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Balnis J, Madrid A, Drake LA, Vancavage R, Tiwari A, Patel VJ, Ramos RB, Schwarz JJ, Yucel R, Singer HA, Alisch RS, Jaitovich A. Blood DNA methylation in post-acute sequelae of COVID-19 (PASC): a prospective cohort study. EBioMedicine 2024; 106:105251. [PMID: 39024897 PMCID: PMC11286994 DOI: 10.1016/j.ebiom.2024.105251] [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: 04/19/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND DNA methylation integrates environmental signals with transcriptional programs. COVID-19 infection induces changes in the host methylome. While post-acute sequelae of COVID-19 (PASC) is a long-term complication of acute illness, its association with DNA methylation is unknown. No universal blood marker of PASC, superseding single organ dysfunctions, has yet been identified. METHODS In this single centre prospective cohort study, PASC, post-COVID without PASC, and healthy participants were enrolled to investigate their symptoms association with peripheral blood DNA methylation data generated with state-of-the-art whole genome sequencing. PASC-induced quality-of-life deterioration was scored with a validated instrument, SF-36. Analyses were conducted to identify potential functional roles of differentially methylated loci, and machine learning algorithms were used to resolve PASC severity. FINDINGS 103 patients with PASC (22.3% male, 77.7% female), 15 patients with previous COVID-19 infection but no PASC (40.0% male, 60.0% female), and 27 healthy volunteers (48.1% male, 51.9% female) were enrolled. Whole genome methylation sequencing revealed 39 differentially methylated regions (DMRs) specific to PASC, each harbouring an average of 15 consecutive positions, that differentiate patients with PASC from the two control groups. Motif analyses of PASC-regulated DMRs identify binding domains for transcription factors regulating circadian rhythm and others. Some DMRs annotated to protein coding genes were associated with changes of RNA expression. Machine learning support vector algorithm and random forest hierarchical clustering reveal 28 unique differentially methylated positions (DMPs) in the genome discriminating patients with better and worse quality of life. INTERPRETATION Blood DNA methylation levels identify PASC, stratify PASC severity, and suggest that DNA motifs are targeted by circadian rhythm-regulating pathways in PASC. FUNDING This project has been funded by the following agencies: NIH-AI173035 (A. Jaitovich and R. Alisch); and NIH-AG066179 (R. Alisch).
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Rachel Vancavage
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Vraj J Patel
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Ramon Bossardi Ramos
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - John J Schwarz
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Recai Yucel
- Department of Epidemiology and Biostatistics, Temple University, PA, USA
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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Cesar-Silva D, Pereira-Dutra FS, Giannini ALM, Maya-Monteiro CM, de Almeida CJG. Lipid compartments and lipid metabolism as therapeutic targets against coronavirus. Front Immunol 2023; 14:1268854. [PMID: 38106410 PMCID: PMC10722172 DOI: 10.3389/fimmu.2023.1268854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023] Open
Abstract
Lipids perform a series of cellular functions, establishing cell and organelles' boundaries, organizing signaling platforms, and creating compartments where specific reactions occur. Moreover, lipids store energy and act as secondary messengers whose distribution is tightly regulated. Disruption of lipid metabolism is associated with many diseases, including those caused by viruses. In this scenario, lipids can favor virus replication and are not solely used as pathogens' energy source. In contrast, cells can counteract viruses using lipids as weapons. In this review, we discuss the available data on how coronaviruses profit from cellular lipid compartments and why targeting lipid metabolism may be a powerful strategy to fight these cellular parasites. We also provide a formidable collection of data on the pharmacological approaches targeting lipid metabolism to impair and treat coronavirus infection.
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Affiliation(s)
- Daniella Cesar-Silva
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Filipe S. Pereira-Dutra
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Lucia Moraes Giannini
- Laboratory of Functional Genomics and Signal Transduction, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa M. Maya-Monteiro
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratory of Endocrinology and Department of Endocrinology and Metabolism, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Cecília Jacques G. de Almeida
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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