biological processes in COVID-19 patients. CONCLUSION Accordingly, due to the potential of studied bacteria on the alteration of ACE, AGTR1, ACE2 genes expression, understanding their correlation with demonstrated miRNAs expression could be valuable. These findings suggest the importance of considering targeted gut microbiota intervention when designing the possible therapeutic strategy for controlling the COVID-19.
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Affiliation(s)
- Sara Ahmadi Badi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Amin Malek
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Alessandro Paolini
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Mahya Rouhollahi Masoumi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Seyed Amirhesam Seyedi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Amir Amanzadeh
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran.
| | - Andrea Masotti
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
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Liu Z, Meng M, Ding S, Zhou X, Feng K, Huang T, Cai YD. Identification of methylation signatures and rules for predicting the severity of SARS-CoV-2 infection with machine learning methods. Front Microbiol 2022; 13:1007295. [PMID: 36212830 PMCID: PMC9537378 DOI: 10.3389/fmicb.2022.1007295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Patients infected with SARS-CoV-2 at various severities have different clinical manifestations and treatments. Mild or moderate patients usually recover with conventional medical treatment, but severe patients require prompt professional treatment. Thus, stratifying infected patients for targeted treatment is meaningful. A computational workflow was designed in this study to identify key blood methylation features and rules that can distinguish the severity of SARS-CoV-2 infection. First, the methylation features in the expression profile were deeply analyzed by a Monte Carlo feature selection method. A feature list was generated. Next, this ranked feature list was fed into the incremental feature selection method to determine the optimal features for different classification algorithms, thereby further building optimal classifiers. These selected key features were analyzed by functional enrichment to detect their biofunctional information. Furthermore, a set of rules were set up by a white-box algorithm, decision tree, to uncover different methylation patterns on various severity of SARS-CoV-2 infection. Some genes (PARP9, MX1, IRF7), corresponding to essential methylation sites, and rules were validated by published academic literature. Overall, this study contributes to revealing potential expression features and provides a reference for patient stratification. The physicians can prioritize and allocate health and medical resources for COVID-19 patients based on their predicted severe clinical outcomes.
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Affiliation(s)
- Zhiyang Liu
- School of Life Sciences, Changchun Sci-Tech University, Changchun, China
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - XiaoChao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
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Sampson C, Liang SY. The Tip of the Spear: Emergency Medicine and Missouri's Response to the COVID-19 Pandemic. MISSOURI MEDICINE 2022; 119:432-436. [PMID: 36337989 PMCID: PMC9616458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The COVID-19 pandemic provided the specialty of emergency medicine the opportunity to showcase what many knew all along: emergency physicians (EP) are well suited to deal with the unknown and can quickly adapt even with incomplete or limited information and resources. Emergency physicians in Missouri served in integral positions locally, nationally and internationally. Missouri EPs published numerous manuscripts on topics from basic science to clinical care. Device innovation also occurred with the development of protective devices for health care workers. As we approach the three-year mark of the COVID-19 pandemic, the burden of clinical care still weighs heavily on EPs. Each wave of the pandemic has brought challenges and spurred EPs to innovate in new ways. As Michigan EP Brian Zink, MD once said "Anyone, Anything, Anytime". These words correctly sum up emergency medicine. When others hesitated to care for COVID-19 patients, EPs stepped up despite uncertainty and risks to their own health. Emergency medicine has led the way and continues to innovate and push the envelope of emergency care.
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Affiliation(s)
- Christopher Sampson
- Department of Emergency Medicine, University of Missouri - Columbia School of Medicine, Columbia, Missouri
| | - Stephen Y Liang
- Department of Emergency Medicine and the Division of Infectious Diseases, Department of Medicine at Washington University School of Medicine, St. Louis, Missouri
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Verschoor CP, Belsky DW, Andrew MK, Haynes L, Loeb M, Pawelec G, McElhaney JE, Kuchel GA. Advanced biological age is associated with improved antibody responses in older high-dose influenza vaccine recipients over four consecutive seasons. Immun Ageing 2022; 19:39. [PMID: 35999604 PMCID: PMC9396565 DOI: 10.1186/s12979-022-00296-7] [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: 05/30/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022]
Abstract
Background Biological aging represents a loss of integrity and functionality of physiological systems over time. While associated with an enhanced risk of adverse outcomes such as hospitalization, disability and death following infection, its role in perceived age-related declines in vaccine responses has yet to be fully elucidated. Using data and biosamples from a 4-year clinical trial comparing immune responses of standard- and high-dose influenza vaccination, we quantified biological age (BA) prior to vaccination in adults over 65 years old (n = 292) using a panel of ten serological biomarkers (albumin, alanine aminotransferase, creatinine, ferritin, free thyroxine, cholesterol, high-density lipoprotein, triglycerides, tumour necrosis factor, interleukin-6) as implemented in the BioAge R package. Hemagglutination inhibition antibody titres against influenza A/H1N1, A/H3N2 and B were quantified prior to vaccination and 4-, 10- and 20- weeks post-vaccination. Results Counter to our hypothesis, advanced BA was associated with improved post-vaccination antibody titres against the different viral types and subtypes. However, this was dependent on both vaccine dose and CMV serostatus, as associations were only apparent for high-dose recipients (d = 0.16–0.26), and were largely diminished for CMV positive high-dose recipients. Conclusions These findings emphasize two important points: first, the loss of physiological integrity related to biological aging may not be a ubiquitous driver of immune decline in older adults; and second, latent factors such as CMV infection (prevalent in up to 90% of older adults worldwide) may contribute to the heterogeneity in vaccine responses of older adults more than previously thought. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-022-00296-7.
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Chen M, Ma Y, Chang W. SARS-CoV-2 and the Nucleus. Int J Biol Sci 2022; 18:4731-4743. [PMID: 35874947 PMCID: PMC9305274 DOI: 10.7150/ijbs.72482] [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: 02/28/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by an RNA virus, SARS-CoV-2. The genome of SARS-CoV-2 lacks a nuclear phase in its life cycle and is replicated in the cytoplasm. However, interfering with nuclear trafficking using pharmacological inhibitors greatly reduces virus infection and virus replication of other coronaviruses is blocked in enucleated cells, suggesting a critical role of the nucleus in virus infection. Here, we summarize the alternations of nuclear pathways caused by SARS-CoV-2, including nuclear translocation pathways, innate immune responses, mRNA metabolism, epigenetic mechanisms, DNA damage response, cytoskeleton regulation, and nuclear rupture. We consider how these alternations contribute to virus replication and discuss therapeutic treatments that target these pathways, focusing on small molecule drugs that are being used in clinical studies.
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Affiliation(s)
- Mengqi Chen
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Yue Ma
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Sci Rep 2022; 12:11714. [PMID: 35810186 PMCID: PMC9271053 DOI: 10.1038/s41598-022-15668-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation of classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.
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Lee Y, Riskedal E, Kalleberg KT, Istre M, Lind A, Lund-Johansen F, Reiakvam O, Søraas AVL, Harris JR, Dahl JA, Hadley CL, Jugessur A. EWAS of post-COVID-19 patients shows methylation differences in the immune-response associated gene, IFI44L, three months after COVID-19 infection. Sci Rep 2022; 12:11478. [PMID: 35798818 PMCID: PMC9261254 DOI: 10.1038/s41598-022-15467-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/23/2022] [Indexed: 11/24/2022] Open
Abstract
Although substantial progress has been made in managing COVID-19, it is still difficult to predict a patient’s prognosis. We explored the epigenetic signatures of COVID-19 in peripheral blood using data from an ongoing prospective observational study of COVID-19 called the Norwegian Corona Cohort Study. A series of EWASs were performed to compare the DNA methylation profiles between COVID-19 cases and controls three months post-infection. We also investigated differences associated with severity and long-COVID. Three CpGs—cg22399236, cg03607951, and cg09829636—were significantly hypomethylated (FDR < 0.05) in COVID-19 positive individuals. cg03607951 is located in IFI44L which is involved in innate response to viral infection and several systemic autoimmune diseases. cg09829636 is located in ANKRD9, a gene implicated in a wide variety of cellular processes, including the degradation of IMPDH2. The link between ANKRD9 and IMPDH2 is striking given that IMPDHs are considered therapeutic targets for COVID-19. Furthermore, gene ontology analyses revealed pathways involved in response to viruses. The lack of significant differences associated with severity and long-COVID may be real or reflect limitations in sample size. Our findings support the involvement of interferon responsive genes in the pathophysiology of COVID-19 and indicate a possible link to systemic autoimmune diseases.
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Affiliation(s)
- Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway
| | | | | | - Mette Istre
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital Ullevaal, 0372, Oslo, Norway
| | | | - Olaug Reiakvam
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Arne V L Søraas
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Jennifer R Harris
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | | | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, P.O. box 7804, 5020, Bergen, Norway
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41
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Attia MH. A cautionary note on altered pace of aging in the COVID-19 era. Forensic Sci Int Genet 2022; 59:102724. [PMID: 35598567 PMCID: PMC9112667 DOI: 10.1016/j.fsigen.2022.102724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/18/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is highly age-dependent due to hi-jacking the molecular control of the immune cells by the severe acute respiratory syndrome-corona virus 2 (SARS-CoV-2) leading to aberrant DNA methylation (DNAm) pattern of blood in comparison to normal individuals. These epigenetic modifications have been linked to perturbations to the epigenetic clock, development of long COVID-19 syndrome, and all-cause mortality risk. I reviewed the effects of COVID-19 on different molecular age markers such as the DNAm, telomere length (TL), and signal joint T-cell receptor excision circle (sjTREC). Integrating the accumulated clinical research data, COVID-19 and novel medical management may alter the pace of aging in adult individuals (<60 years). As such, COVID-19 might be a confounder in epigenetic age estimation similar to life style diversities, pathogens and pathologies which may influence the interpretation of DNAm data. Similarly, the SARS-CoV-2 affects T-lymphocyte function with possible influence on sjTREC levels. In contrast, TL measurements performed years before the SARS-CoV-2 pandemic proved that short TL predisposes to severe COVID- 19 independently from chronological age. However, the persistence of COVID-19 epigenetic scars and the durability of the immune response after vaccination and their effect on the ongoing pace of aging are still unknown. In the light of these data, the heterogeneous nature of the samples in these studies mandates a systematic evaluation of the currrent methods. SARS-CoV-2 may modify the reliability of the age estimation models in real casework because blood is the most common biological sample encountered in forensic contexts.
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42
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Breen EC, Sehl ME, Shih R, Langfelder P, Wang R, Horvath S, Bream JH, Duggal P, Martinson J, Wolinsky SM, Martínez-Maza O, Ramirez CM, Jamieson BD. Accelerated aging with HIV begins at the time of initial HIV infection. iScience 2022; 25:104488. [PMID: 35880029 PMCID: PMC9308149 DOI: 10.1016/j.isci.2022.104488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/06/2021] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Living with HIV infection is associated with early onset of aging-related chronic conditions, sometimes described as accelerated aging. Epigenetic DNA methylation patterns can evaluate acceleration of biological age relative to chronological age. The impact of initial HIV infection on five epigenetic measures of aging was examined before and approximately 3 years after HIV infection in the same individuals (n=102). Significant epigenetic age acceleration (median 1.9-4.8 years) and estimated telomere length shortening (all p≤ 0.001) were observed from pre-to post-HIV infection, and remained significant in three epigenetic measures after controlling for T cell changes. No acceleration was seen in age- and time interval-matched HIV-uninfected controls. Changes in genome-wide co-methylation clusters were also significantly associated with initial HIV infection (p≤ 2.0 × 10-4). These longitudinal observations clearly demonstrate an early and substantial impact of HIV infection on the epigenetic aging process, and suggest a role for HIV itself in the earlier onset of clinical aging.
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Affiliation(s)
- Elizabeth Crabb Breen
- Cousins Center for Psychoneuroimmunology, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mary E. Sehl
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roger Shih
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Peter Langfelder
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ruibin Wang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MA 21205, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA,Altos Labs, San Diego, CA 92121, USA
| | - Jay H. Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MA 21205, USA
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Otoniel Martínez-Maza
- Departments of Obstetrics & Gynecology and Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Christina M. Ramirez
- Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beth D. Jamieson
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA,Corresponding author
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43
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Huoman J, Sayyab S, Apostolou E, Karlsson L, Porcile L, Rizwan M, Sharma S, Das J, Rosén A, Lerm M. Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro. Epigenetics 2022; 17:1875-1891. [PMID: 35758003 PMCID: PMC9665140 DOI: 10.1080/15592294.2022.2089471] [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] [Indexed: 11/29/2022] Open
Abstract
A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.
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Affiliation(s)
- Johanna Huoman
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Shumaila Sayyab
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Eirini Apostolou
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lovisa Karlsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucas Porcile
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Muhammad Rizwan
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sumit Sharma
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jyotirmoy Das
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anders Rosén
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria Lerm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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44
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Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution. Genes (Basel) 2022; 13:genes13071109. [DOI: 10.3390/genes13071109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell transcriptome studies have revealed immune dysfunction in COVID-19 patients, including lymphopenia, T cell exhaustion, and increased levels of pro-inflammatory cytokines, while DNA methylation plays an important role in the regulation of immune response and inflammatory response. The specific cell types of immune responses regulated by DNA methylation in COVID-19 patients will be better understood by exploring the COVID-19 DNA methylation variation at the cell-type level. Here, we developed an analytical pipeline to explore single-cell DNA methylation variations in COVID-19 patients by transferring bulk-tissue-level knowledge to the single-cell level. We discovered that the methylation variations in the whole blood of COVID-19 patients showed significant cell-type specificity with remarkable enrichment in gamma-delta T cells and presented a phenomenon of hypermethylation and low expression. Furthermore, we identified five genes whose methylation variations were associated with several cell types. Among them, S100A9, AHNAK, and CX3CR1 have been reported as potential COVID-19 biomarkers previously, and the others (TRAF3IP3 and LFNG) are closely associated with the immune and virus-related signaling pathways. We propose that they might serve as potential epigenetic biomarkers for COVID-19 and could play roles in important biological processes such as the immune response and antiviral activity.
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45
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Fava VM, Bourgey M, Nawarathna PM, Orlova M, Cassart P, Vinh DC, Cheng MP, Bourque G, Schurr E, Langlais D. A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19. SCIENCE ADVANCES 2022; 8:eabm2510. [PMID: 35648852 PMCID: PMC9159580 DOI: 10.1126/sciadv.abm2510] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Despite the availability of highly efficacious vaccines, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lacks effective drug treatment, which results in a high rate of mortality. To address this therapeutic shortcoming, we applied a systems biology approach to the study of patients hospitalized with severe COVID. We show that, at the time of hospital admission, patients who were equivalent on the clinical ordinal scale displayed significant differential monocyte epigenetic and transcriptomic attributes between those who would survive and those who would succumb to COVID-19. We identified messenger RNA metabolism, RNA splicing, and interferon signaling pathways as key host responses overactivated by patients who would not survive. Those pathways are prime drug targets to reduce mortality of critically ill patients with COVID-19, leading us to identify tacrolimus, zotatifin, and nintedanib as three strong candidates for treatment of severely ill patients at the time of hospital admission.
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Affiliation(s)
- Vinicius M. Fava
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pubudu M. Nawarathna
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Marianna Orlova
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pauline Cassart
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Donald C. Vinh
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
| | - Matthew Pellan Cheng
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
- Corresponding author. (D.L.); (E.S.)
| | - David Langlais
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
- Corresponding author. (D.L.); (E.S.)
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46
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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: 15] [Impact Index Per Article: 7.5] [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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47
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Liu Z, Kilic G, Li W, Bulut O, Gupta MK, Zhang B, Qi C, Peng H, Tsay HC, Soon CF, Mekonnen YA, Ferreira AV, van der Made CI, van Cranenbroek B, Koenen HJPM, Simonetti E, Diavatopoulos D, de Jonge MI, Müller L, Schaal H, Ostermann PN, Cornberg M, Eiz-Vesper B, van de Veerdonk F, van Crevel R, Joosten LAB, Domínguez-Andrés J, Xu CJ, Netea MG, Li Y. Multi-Omics Integration Reveals Only Minor Long-Term Molecular and Functional Sequelae in Immune Cells of Individuals Recovered From COVID-19. Front Immunol 2022; 13:838132. [PMID: 35464396 PMCID: PMC9022455 DOI: 10.3389/fimmu.2022.838132] [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: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
The majority of COVID-19 patients experience mild to moderate disease course and recover within a few weeks. An increasing number of studies characterized the long-term changes in the specific anti-SARS-CoV-2 immune responses, but how COVID-19 shapes the innate and heterologous adaptive immune system after recovery is less well known. To comprehensively investigate the post-SARS-CoV-2 infection sequelae on the immune system, we performed a multi-omics study by integrating single-cell RNA-sequencing, single-cell ATAC-sequencing, genome-wide DNA methylation profiling, and functional validation experiments in 14 convalescent COVID-19 and 15 healthy individuals. We showed that immune responses generally recover without major sequelae after COVID-19. However, subtle differences persist at the transcriptomic level in monocytes, with downregulation of the interferon pathway, while DNA methylation also displays minor changes in convalescent COVID-19 individuals. However, these differences did not affect the cytokine production capacity of PBMCs upon different bacterial, viral, and fungal stimuli, although baseline release of IL-1Ra and IFN-γ was higher in convalescent individuals. In conclusion, we propose that despite minor differences in epigenetic and transcriptional programs, the immune system of convalescent COVID-19 patients largely recovers to the homeostatic level of healthy individuals.
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Affiliation(s)
- Zhaoli Liu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Gizem Kilic
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wenchao Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Ozlem Bulut
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Bowen Zhang
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Cancan Qi
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Hsin-Chieh Tsay
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Chai Fen Soon
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Yonatan Ayalew Mekonnen
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Anaísa Valido Ferreira
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Caspar I van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bram van Cranenbroek
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Elles Simonetti
- Laboratory of Pediatric Infectious Diseases, Radboud Centre for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dimitri Diavatopoulos
- Laboratory of Pediatric Infectious Diseases, Radboud Centre for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marien I de Jonge
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisa Müller
- Institute of Virology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Dusseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Dusseldorf, Germany
| | - Philipp N Ostermann
- Institute of Virology, University Hospital Duesseldorf, Medical Faculty, Heinrich Heine University Duesseldorf, Dusseldorf, Germany
| | - Markus Cornberg
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Frank van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
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48
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Cao X, Li W, Wang T, Ran D, Davalos V, Planas-Serra L, Pujol A, Esteller M, Wang X, Yu H. Accelerated biological aging in COVID-19 patients. Nat Commun 2022; 13:2135. [PMID: 35440567 PMCID: PMC9018863 DOI: 10.1038/s41467-022-29801-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/30/2022] [Indexed: 01/01/2023] Open
Abstract
Chronological age is a risk factor for SARS-CoV-2 infection and severe COVID-19. Previous findings indicate that epigenetic age could be altered in viral infection. However, the epigenetic aging in COVID-19 has not been well studied. In this study, DNA methylation of the blood samples from 232 healthy individuals and 413 COVID-19 patients is profiled using EPIC methylation array. Epigenetic ages of each individual are determined by applying epigenetic clocks and telomere length estimator to the methylation profile of the individual. Epigenetic age acceleration is calculated and compared between groups. We observe strong correlations between the epigenetic clocks and individual's chronological age (r > 0.8, p < 0.0001). We also find the increasing acceleration of epigenetic aging and telomere attrition in the sequential blood samples from healthy individuals and infected patients developing non-severe and severe COVID-19. In addition, the longitudinal DNA methylation profiling analysis find that the accumulation of epigenetic aging from COVID-19 syndrome could be partly reversed at late clinic phases in some patients. In conclusion, accelerated epigenetic aging is associated with the risk of SARS-CoV-2 infection and developing severe COVID-19. In addition, the accumulation of epigenetic aging from COVID-19 may contribute to the post-COVID-19 syndrome among survivors.
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Affiliation(s)
- Xue Cao
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China.,Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjuan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Wang
- Research & Development, Thermo Fisher Scientific Inc., Los Angeles, CA, USA
| | - Dongzhi Ran
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.,Key Laboratory of Biochemistry and Molecular Pharmacology, Department of Pharmacology, Chongqing Medical University, Chongqing, China
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xiaolin Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huichuan Yu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China. .,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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49
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Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods C. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. RESEARCH SQUARE 2022:rs.3.rs-1479864. [PMID: 35411343 PMCID: PMC8996625 DOI: 10.21203/rs.3.rs-1479864/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associate with mild or moderate symptoms are already robust and include severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity is marked by upregulation classical antiviral pathways including those regulating IRF1 and IRF7, whereas in moderate disease these classical antiviral signals diminish suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.
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50
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Mahmoodpoor A, Sanaie S, Roudbari F, Sabzevari T, Sohrabifar N, Kazeminasab S. Understanding the role of telomere attrition and epigenetic signatures in COVID-19 severity. Gene 2022; 811:146069. [PMID: 34848322 PMCID: PMC8634871 DOI: 10.1016/j.gene.2021.146069] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/12/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022]
Abstract
Within the past several decades, the emergence and spread of infectious diseases with pandemic potential have endangered human lives. Coronavirus disease 2019 (COVID-19) outbreak represents an unprecedented threat for all health systems worldwide. The clinical spectrum of COVID-19 is highly heterogeneous, ranging from asymptomatic and mild upper respiratory tract illness to severe interstitial pneumonia with respiratory failure and even death. Highly age-dependent patterns of immune response potentially explain the higher rates of the severe forms of COVID-19 in elderly patients. However, genetic and epigenetic architecture can influence multiple biological processes during the lifespan, therefore as far as our knowledge shows, vulnerability to viral infection concerning telomere length and epigenetic signature is not a new idea. This review aims is to summarize the current understanding of the role of telomere length and epigenetic mechanisms on the severity of COVID-19. The current knowledge highlights the significant association between the shorter telomere length and the higher risk of developing severe COVID-19. Differential DNA methylation patterns and miRNA expression profiles imply that these hallmarks can play a pivotal role in COVID- 19 pathogenesis. Understanding the causes of inter-individual variations in COVID-19 outcomes could provide clues to the development of the personalized therapeutic intervention.
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Affiliation(s)
- Ata Mahmoodpoor
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sarvin Sanaie
- Neurosciences Research center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Tara Sabzevari
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasim Sohrabifar
- Cardiovascular Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Kazeminasab
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Vice-Chancellor, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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