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Liang S, Zheng YY, Pan Y. Blood transcriptome analysis uncovered COVID-19-myocarditis crosstalk. Microb Pathog 2024; 189:106587. [PMID: 38373644 DOI: 10.1016/j.micpath.2024.106587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND The condition of COVID-19-related myocarditis has emerged as a prominent contributor to COVID-19 mortality. As the epidemic persists, its incidence continues to rise. Despite ongoing efforts, the elucidation of COVID-19-related myocarditis underlying molecular mechanisms still requires further investigation. METHODS Hub genes for COVID-19-related myocarditis were screened by integrating gene expression profile analysis via differential expression in COVID-19 (GSE196822) and myocarditis (GSE148153 and GSE147517). After verification with independent datasets (GSE211979, GSE167028, GSE178491 and GSE215865), the hub genes were studied using a range of systems-biology approaches, such as ceRNA, TF-mRNA networks and PPI networks, as well as gene ontology, pathway enrichment, immune infiltration analysis and drug target identification. RESULTS TBKBP1 and ERGIC1 were identified as COVID-19-related myocarditis hub genes via integrated bioinformatics analysis. In addition, receiver operating characteristic curves constructed based on the expression levels of TBKBP1 and ERGIC1 could effectively distinguish healthy control individuals from patients with COVID-19. Functional enrichment analysis suggested several enriched biological pathways related to inflammation and immune response. Immune cell changes correlated with TBKBP1 and ERGIC1 levels in patients with COVID-19 or patients with COVID-19 and myocarditis. Tamibarotene, methotrexate and theophylline were identified as a potential drug targeting TBKBP1 and ERGIC1. CONCLUSION TBKBP1 and ERGIC1 were identified as crucial genes in the development of COVID-19-related myocarditis and have demonstrated a strong association with innate antiviral immunity. The present work may be helpful for further investigation of the molecular mechanisms and new therapeutic drug targets correlated with myocarditis in COVID-19.
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Affiliation(s)
- Shuang Liang
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China.
| | - Ying-Ying Zheng
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
| | - Ying Pan
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
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Sorosina M, Barizzone N, Clarelli F, Anand S, Lupoli S, Salvi E, Mangano E, Bordoni R, Roostaei T, Mascia E, Zuccalà M, Vecchio D, Cavalla P, Santoro S, Ferrè L, Zollo A, Barlassina C, Cusi D, Martinelli V, Comi G, Leone M, Filippi M, Patsopoulos NA, De Jager PL, De Bellis G, Esposito F, D'Alfonso S, Martinelli Boneschi F. A multi-step genomic approach prioritized TBKBP1 gene as relevant for multiple sclerosis susceptibility. J Neurol 2022; 269:4510-4522. [PMID: 35545683 PMCID: PMC9294010 DOI: 10.1007/s00415-022-11109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Background Over 200 genetic loci have been associated with multiple sclerosis (MS) explaining ~ 50% of its heritability, suggesting that additional mechanisms may account for the “missing heritability” phenomenon. Objective To analyze a large cohort of Italian individuals to identify markers associated with MS with potential functional impact in the disease. Methods We studied 2571 MS and 3234 healthy controls (HC) of continental Italian origin. Discovery phase included a genome wide association study (1727 MS, 2258 HC), with SNPs selected according to their association in the Italian cohort only or in a meta-analysis of signals with a cohort of European ancestry (4088 MS, 7144 HC). Top associated loci were then tested in two Italian cohorts through array-based genotyping (903 MS, 884 HC) and pool-based target sequencing (588 MS, 408 HC). Finally, functional prioritization through conditional eQTL and mQTL has been performed. Results Top associated signals overlap with already known MS loci on chromosomes 3 and 17. Three SNPs (rs4267364, rs8070463, rs67919208), all involved in the regulation of TBKBP1, were prioritized to be functionally relevant. Conclusions No evidence of novel signal of association with MS specific for the Italian continental population has been found; nevertheless, two MS loci seems to play a relevant role, raising the interest to further investigations for TBKBP1 gene. Supplementary Information The online version contains supplementary material available at 10.1007/s00415-022-11109-8.
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Affiliation(s)
- Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Nadia Barizzone
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Eastern Piedmont, Avogadro University, 28100, Novara, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Santosh Anand
- Department of Informatics, Systems and Communications (DISCo), University of Milano-Bicocca, Milan, Italy
| | - Sara Lupoli
- Department of Health Sciences, University of Milan, 20139, Milan, Italy
| | - Erika Salvi
- Department of Health Sciences, University of Milan, 20139, Milan, Italy
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133, Milan, Italy
| | - Eleonora Mangano
- National Research Council of Italy, Institute for Biomedical Technologies, Segrate, 20090, Milan, Italy
| | - Roberta Bordoni
- National Research Council of Italy, Institute for Biomedical Technologies, Segrate, 20090, Milan, Italy
| | - Tina Roostaei
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Miriam Zuccalà
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Eastern Piedmont, Avogadro University, 28100, Novara, Italy
| | - Domizia Vecchio
- MS Centre, SCDU Neurology, AOU Maggiore Della Carità, Department of Translational Medicine, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Eastern Piedmont Avogadro, 28100, Novara, Italy
| | - Paola Cavalla
- MS Center, Department of Neuroscience and Mental Health, City of Health and Science University Hospital of Torino, 10126, Turin, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Laura Ferrè
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Alen Zollo
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, 20122, Milan, Italy
| | | | - Daniele Cusi
- National Research Council of Italy, Institute for Biomedical Technologies, Segrate, 20090, Milan, Italy
- Bio4Dreams, Business Nursery for Life Sciences, Piazzale Principessa Clotilde 4/A, 20121, Milan, Italy
| | - Vittorio Martinelli
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giancarlo Comi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Maurizio Leone
- SC Neurologia, Dipartimento Di Scienze Mediche, IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- Vita-Salute San Raffaele University, 20132, Milan, Italy
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- Neurophysiology Unit, IRCCS San Raffaele Scientific Institute, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Gianluca De Bellis
- National Research Council of Italy, Institute for Biomedical Technologies, Segrate, 20090, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Eastern Piedmont, Avogadro University, 28100, Novara, Italy
| | - Filippo Martinelli Boneschi
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, 20122, Milan, Italy.
- Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
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