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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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Belmonte T, Perez-Pons M, Benítez ID, Molinero M, García-Hidalgo MC, Rodríguez-Muñoz C, Gort-Paniello C, Moncusí-Moix A, Madè A, Devaux Y, Martelli F, Ortega A, González J, Torres G, Barbé F, de Gonzalo-Calvo D. Addressing the unsolved challenges in microRNA-based biomarker development: Suitable endogenous reference microRNAs for SARS-CoV-2 infection severity. Int J Biol Macromol 2024; 269:131926. [PMID: 38688344 DOI: 10.1016/j.ijbiomac.2024.131926] [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: 09/20/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Circulating cell-free microRNAs (miRNAs) are promising biomarkers for medical decision-making. Suitable endogenous controls are essential to ensure reproducibility. We aimed to identify and validate endogenous reference miRNAs for qPCR data normalization in samples from SARS-CoV-2-infected hospitalized patients. We used plasma samples (n = 170) from COVID-19 patients collected at hospital admission (COVID-Ponent project, www.clinicaltrials.gov/NCT04824677). First, 179 miRNAs were profiled using RT-qPCR. After stability assessment, candidates were validated using the same methodology. miRNA stability was analyzed using the geNorm, NormFinder and BestKeeper algorithms. Stability was further evaluated using an RNA-seq dataset derived from COVID-19 hospitalized patients, along with plasma samples from patients with critical COVID-19 profiled using RT-qPCR. In the screening phase, after strict control of expression levels, stability assessment selected eleven candidates (miR-17-5p, miR-20a-5p, miR-30e-5p, miR-106a-5p, miR-151a-5p, miR-185-5p, miR-191-5p, miR-423-3p, miR-425-5p, miR-484 and miR-625-5p). In the validation phase, all algorithms identified miR-106a-5p and miR-484 as top endogenous controls. No association was observed between these miRNAs and clinical or sociodemographic characteristics. Both miRNAs were stably detected and showed low variability in the additional analyses. In conclusion, a 2-miRNA panel composed of miR-106a-5p and miR-484 constitutes a first-line normalizer for miRNA-based biomarker development using qPCR in hospitalized patients infected with SARS-CoV-2.
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Affiliation(s)
- Thalia Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Carlos Rodríguez-Muñoz
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Alisia Madè
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 MI, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 MI, Italy
| | - Alicia Ortega
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Gerencia Regional de Salud de Castilla y León, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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Tucker EJ, Wong SW, Marri S, Ali S, Fedele AO, Michael MZ, Rojas-Canales D, Li JY, Lim CK, Gleadle JM. SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection. iScience 2024; 27:108719. [PMID: 38226175 PMCID: PMC10788221 DOI: 10.1016/j.isci.2023.108719] [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: 06/23/2023] [Revised: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Many viruses produce microRNAs (miRNAs), termed viral miRNAs (v-miRNAs), with the capacity to target host gene expression. Bioinformatic and cell culture studies suggest that SARS-CoV-2 can also generate v-miRNAs. This patient-based study defines the SARS-CoV-2 encoded small RNAs present in nasopharyngeal swabs of patients with COVID-19 infection using small RNA-seq. A specific conserved sequence (CoV2-miR-O8) is defined that is not expressed in other coronaviruses but is preserved in all SARS-CoV-2 variants. CoV2-miR-O8 is highly represented in nasopharyngeal samples from patients with COVID-19 infection, is detected by RT-PCR assays in patients, has features consistent with Dicer and Drosha generation as well as interaction with Argonaute and targets specific human microRNAs.
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Affiliation(s)
- Elise J. Tucker
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Soon Wei Wong
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Shashikanth Marri
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Saira Ali
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Anthony O. Fedele
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
| | - Michael Z. Michael
- College of Medicine and Public Health, Flinders University, SA, Australia
- Department of Gastroenterology, Flinders Medical Centre, SA, Australia
| | - Darling Rojas-Canales
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Jordan Y. Li
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Chuan Kok Lim
- Infectious Diseases Laboratories, SA Pathology, SA, Australia
| | - Jonathan M. Gleadle
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
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Chen WC, Hu SY, Shen CF, Cheng MH, Hong JJ, Shen CJ, Cheng CM. COVID-19 Vaccination in Pregnancy: Pilot Study for Maternal and Neonatal MicroRNA Profiles. Vaccines (Basel) 2023; 11:1814. [PMID: 38140218 PMCID: PMC10747030 DOI: 10.3390/vaccines11121814] [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: 10/08/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
This pilot study explores alterations in miRNA profiles among pregnant women and their neonates upon receiving different doses of COVID-19 vaccines. Blood samples, including maternal blood (MB) and neonatal cord blood (CB), collected from five pregnant women were scrutinized using the miRNA PanelChip Analysis System, identifying nine distinct miRNAs, including miR-451a and miR-1972, which exhibited significant downregulation with two vaccine doses in both MB and CB. When compared with women vaccinated with four doses, miR-486-5p, miR-451a, and miR-1972 in the two-dose group also showed notable downregulation. Evaluating recipients of three and four doses, miR-423-5p and miR-1972 expression were significantly reduced in both MB and CB. Further comparative analysis highlighted a decline in miR-223-3p expression with increasing vaccine doses, while miR15a-5p, miR-16-5p, and miR-423-5p showed an upward trend. Notably, miR-451a, miR-1972, and miR-423-5p levels varied across doses and were associated with pathways such as "PI3K-Akt", "neurotrophin signaling", and "cortisol synthesis", suggesting the profound influence of vaccination on diverse molecular mechanisms. Our research has uncovered that escalating vaccine dosages impact miRNA profiles, which may be associated with the immunological response mechanisms in both the mother and fetus, thus indicating a substantial impact of vaccination on various molecular processes.
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Affiliation(s)
- Wei-Chun Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; (W.-C.C.); (S.-Y.H.)
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Obstetrics and Gynecology, New Taipei City Municipal Tucheng Hospital, New Taipei City 236, Taiwan
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu 300, Taiwan
- School of Traditional Chinese Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Shu-Yu Hu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; (W.-C.C.); (S.-Y.H.)
| | - Ching-Fen Shen
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Mei-Hsiu Cheng
- Taiwan Business Development Department, Inti Taiwan, Inc., Hsinchu 302, Taiwan; (M.-H.C.); (J.-J.H.)
| | - Jun-Jie Hong
- Taiwan Business Development Department, Inti Taiwan, Inc., Hsinchu 302, Taiwan; (M.-H.C.); (J.-J.H.)
| | - Ching-Ju Shen
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; (W.-C.C.); (S.-Y.H.)
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu 300, Taiwan
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Rojas-Cruz AF, Bermúdez-Santana CI. Computational Prediction of RNA-RNA Interactions between Small RNA Tracks from Betacoronavirus Nonstructural Protein 3 and Neurotrophin Genes during Infection of an Epithelial Lung Cancer Cell Line: Potential Role of Novel Small Regulatory RNA. Viruses 2023; 15:1647. [PMID: 37631989 PMCID: PMC10458423 DOI: 10.3390/v15081647] [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: 07/13/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Whether RNA-RNA interactions of cytoplasmic RNA viruses, such as Betacoronavirus, might end in the biogenesis of putative virus-derived small RNAs as miRNA-like molecules has been controversial. Even more, whether RNA-RNA interactions of wild animal viruses may act as virus-derived small RNAs is unknown. Here, we address these issues in four ways. First, we use conserved RNA structures undergoing negative selection in the genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 circulating in different bat species, intermediate animals, and human hosts. Second, a systematic literature review was conducted to identify Betacoronavirus-targeting hsa-miRNAs involved in lung cell infection. Third, we employed sophisticated long-range RNA-RNA interactions to refine the seed sequence homology of hsa-miRNAs with conserved RNA structures. Fourth, we used high-throughput RNA sequencing of a Betacoronavirus-infected epithelial lung cancer cell line (Calu-3) to validate the results. We proposed nine potential virus-derived small RNAs: two vsRNAs in SARS-CoV (Bats: SB-vsRNA-ORF1a-3p; SB-vsRNA-S-5p), one vsRNA in MERS-CoV (Bats: MB-vsRNA-ORF1b-3p), and six vsRNAs in SARS-CoV-2 (Bats: S2B-vsRNA-ORF1a-5p; intermediate animals: S2I-vsRNA-ORF1a-5p; and humans: S2H-vsRNA-ORF1a-5p, S2H-vsRNA-ORF1a-3p, S2H-vsRNA-ORF1b-3p, S2H-vsRNA-ORF3a-3p), mainly encoded by nonstructural protein 3. Notably, Betacoronavirus-derived small RNAs targeted 74 differentially expressed genes in infected human cells, of which 55 upregulate the molecular mechanisms underlying acute respiratory distress syndrome (ARDS), and the 19 downregulated genes might be implicated in neurotrophin signaling impairment. These results reveal a novel small RNA-based regulatory mechanism involved in neuropathogenesis that must be further studied to validate its therapeutic use.
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Affiliation(s)
- Alexis Felipe Rojas-Cruz
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Clara Isabel Bermúdez-Santana
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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Abyadeh M, Yadav VK, Kaya A. Common molecular signatures between coronavirus infection and Alzheimer's disease reveal targets for drug development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544970. [PMID: 37398415 PMCID: PMC10312734 DOI: 10.1101/2023.06.14.544970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cognitive decline has been reported as a common consequence of COVID-19, and studies have suggested a link between COVID-19 infection and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. To shed light on this link, we conducted an integrated genomic analysis using a novel Robust Rank Aggregation method to identify common transcriptional signatures of the frontal cortex, a critical area for cognitive function, between individuals with AD and COVID-19. We then performed various analyses, including the KEGG pathway, GO ontology, protein-protein interaction, hub gene, gene-miRNA, and gene-transcription factor interaction analyses to identify molecular components of biological pathways that are associated with AD in the brain also show similar changes in severe COVID-19. Our findings revealed the molecular mechanisms underpinning the association between COVID-19 infection and AD development and identified several genes, miRNAs, and TFs that may be targeted for therapeutic purposes. However, further research is needed to investigate the diagnostic and therapeutic applications of these findings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Vijay K. Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284 USA
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Abyadeh M, Yadav VK, Kaya A. Common Molecular Signatures Between Coronavirus Infection and Alzheimer's Disease Reveal Targets for Drug Development. J Alzheimers Dis 2023; 95:995-1011. [PMID: 37638446 DOI: 10.3233/jad-230684] [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] [Indexed: 08/29/2023]
Abstract
BACKGROUND Cognitive decline is a common consequence of COVID-19, and studies suggest a link between COVID-19 and Alzheimer's disease (AD). However, the molecular mechanisms underlying this association remain unclear. OBJECTIVE To understand the potential molecular mechanisms underlying the association between COVID-19 and AD development, and identify the potential genetic targets for pharmaceutical approaches to reduce the risk or delay the development of COVID-19-related neurological pathologies. METHODS We analyzed transcriptome datasets of 638 brain samples using a novel Robust Rank Aggregation method, followed by functional enrichment, protein-protein, hub genes, gene-miRNA, and gene-transcription factor (TF) interaction analyses to identify molecular markers altered in AD and COVID-19 infected brains. RESULTS Our analyses of frontal cortex from COVID-19 and AD patients identified commonly altered genes, miRNAs and TFs. Functional enrichment and hub gene analysis of these molecular changes revealed commonly altered pathways, including downregulation of the cyclic adenosine monophosphate (cAMP) signaling and taurine and hypotaurine metabolism, alongside upregulation of neuroinflammatory pathways. Furthermore, gene-miRNA and gene-TF network analyses provided potential up- and downstream regulators of identified pathways. CONCLUSION We found that downregulation of cAMP signaling pathway, taurine metabolisms, and upregulation of neuroinflammatory related pathways are commonly altered in AD and COVID-19 pathogenesis, and may make COVID-19 patients more susceptible to cognitive decline and AD. We also identified genetic targets, regulating these pathways that can be targeted pharmaceutically to reduce the risk or delay the development of COVID-19-related neurological pathologies and AD.
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Affiliation(s)
- Morteza Abyadeh
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
| | - Vijay K Yadav
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Common wealth University, Richmond, VA, USA
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