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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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2
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Maqbool M, Hussain MS, Shaikh NK, Sultana A, Bisht AS, Agrawal M. Noncoding RNAs in the COVID-19 Saga: An Untold Story. Viral Immunol 2024. [PMID: 38968365 DOI: 10.1089/vim.2024.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024] Open
Affiliation(s)
- Mudasir Maqbool
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, India
| | - Md Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Nusrat K Shaikh
- Department of Quality Assurance, Smt. N. M. Padalia Pharmacy College, Ahmedabad, India
| | - Ayesha Sultana
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya University, Mangalore, India
| | - Ajay Singh Bisht
- Shri Guru Ram Rai University School of Pharmaceutical Sciences, Dehradun, India
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K. R. Mangalam University, Gurugram, India
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Bermudez-Santana CI, Gallego-Gómez JC. Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses 2024; 16:804. [PMID: 38793685 PMCID: PMC11125801 DOI: 10.3390/v16050804] [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: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.
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Affiliation(s)
- Clara Isabel Bermudez-Santana
- Computational and theoretical RNomics Group, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Gallego-Gómez
- Grupo de Medicina de Traslación, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
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4
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Gamero-de-Luna EJ, Sánchez-Jaén MR. [Genetic factors associated with long COVID]. Semergen 2024; 50:102187. [PMID: 38277732 DOI: 10.1016/j.semerg.2023.102187] [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: 09/19/2023] [Accepted: 10/01/2023] [Indexed: 01/28/2024]
Abstract
INTRODUCTION The variability in expression and evolution of COVID is not completely explained by clinical factors. In fact, genetic factors play an important role. Moreover, it is unknown whether the genetic factor that contribute to susceptibility and severity are also involved in the onset and evolution of long-COVID. The objective of this review is to gather information from literature to understand which genetic factors are involved in the onset of persistent COVID. MATERIAL AND METHODS Systematic review in PubMed and bioRxiv and medRxiv repositories based on MeSH-descriptors and MeSH-terms related to COVID and genetic factors. Using these terms 2715 articles were pooled. An initial screening performed by authors independently, selected 205 articles of interest. A final deeper screening a total of 85 articles were chosen for complete reading and summarized in this review. RESULTS Although ACE2 and TMPSS6 are involved in COVID susceptibility, their involvement in long-COVID has not been found. On the other hand, the severity of the disease and the onset of long-COVID has been associated with different genes involved in the inflammatory and immune response. Particularly interesting has been the association found with the FOXP4 locus. CONCLUSIONS Although studies on long-COVID are insufficient to fully comprehend the cause, it is clear that the current identified genetic factors do not fully explain the progression and onset of long-COVID. Other factors such as polygenic action, pleiotropic genes, the microbiota and epigenetic changes must be considered and studied.
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Affiliation(s)
- E J Gamero-de-Luna
- Medicina Familiar y Comunitaria, Centro de Salud El Juncal, Sevilla, España; GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España.
| | - M R Sánchez-Jaén
- GT Medicina Genómica Personalizada y Enfermedades Raras, SEMERGEN, España; Medicina Familiar y Comunitaria, Centro de Salud de Fabero, León, España
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Shbeer AM. Mystery of COVID 19: Focusing on important ncRNAs and effective signaling pathways. Pathol Res Pract 2024; 255:155155. [PMID: 38354486 DOI: 10.1016/j.prp.2024.155155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
This article provides a thorough investigation of the essential role of non-coding RNAs (ncRNAs) in the context of COVID-19, emphasizing their impact on the complex molecular dynamics of the viral infection. By conducting a systematic review of existing literature, we identify key ncRNAs involved in different stages of the viral life cycle, modulation of host immune response, and disease progression. The importance of microRNAs, long non-coding RNAs, and other ncRNA types emerges as influential factors in shaping the interaction between the host and the virus. Additionally, the study delves into the effective signaling pathways linked to COVID-19 pathogenesis, uncovering intricate molecular cascades that govern viral entry, replication, and host cell response. This exploration encompasses established pathways such as IL-6/JAK/STAT signaling, highlighting their interplay within the context of COVID-19. By synthesizing this knowledge, our aim is not only to enhance our understanding of the molecular complexities of COVID-19 but also to reveal potential therapeutic targets. Through elucidating the interaction between ncRNAs and signaling pathways, our article seeks to contribute to ongoing efforts in developing targeted interventions against COVID-19, ultimately advancing our ability to address this global health crisis.
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Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
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6
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Sefatjoo Z, Mohebbi SR, Hosseini SM, Shoraka S, Saeedi Niasar M, Baghaei K, Meyfour A, Sadeghi A, Malekpour H, Asadzadeh Aghdaei H, Zali MR. Evaluation of long non-coding RNAs EGOT, NRAV, NRIR and mRNAs ISG15 and IFITM3 expressions in COVID-19 patients. Cytokine 2024; 175:156495. [PMID: 38184893 DOI: 10.1016/j.cyto.2023.156495] [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: 03/27/2023] [Revised: 08/26/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Individuals with Coronavirus Disease 2019 (COVID-19) may show no symptoms to moderate or severe complications. This variation may be due to differences in the strength of the immune response, including a delayed interferon (IFN) response in asymptomatic patients and higher IFN levels in severe patients. Some long non-coding RNAs (lncRNAs), as regulators of the IFN pathway, may contribute to the emergence of different COVID-19 symptoms. This study aimed to comparatively investigate the relationship between lncRNAs (eosinophil granule ontogeny transcript (EGOT), negative regulator of antiviral response (NRAV), and negative regulator of interferon response (NRIR)), alongside interferon-stimulated genes (ISGs) like ISG-15 and interferon-induced transmembrane protein 3 (IFITM3) in COVID-19 patients with asymptomatic, moderate, and severe symptoms. Buffy coat samples were collected from 17 asymptomatic, 23 moderate, 22 severe patients, and 44 healthy controls. Quantitative real-time PCR was utilized to determine the expression levels. In a comparison between COVID-19 patients and healthy individuals, higher expression levels of EGOT and NRAV were observed in severe and moderate patients. NRIR expression was increased across all patient groups. Meanwhile, ISG15 expression decreased in all patient groups, and the moderate group showed a significant decrease in IFITM3 expression. Comparing COVID-19 patient groups, EGOT expression was significantly higher in moderate COVID-19 patients compared to asymptomatic patients. NRAV was higher in moderate and severe patients compared to asymptomatic. NRIR levels did not differ significantly between the COVID-19 patient groups. ISG15 was higher in moderate and severe patients compared to asymptomatic. IFITM3 expression was significantly higher in severe patients compared to the moderate group. In severe COVID-19 patients, EGOT expression was positively correlated with NRAV levels. EGOT and NRAV showed a significant positive correlation in asymptomatic patients, and both were positively correlated with IFITM3 expression. This study suggests that EGOT, NRAV, NRIR, ISG15, and IFITM3 may serve as diagnostic biomarkers for COVID-19. The lncRNA NRAV may be a good biomarker in a prognostic panel between asymptomatic and severe patients in combination with other high-sensitivity biomarkers. EGOT, NRAV, and ISG15 could also be considered as specific biomarkers in a prognostic panel comparing asymptomatic and moderate patients with other high-sensitivity biomarkers.
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Affiliation(s)
- Zahra Sefatjoo
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Shahrzad Shoraka
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Saeedi Niasar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Habib Malekpour
- Research and Development Center, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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Luo M, Wang C, Guo J, Wen K, Yang C, Ni K, Liu L, Pan Y, Li J, Deng L. High Stretch Modulates cAMP/ATP Level in Association with Purine Metabolism via miRNA-mRNA Interactions in Cultured Human Airway Smooth Muscle Cells. Cells 2024; 13:110. [PMID: 38247802 PMCID: PMC10813996 DOI: 10.3390/cells13020110] [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: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024] Open
Abstract
High stretch (>10% strain) of airway smooth muscle cells (ASMCs) due to mechanical ventilation (MV) is postulated to contribute to ventilator-induced lung injury (VILI), but the underlying mechanisms remain largely unknown. We hypothesized that ASMCs may respond to high stretch via regulatory miRNA-mRNA interactions, and thus we aimed to identify high stretch-responsive cellular events and related regulating miRNA-mRNA interactions in cultured human ASMCs with/without high stretch. RNA-Seq analysis of whole genome-wide miRNAs revealed 12 miRNAs differentially expressed (DE) in response to high stretch (7 up and 5 down, fold change >2), which target 283 DE-mRNAs as identified by a parallel mRNA sequencing and bioinformatics analysis. The KEGG and GO analysis further indicated that purine metabolism was the first enriched event in the cells during high stretch, which was linked to miR-370-5p-PDE4D/AK7. Since PDE4D/AK7 have been previously linked to cAMP/ATP metabolism in lung diseases and now to miR-370-5p in ASMCs, we thus evaluated the effect of high stretch on the cAMP/ATP level inside ASMCs. The results demonstrated that high stretch modulated the cAMP/ATP levels inside ASMCs, which could be largely abolished by miR-370-5p mimics. Together, these findings indicate that miR-370-5p-PDE4D/AK7 mediated high stretch-induced modulation of cAMP and ATP synthesis inside ASMCs. Furthermore, such interactive miRNA-mRNA pairs may provide new insights for the discovery of effective biomarkers/therapeutic targets for the diagnosis and treatment of VILI and other MV-associated respiratory diseases.
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Affiliation(s)
- Mingzhi Luo
- Correspondence: (M.L.); (L.D.); Tel.: +86-136-1611-9565 (M.L.); +86-136-8520-7009 (L.D.)
| | | | | | | | | | | | | | | | | | - Linhong Deng
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, School of Medical and Health Engineering, Changzhou University, Changzhou 213164, China (K.W.)
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8
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Narayanan SA, Jamison DA, Guarnieri JW, Zaksas V, Topper M, Koutnik AP, Park J, Clark KB, Enguita FJ, Leitão AL, Das S, Moraes-Vieira PM, Galeano D, Mason CE, Trovão NS, Schwartz RE, Schisler JC, Coelho-Dos-Reis JGA, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection. Eur J Hum Genet 2024; 32:10-20. [PMID: 37938797 PMCID: PMC10772081 DOI: 10.1038/s41431-023-01462-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 11/09/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.
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Affiliation(s)
- S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32301, USA.
| | - David A Jamison
- COVID-19 International Research Team, Medford, MA, 02155, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Michael Topper
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Departments of Oncology and Medicine and the Sidney Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andrew P Koutnik
- Human Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, FL, 32502, USA
- Sansum Diabetes Research Institute, Santa Barbara, CA, 93015, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 10065, USA
| | - Kevin B Clark
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Cures Within Reach, Chicago, IL, 60602, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation's Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), Philadelphia, PA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, 10016, USA
- Peace Innovation Institute, The Hague 2511, Netherlands and Stanford University, Palo Alto, 94305, CA, USA
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Saswati Das
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Mannohar Lohia Hospital, New Delhi, 110001, India
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC) and Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
| | - Diego Galeano
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA, 02155, USA
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jordana G A Coelho-Dos-Reis
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Basic and Applied Virology Lab, Department of Microbiology, Institute for Biological Sciences (ICB), Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Bioinformatics and Computational Biology Program, Center for Metabolomics, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Santa Clara, CA, 94035, USA.
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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10
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Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
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Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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12
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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13
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The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients. Viruses 2023; 15:v15020433. [PMID: 36851647 PMCID: PMC9958880 DOI: 10.3390/v15020433] [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: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the molecular mechanisms behind the development of disease severity are still not clearly understood. Recent studies demonstrated that SARS-CoV-2 alters the host cell splicing and transcriptional response to overcome the host immune response that provides the virus with favorable conditions to replicate efficiently within the host cells. In several disease conditions, aberrant splicing could lead to the development of novel chimeric transcripts that could promote the functional alternations of the cell. As severe SARS-CoV-2 infection was reported to cause abnormal splicing in the infected cells, we could expect the generation and expression of novel chimeric transcripts. However, no study so far has attempted to check whether novel chimeric transcripts are expressed in severe SARS-CoV-2 infections. In this study, we analyzed several publicly available blood transcriptome datasets of severe COVID-19, mild COVID-19, other severe respiratory viral infected patients, and healthy individuals. We identified 424 severe COVID-19 -specific chimeric transcripts, 42 of which were recurrent. Further, we detected 189 chimeric transcripts common to severe COVID-19 and multiple severe respiratory viral infections. Pathway and gene enrichment analysis of the parental genes of these two subsets of chimeric transcripts reveals that these are potentially involved in immune-related processes, interferon signaling, and inflammatory responses, which signify their potential association with immune dysfunction leading to the development of disease severity. Our study provides the first detailed expression landscape of chimeric transcripts in severe COVID-19 and other severe respiratory viral infections.
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14
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Mukherjee SB, Mukherjee S, Detroja R, Frenkel-Morgenstern M. The landscape of differential splicing and transcript alternations in severe COVID-19 infection. FEBS J 2023. [PMID: 36628954 DOI: 10.1111/febs.16723] [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: 06/28/2022] [Revised: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Viral infections can modulate the widespread alternations of cellular splicing, favouring viral replication within the host cells by overcoming host immune responses. However, how SARS-CoV-2 induces host cell differential splicing and affects the landscape of transcript alternation in severe COVID-19 infection remains elusive. Understanding the differential splicing and transcript alternations in severe COVID-19 infection may improve our molecular insights into the SARS-CoV-2 pathogenesis. In this study, we analysed the publicly available blood and lung transcriptome data of severe COVID-19 patients, blood transcriptome data of recovered COVID-19 patients at 12-, 16- and 24-week postinfection and healthy controls. We identified a significant transcript isoform switching in the individual blood and lung RNA-seq data of severe COVID-19-infected patients and 25 common genes that alter their transcript isoform in both blood and lung samples. Altered transcripts show significant loss of the open reading frame, functional domains and switch from coding to noncoding transcript, impacting normal cellular functions. Furthermore, we identified the expression of several novel recurrent chimeric transcripts in the blood samples from severe COVID-19 patients. Moreover, the analysis of the isoform switching into blood samples from recovered COVID-19 patients highlights that there is no significant isoform switching in 16- and 24-week postinfection, and the levels of expressed chimeric transcripts are reduced. This finding emphasizes that SARS-CoV-2 severe infection induces widespread splicing in the host cells, which could help the virus alter the host immune responses and facilitate the viral replication within the host and the efficient translation of viral proteins.
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Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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15
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Ding J, Chen J, Yin X, Zhou J. Current understanding on long non-coding RNAs in immune response to COVID-19. Virus Res 2023; 323:198956. [PMID: 36208691 PMCID: PMC9532266 DOI: 10.1016/j.virusres.2022.198956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/11/2022] [Accepted: 10/03/2022] [Indexed: 01/25/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic threatening the lives and health of people worldwide. Currently, there are no effective therapies or available vaccines for COVID-19. The molecular mechanism causing acute immunopathological diseases in severe COVID-19 is being investigated. Long noncoding RNAs (lncRNAs) have been proven to be involved in many viral infections, such as hepatitis, influenza and acquired immune deficiency syndrome. Many lncRNAs present differential expression between normal tissue and virus-infected tissue. However, the role of lncRNAs in SARS-CoV-2 infection has not been fully elucidated. This study aimed to review the relationship between lncRNAs and viral infection, interferon and cytokine storms in COVID-19, hoping to provide novel insights into promising targets for COVID-19 treatment.
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Affiliation(s)
- Jing Ding
- Department of Medical Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jing Chen
- Department of Medical Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Xude Yin
- Department of Medical Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jin Zhou
- Department of Medical Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
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16
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Pelisek J, Reutersberg B, Greber UF, Zimmermann A. Vascular dysfunction in COVID-19 patients: update on SARS-CoV-2 infection of endothelial cells and the role of long non-coding RNAs. Clin Sci (Lond) 2022; 136:1571-1590. [PMID: 36367091 PMCID: PMC9652506 DOI: 10.1042/cs20220235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 08/16/2023]
Abstract
Although COVID-19 is primarily a respiratory disease, it may affect also the cardiovascular system. COVID-19 patients with cardiovascular disorder (CVD) develop a more severe disease course with a significantly higher mortality rate than non-CVD patients. A common denominator of CVD is the dysfunction of endothelial cells (ECs), increased vascular permeability, endothelial-to-mesenchymal transition, coagulation, and inflammation. It has been assumed that clinical complications in COVID-19 patients suffering from CVD are caused by SARS-CoV-2 infection of ECs through the angiotensin-converting enzyme 2 (ACE2) receptor and the cellular transmembrane protease serine 2 (TMPRSS2) and the consequent dysfunction of the infected vascular cells. Meanwhile, other factors associated with SARS-CoV-2 entry into the host cells have been described, including disintegrin and metalloproteinase domain-containing protein 17 (ADAM17), the C-type lectin CD209L or heparan sulfate proteoglycans (HSPG). Here, we discuss the current data about the putative entry of SARS-CoV-2 into endothelial and smooth muscle cells. Furthermore, we highlight the potential role of long non-coding RNAs (lncRNAs) affecting vascular permeability in CVD, a process that might exacerbate disease in COVID-19 patients.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zürich, Zürich, Switzerland
| | | | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Switzerland
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17
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Liu J, Ji Q, Cheng F, Chen D, Geng T, Huang Y, Zhang J, He Y, Song T. The lncRNAs involved in regulating the RIG-I signaling pathway. Front Cell Infect Microbiol 2022; 12:1041682. [PMID: 36439216 PMCID: PMC9682092 DOI: 10.3389/fcimb.2022.1041682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 09/23/2023] Open
Abstract
Understanding the targets and interactions of long non-coding RNAs (lncRNAs) related to the retinoic acid-inducible gene-I (RIG-I) signaling pathway is essential for developing interventions, which would enable directing the host inflammatory response regulation toward protective immunity. In the RIG-I signaling pathway, lncRNAs are involved in the important processes of ubiquitination, phosphorylation, and glycolysis, thus promoting the transport of the interferon regulatory factors 3 and 7 (IRF3 and IRF7) and the nuclear factor kappa B (NF-κB) into the nucleus, and activating recruitment of type I interferons (IFN-I) and inflammatory factors to the antiviral action site. In addition, the RIG-I signaling pathway has recently been reported to contain the targets of coronavirus disease-19 (COVID-19)-related lncRNAs. The molecules in the RIG-I signaling pathway are directly regulated by the lncRNA-microRNAs (miRNAs)-messenger RNA (mRNA) axis. Therefore, targeting this axis has become a novel strategy for the diagnosis and treatment of cancer. In this paper, the studies on the regulation of the RIG-I signaling pathway by lncRNAs during viral infections and cancer are comprehensively analyzed. The aim is to provide a solid foundation of information for conducting further detailed studies on lncRNAs and RIG-I in the future and also contribute to clinical drug development.
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Affiliation(s)
- Jing Liu
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Qinglu Ji
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Feng Cheng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Dengwang Chen
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Tingting Geng
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yueyue Huang
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi, China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, China
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18
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Saha Detroja T, Detroja R, Mukherjee S, Samson AO. Identifying Hub Genes Associated with Neoadjuvant Chemotherapy Resistance in Breast Cancer and Potential Drug Repurposing for the Development of Precision Medicine. Int J Mol Sci 2022; 23:ijms232012628. [PMID: 36293493 PMCID: PMC9603969 DOI: 10.3390/ijms232012628] [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: 09/24/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
Breast cancer is the second leading cause of morbidity and mortality in women worldwide. Despite advancements in the clinical application of neoadjuvant chemotherapy (NAC), drug resistance remains a major concern hindering treatment efficacy. Thus, identifying the key genes involved in driving NAC resistance and targeting them with known potential FDA-approved drugs could be applied to advance the precision medicine strategy. With this aim, we performed an integrative bioinformatics study to identify the key genes associated with NAC resistance in breast cancer and then performed the drug repurposing to identify the potential drugs which could use in combination with NAC to overcome drug resistance. In this study, we used publicly available RNA-seq datasets from the samples of breast cancer patients sensitive and resistant to chemotherapy and identified a total of 1446 differentially expressed genes in NAC-resistant breast cancer patients. Next, we performed gene co-expression network analysis to identify significantly co-expressed gene modules, followed by MCC (Multiple Correlation Clustering) clustering algorithms and identified 33 key hub genes associated with NAC resistance. mRNA–miRNA network analysis highlighted the potential impact of these hub genes in altering the regulatory network in NAC-resistance breast cancer cells. Further, several hub genes were found to be significantly involved in the poor overall survival of breast cancer patients. Finally, we identified FDA-approved drugs which could be useful for potential drug repurposing against those hub genes. Altogether, our findings provide new insight into the molecular mechanisms of NAC resistance and pave the way for drug repurposing techniques and personalized treatment to overcome NAC resistance in breast cancer.
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Affiliation(s)
| | - Rajesh Detroja
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Sumit Mukherjee
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
- Correspondence: (S.M.); (A.O.S.)
| | - Abraham O. Samson
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Correspondence: (S.M.); (A.O.S.)
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Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance. Int J Biol Macromol 2022; 222:1538-1550. [PMID: 36152703 PMCID: PMC9492401 DOI: 10.1016/j.ijbiomac.2022.09.105] [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: 01/12/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 12/18/2022]
Abstract
The recently developed pathogenic virus, SARS-CoV-2, was found in the Hubei Province, China. Giving rise to a broad spectrum of symptoms, SARS-CoV-2 rapidly spread across the globe, causing multi-systemic and dangerous complications, with death in extreme cases. Thereby, the number of research cases increases every day on preventing infection and treating its resulting damage. Accumulating evidence suggests noncoding RNAs (ncRNAs) are necessary for modifying virus infection and antiviral immune reaction, along with biological processes regulating SARS-CoV-2 and subsequent disease states. Therefore, understanding these mechanisms might provide a further understanding of the pathogenesis and feasible therapy alternatives against SARS-CoV2. Consequently, the molecular biology of SARS-CoV-2, ncRNA's role in its infection, and various RNA therapy tactics against the virus have been presented in this review section.
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Hsa_circ_0000479/Hsa-miR-149-5p/RIG-I, IL-6 Axis: A Potential Novel Pathway to Regulate Immune Response against COVID-19. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2762582. [PMID: 36081604 PMCID: PMC9448594 DOI: 10.1155/2022/2762582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/12/2022] [Accepted: 08/08/2022] [Indexed: 12/27/2022]
Abstract
Background. COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global pandemic and mortality of people around the world. Some circular RNAs (circRNAs), one of the new types of noncoding RNAs (ncRNAs), act as competing endogenous RNAs (ceRNAs) and compete with mRNAs for shared miRNAs, to regulate gene expression. In the present study, we aimed to evaluate the expression and roles of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 in COVID-19 infection. Materials and Methods. After extraction of total RNA from peripheral blood mononuclear cells (PBMC) of 50 patients with symptomatic COVID-19, 50 patients with nonsymptomatic COVID-19, and 50 normal controls, cDNA synthesis was performed. Online in silico tools were applied to evaluate the interaction between the genes in the hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis, and its role in COVID-19-related pathways. Quantification of the expression of these genes and confirmation of their interaction was done using the quantitative real-time PCR (qRT-PCR) technique. Results. The expression levels of hsa_circ_0000479, RIG-I, and IL-6 were increased in COVID-19 patients compared to healthy controls, while hsa-miR-149-5p expression was decreased. Moreover, there was a significant negative correlation between hsa-miR-149-5p and hsa_circ_0000479, RIG-I, IL-6 expressions, and also a positive expression correlation between hsa_circ_0000479 and IL-6, RIG-I. Then, bioinformatics tools revealed the role of hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis in PI3K-AKT and STAT3 signaling pathways. Conclusion. Upregulation of hsa_circ_0000479, RIG-I, and IL-6, and downregulation of hsa-miR-149-5p, along with correlation studies, indicate that hsa_circ_0000479/hsa-miR-149-5p/RIG-I, IL-6 axis could play a role in regulating the immune response against SARS-CoV-2. However, more studies are needed in this area.
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Ferroptosis-Related Long Noncoding RNAs Have Excellent Predictive Ability for Multiomic Characteristics of Bladder Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9316847. [PMID: 36071865 PMCID: PMC9444476 DOI: 10.1155/2022/9316847] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
Background The role of ferroptosis-related long non-coding RNAs (lncRNAs) in bladder cancer remains elusive. This study is aimed at examining the prognostic role of ferroptosis-related lncRNAs in bladder cancer. Materials and Methods The transcriptomic matrix and clinical information of patients with bladder cancer were obtained from The Cancer Genome Atlas (TCGA) database. A ferroptosis-related lncRNA signature was developed via the least absolute shrinkage and selection operator (LASSO) analysis using data from the training cohort, and the signature was further validated using data from the test cohort. The role of AC006160.1, the most significant lncRNA in the risk signature, was examined in various cell lines including SV-HUC-1, BIU-87, HT-1376, T24, RT4, RT-112, 5637, and UMUC3. The pcDNA3.1-AC006160.1 plasmid was constructed and transfected into the bladder cancer cell lines T24 and BIU-87. In addition, cell proliferation, colony formation, transwell, and wound healing assays were performed to examine the biological function of AC006160.1 in T24 and BIU-87 cell lines. Results Two clusters were identified through consensus clustering based on prognostic ferroptosis-related lncRNAs. A 5-lncRNA risk signature was successfully constructed using data from the training cohort and validated using data from the test cohort. The risk signature had excellent ability to predict survival outcomes, clinical stages, pathological grades, expression of immune checkpoints, and immunotherapeutic responses in bladder cancer samples. Furthermore, AC006160.1 expression was found to be lower in the cancer cell lines BIU-87, T24, RT4, RT-112, and 5637 than in the normal control cell line SV-HUC-1. Cell proliferation, colony formation, transwell migration, and wound healing assays validated that overexpression of AC006160.1 significantly inhibited the proliferation and invasion abilities of both T24 and BIU-87 cells. Drug sensitivity analysis revealed that patients with high expression of AC006160.1 were sensitive to metformin and methotrexate, and the results were further validated via in vitro drug experiments. Conclusions Ferroptosis-related lncRNAs play a vital role in predicting the multiomic characteristics of bladder cancer. The lncRNA AC006160.1 serves as a protective factor for the development of bladder cancer.
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22
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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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23
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Zhong Y, Ashley CL, Steain M, Ataide SF. Assessing the suitability of long non-coding RNAs as therapeutic targets and biomarkers in SARS-CoV-2 infection. Front Mol Biosci 2022; 9:975322. [PMID: 36052163 PMCID: PMC9424846 DOI: 10.3389/fmolb.2022.975322] [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: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts that are over 200 nucleotides and rarely encode proteins or peptides. They regulate gene expression and protein activities and are heavily involved in many cellular processes such as cytokine secretion in respond to viral infection. In severe COVID-19 cases, hyperactivation of the immune system may cause an abnormally sharp increase in pro-inflammatory cytokines, known as cytokine release syndrome (CRS), which leads to severe tissue damage or even organ failure, raising COVID-19 mortality rate. In this review, we assessed the correlation between lncRNAs expression and cytokine release syndrome by comparing lncRNA profiles between COVID-19 patients and health controls, as well as between severe and non-severe cases. We also discussed the role of lncRNAs in CRS contributors and showed that the lncRNA profiles display consistency with patients’ clinic symptoms, thus suggesting the potential of lncRNAs as drug targets or biomarkers in COVID-19 treatment.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Caroline L. Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sandro Fernandes Ataide
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Sandro Fernandes Ataide,
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24
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Tanuj GN, Khan O, Malla WA, Rajak KK, Chandrashekar S, Kumar A, Dhara S, Gupta PK, Mishra BP, Dutt T, Gandham R, Sajjanar B. Integrated analysis of long-noncoding RNA and circular RNA expression in Peste-des-Petits-Ruminants Virus (PPRV) infected marmoset B lymphocyte (B95a) cells. Microb Pathog 2022; 170:105702. [DOI: 10.1016/j.micpath.2022.105702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/26/2022] [Accepted: 07/31/2022] [Indexed: 10/15/2022]
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25
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Das D, Podder S. Deregulation of ceRNA Networks in Frontal Cortex and Choroid Plexus of Brain during SARS-CoV-2 Infection Aggravates Neurological Manifestations: An Insight from Bulk and Single-Cell Transcriptomic Analyses. Adv Biol (Weinh) 2022; 6:e2101310. [PMID: 35661455 PMCID: PMC9348399 DOI: 10.1002/adbi.202101310] [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: 11/30/2021] [Revised: 05/20/2022] [Indexed: 01/28/2023]
Abstract
Although transcriptomic studies of SARS-CoV-2-infected brains have depicted variability in gene expression, the landscape of deregulated cell-specific regulatory circuits has not been elucidated yet. Hence, bulk and single-cell RNA-seq data are analyzed to gain detailed insights. Initially, two ceRNA networks with 19 and 3 differentially expressed (DE) hub lncRNAs are reconstructed in SARS-CoV-2 infected Frontal Cortex (FC) and Choroid Plexus (CP), respectively. Functional and pathway enrichment analyses of downstream mRNAs of deregulated ceRNA axes demonstrate impairment of neurological processes. Mapping of hub lncRNA-mRNA pairs from bulk RNA-seq with snRNA-seq data has indicated that NORAD, NEAT1, and STXBP5-AS1 are downregulated across 4, 4, and 2 FC cell types, respectively. At the same time, MIRLET7BHG and MALAT1 are upregulated in excitatory neurons of FC and neurons of CP, respectively. Here, it is hypothesized that downregulation of NORAD, NEAT1, and STXBP5-AS1, and upregulation of MIRLET7BHG and MALAT1 might deregulate respectively 51, 6, and 37, and 31 and 19 mRNAs in cell types of FC and CP. Afterward, 13 therapeutic miRNAs are traced that might safeguard against deregulated lncRNA-mRNA pairs of NORAD, NEAT1, and MIRLET7BHG in FC. This study helps to explain the plausible mechanism of post-COVID neurological manifestation and also to devise therapeutics against it.
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Affiliation(s)
- Deepyaman Das
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
| | - Soumita Podder
- Department of MicrobiologyRaiganj UniversityRaiganjUttar DinajpurWest Bengal733134India
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26
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Saha C, Laha S, Chatterjee R, Bhattacharyya NP. Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis. Noncoding RNA 2021; 7:74. [PMID: 34940755 PMCID: PMC8708613 DOI: 10.3390/ncrna7040074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022] Open
Abstract
Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated genes in COVID-19 remain largely unknown. In the present communication, reanalyzing publicly available gene expression data, we observed that 66 lncRNA and 5491 PCG were deregulated in more than one experimental condition. Combining our earlier published results and using different publicly available resources, it was observed that 72 deregulated lncRNA interacted with 3228 genes/proteins. Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection. The majority of the deregulated lncRNA and PCG were targets of at least one of the transcription factors (TFs), interferon responsive factors (IRFs), signal transducer, and activator of transcription (STATs), NFκB, MYC, and RELA/p65. Deregulated 1069 PCG was joint targets of lncRNA and TF. These joint targets are significantly enriched with pathways relevant for SARS-CoV-2 infection indicating that joint regulation of PCG could be one of the mechanisms for deregulation. Over all this manuscript showed possible involvement of lncRNA and mechanisms of deregulation of PCG in the pathogenesis of COVID-19.
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Affiliation(s)
- Chinmay Saha
- Department of Genome Science, School of Interdisciplinary Studies, University of Kalyani, Nadia 741235, India;
| | - Sayantan Laha
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India; (S.L.); (R.C.)
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India; (S.L.); (R.C.)
| | - Nitai P. Bhattacharyya
- Department of Endocrinology and Metabolism, Institute of Post Graduate Medical Education & Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata 700020, India
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27
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Natarelli L, Virgili F, Weber C. SARS-CoV-2, Cardiovascular Diseases, and Noncoding RNAs: A Connected Triad. Int J Mol Sci 2021; 22:12243. [PMID: 34830125 PMCID: PMC8620514 DOI: 10.3390/ijms222212243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by important respiratory impairments frequently associated with severe cardiovascular damages. Moreover, patients with pre-existing comorbidity for cardiovascular diseases (CVD) often present a dramatic increase in inflammatory cytokines release, which increases the severity and adverse outcomes of the infection and, finally, mortality risk. Despite this evident association at the clinical level, the mechanisms linking CVD and COVID-19 are still blurry and unresolved. Noncoding RNAs (ncRNAs) are functional RNA molecules transcribed from DNA but usually not translated into proteins. They play an important role in the regulation of gene expression, either in relatively stable conditions or as a response to different stimuli, including viral infection, and are therefore considered a possible important target in the design of specific drugs. In this review, we introduce known associations and interactions between COVID-19 and CVD, discussing the role of ncRNAs within SARS-CoV-2 infection from the perspective of the development of efficient pharmacological tools to treat COVID-19 patients and taking into account the equally dramatic associated consequences, such as those affecting the cardiovascular system.
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Affiliation(s)
- Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), 800336 Munich, Germany;
| | - Fabio Virgili
- Research Center for Food and Nutrition, Council for Agricultural Research and Economics, 00178 Rome, Italy;
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), 800336 Munich, Germany;
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 HX Maastricht, The Netherlands
- Munich Cluster for Systems Neurology (SyNergy), Institute for Stroke and Dementia Research, 81377 Munich, Germany
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28
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Roy RK, Sharma U, Wasson MK, Jain A, Hassan MI, Prakash H. Macrophage Activation Syndrome and COVID 19: Impact of MAPK Driven Immune-Epigenetic Programming by SARS-Cov-2. Front Immunol 2021; 12:763313. [PMID: 34659270 PMCID: PMC8519338 DOI: 10.3389/fimmu.2021.763313] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/20/2021] [Indexed: 01/08/2023] Open
Affiliation(s)
- Roshan Kumar Roy
- Amity Institute of Virology and Immunology, Amity University, NOIDA, Udham Singh Nagar, India
| | - Uttam Sharma
- Department of Zoology, Central University of Punjab, Bathinda, India
| | - Mishi Kaushal Wasson
- Amity Institute of Virology and Immunology, Amity University, NOIDA, Udham Singh Nagar, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, NOIDA, Udham Singh Nagar, India
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29
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Yang Q, Lin F, Wang Y, Zeng M, Luo M. Long Noncoding RNAs as Emerging Regulators of COVID-19. Front Immunol 2021; 12:700184. [PMID: 34408749 PMCID: PMC8366413 DOI: 10.3389/fimmu.2021.700184] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which has high incidence rates with rapid rate of transmission, is a pandemic that spread across the world, resulting in more than 3,000,000 deaths globally. Currently, several drugs have been used for the clinical treatment of COVID-19, such as antivirals (radecivir, baritinib), monoclonal antibodies (tocilizumab), and glucocorticoids (dexamethasone). Accumulating evidence indicates that long noncoding RNAs (lncRNAs) are essential regulators of virus infections and antiviral immune responses including biological processes that are involved in the regulation of COVID-19 and subsequent disease states. Upon viral infections, cellular lncRNAs directly regulate viral genes and influence viral replication and pathology through virus-mediated changes in the host transcriptome. Additionally, several host lncRNAs could help the occurrence of viral immune escape by inhibiting type I interferons (IFN-1), while others could up-regulate IFN-1 production to play an antiviral role. Consequently, understanding the expression and function of lncRNAs during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection will provide insights into the development of lncRNA-based methods. In this review, we summarized the current findings of lncRNAs in the regulation of the strong inflammatory response, immune dysfunction and thrombosis induced by SARS-CoV-2 infection, discussed the underlying mechanisms, and highlighted the therapeutic challenges of COVID-19 treatment and its future research directions.
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Affiliation(s)
- Qinzhi Yang
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, The School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Fang Lin
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, The School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yanan Wang
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, The School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Min Zeng
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Mao Luo
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology of Department of Pharmacology, The School of Pharmacy, Southwest Medical University, Luzhou, China
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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30
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Schoeman D, Fielding BC. Human Coronaviruses: Counteracting the Damage by Storm. Viruses 2021; 13:1457. [PMID: 34452323 PMCID: PMC8402835 DOI: 10.3390/v13081457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 18 years, three highly pathogenic human (h) coronaviruses (CoVs) have caused severe outbreaks, the most recent causative agent, SARS-CoV-2, being the first to cause a pandemic. Although much progress has been made since the COVID-19 pandemic started, much about SARS-CoV-2 and its disease, COVID-19, is still poorly understood. The highly pathogenic hCoVs differ in some respects, but also share some similarities in clinical presentation, the risk factors associated with severe disease, and the characteristic immunopathology associated with the progression to severe disease. This review aims to highlight these overlapping aspects of the highly pathogenic hCoVs-SARS-CoV, MERS-CoV, and SARS-CoV-2-briefly discussing the importance of an appropriately regulated immune response; how the immune response to these highly pathogenic hCoVs might be dysregulated through interferon (IFN) inhibition, antibody-dependent enhancement (ADE), and long non-coding RNA (lncRNA); and how these could link to the ensuing cytokine storm. The treatment approaches to highly pathogenic hCoV infections are discussed and it is suggested that a greater focus be placed on T-cell vaccines that elicit a cell-mediated immune response, using rapamycin as a potential agent to improve vaccine responses in the elderly and obese, and the potential of stapled peptides as antiviral agents.
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Affiliation(s)
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town 7535, South Africa;
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31
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Devadoss D, Acharya A, Manevski M, Pandey K, Borchert GM, Nair M, Mirsaeidi M, Byrareddy SN, Chand HS. Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.13.21257152. [PMID: 34031668 PMCID: PMC8142670 DOI: 10.1101/2021.05.13.21257152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Respiratory epithelial cells are the primary target for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated the 3D human airway tissue model to evaluate innate epithelial cell responses to SARS-CoV-2 infection. A SARS-CoV-2 clinical isolate productively infected the 3D-airway model with a time-dependent increase in viral load (VL) and concurrent upregulation of airway immunomodulatory factors ( IL-6, ICAM-1 , and SCGB1A1 ) and respiratory mucins ( MUC5AC, MUC5B, MUC2 , and MUC4) , and differential modulation of select long noncoding RNAs (lncRNAs i.e., LASI, TOSL, NEAT1 , and MALAT1 ). Next, we examined these immunomodulators in the COVID-19 patient nasopharyngeal swab samples collected from subjects with high- or low-VLs (∼100-fold difference). As compared to low-VL, high-VL patients had prominent mucoinflammatory signature with elevated expression of IL-6, ICAM-1, SCGB1A1, SPDEF, MUC5AC, MUC5B , and MUC4 . Interestingly, LASI, TOSL , and NEAT1 lncRNA expressions were also markedly elevated in high-VL patients with no change in MALAT1 expression. In addition, dual-staining of LASI and SARS-CoV-2 nucleocapsid N1 RNA showed predominantly nuclear/perinuclear localization at 24 hpi in 3D-airway model as well as in high-VL COVID-19 patient nasopharyngeal cells, which exhibited high MUC5AC immunopositivity. Collectively, these findings suggest SARS-CoV-2 induced lncRNAs may play a role in acute mucoinflammatory response observed in symptomatic COVID-19 patients.
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