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Panda M, Kalita E, Singh S, Kumar K, Rao A, Prajapati VK. MiRNA-SARS-CoV-2 dialogue and prospective anti-COVID-19 therapies. Life Sci 2022; 305:120761. [PMID: 35787998 PMCID: PMC9249409 DOI: 10.1016/j.lfs.2022.120761] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
Abstract
COVID-19 is a highly transmissible disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), affects 226 countries and continents, and has resulted in >6.2 million deaths worldwide. Despite the efforts of all scientific institutions worldwide to identify potential therapeutics, no specific drug has been approved by the FDA to treat the COVID-19 patient. SARS-CoV-2 variants of concerns make the potential of publicly known therapeutics to respond to and detect disease onset highly improbable. The quest for universal therapeutics pointed to the ability of RNA-based molecules to shield and detect the adverse effects of the COVID-19 illness. One such candidate, miRNA (microRNA), works on regulating the differential expression of the target gene post-transcriptionally. The prime focus of this review is to report the critical miRNA molecule and their regular expression in patients with COVID-19 infection and associated comorbidities. Viral and host miRNAs control the etiology of COVID-19 infection throughout the life cycle and host inflammatory response, where host miRNAs are identified as a double-edged showing as a proviral and antiviral response. The review also covered the role of viral miRNAs in mediating host cell signaling expression during disease pathology. Studying molecular interactions between the host and the SARS-CoV-2 virus during COVID-19 pathogenesis offers the chance to use miRNA-based therapeutics to reduce the severity of the illness. By utilizing an appropriate delivery vehicle, these small non-coding RNA could be envisioned as a promising biomarker in designing a practical RNAi-based treatment approach of clinical significance.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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Micro-Players of Great Significance-Host microRNA Signature in Viral Infections in Humans and Animals. Int J Mol Sci 2022; 23:ijms231810536. [PMID: 36142450 PMCID: PMC9504570 DOI: 10.3390/ijms231810536] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Over time, more and more is becoming known about micro-players of great significance. This is particularly the case for microRNAs (miRNAs; miR), which have been found to participate in the regulation of many physiological and pathological processes in both humans and animals. One such process is viral infection in humans and animals, in which the host miRNAs—alone or in conjunction with the virus—interact on two levels: viruses may regulate the host’s miRNAs to evade its immune system, while the host miRNAs can play anti- or pro-viral roles. The purpose of this comprehensive review is to present the key miRNAs involved in viral infections in humans and animals. We summarize the data in the available literature, indicating that the signature miRNAs in human viral infections mainly include 12 miRNAs (i.e., miR-155, miR-223, miR-146a, miR-122, miR-125b, miR-132, miR-34a, miR -21, miR-16, miR-181 family, let-7 family, and miR-10a), while 10 miRNAs are commonly found in animals (i.e., miR-155, miR-223, miR-146a, miR-145, miR-21, miR-15a/miR-16 cluster, miR-181 family, let-7 family, and miR-122) in this context. Knowledge of which miRNAs are involved in different viral infections and the biological functions that they play can help in understanding the pathogenesis of viral diseases, facilitating the future development of therapeutic agents for both humans and animals.
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Jusic A, Stellos K, Ferreira L, Baker AH, Devaux Y. (Epi)transcriptomics in cardiovascular and neurological complications of COVID-19. JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY PLUS 2022; 1:100013. [PMID: 36164464 PMCID: PMC9330360 DOI: 10.1016/j.jmccpl.2022.100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 06/16/2023]
Abstract
Although systemic inflammation and pulmonary complications increase the mortality rate in COVID-19, a broad spectrum of cardiovascular and neurological complications can also contribute to significant morbidity and mortality. The molecular mechanisms underlying cardiovascular and neurological complications during and after SARS-CoV-2 infection are incompletely understood. Recently reported perturbations of the epitranscriptome of COVID-19 patients indicate that mechanisms including those derived from RNA modifications and non-coding RNAs may play a contributing role in the pathogenesis of COVID-19. In this review paper, we gathered recently published studies investigating (epi)transcriptomic fluctuations upon SARS-CoV-2 infection, focusing on the brain-heart axis since neurological and cardiovascular events and their sequelae are of utmost prevalence and importance in this disease.
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Affiliation(s)
- Amela Jusic
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina
| | - Konstantinos Stellos
- Department of Cardiovascular Research, European Centre for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Heidelberg/Mannheim Partner Site, Mannheim, Germany
- Department of Cardiology, University Hospital Mannheim, Mannheim, Germany
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lino Ferreira
- CNC-Center for Neurosciences and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
- Faculty of Medicine, University Coimbra, 3000-548 Coimbra, Portugal
| | - Andrew H. Baker
- Centre for Cardiovascular Science, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
- CARIM Institute, University of Maastricht, Universiteitssingel 50, 6200 MD Maastricht, the Netherlands
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
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Mortazavi-Jahromi SS, Aslani M. Dysregulated miRNAs network in the critical COVID-19: An important clue for uncontrolled immunothrombosis/thromboinflammation. Int Immunopharmacol 2022; 110:109040. [PMID: 35839566 PMCID: PMC9271492 DOI: 10.1016/j.intimp.2022.109040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Known as a pivotal immunohemostatic response, immunothrombosis is activated to restrict the diffusion of pathogens. This beneficial intravascular defensive mechanism represents the close interaction between the immune and coagulation systems. However, its uncontrolled form can be life-threatening to patients with the critical coronavirus disease 2019 (COVID-19). Hyperinflammation and ensuing cytokine storm underlie the activation of the coagulation system, something which results in the provocation of more immune-inflammatory responses by the thrombotic mediators. This vicious cycle causes grave clinical complications and higher risks of mortality. Classified as an evolutionarily conserved family of the small non-coding RNAs, microRNAs (miRNAs) serve as the fine-tuners of genes expression and play a key role in balancing the pro/anticoagulant and pro-/anti-inflammatory factors maintaining homeostasis. Therefore, any deviation from their optimal expression levels or efficient functions can lead to severe complications. Despite their extensive effects on the molecules and processes involved in uncontrolled immunothrombosis, some genetic agents and uncontrolled immunothrombosis-induced interfering factors (e.g., miRNA-single nucleotide polymorphysms (miR-SNPs), the complement system components, nicotinamide adenine dinucleotide phosphate (NADPH) oxidases, and reactive oxygen species (ROS)) have apparently disrupted their expressions/functions. This review study aims to give an overview of the role of miRNAs in the context of uncontrolled immunothrombosis/thromboinflammation accompanied by some presumptive interfering factors affecting their expressions/functions in the critical COVID-19. Detecting, monitoring, and resolving these interfering agents mafy facilitate the design and development of the novel miRNAs-based therapeutic approaches to the reduction of complications incidence and mortality in patients with the critical COVID-19.
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Affiliation(s)
- Seyed Shahabeddin Mortazavi-Jahromi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Cellular and Molecular Biology, Kish International Campus, University of Tehran, Kish, Iran.
| | - Mona Aslani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Roustai Geraylow K, Hemmati R, Kadkhoda S, Ghafouri-Fard S. miRNA expression in COVID-19. GENE REPORTS 2022; 28:101641. [PMID: 35875722 PMCID: PMC9288248 DOI: 10.1016/j.genrep.2022.101641] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/25/2022] [Accepted: 07/10/2022] [Indexed: 11/02/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is regarded as a challenge in health system. Several studies have assessed the immune-related aspect of this disorder to identify the host-related factors that affect the course of COVID-19. microRNAs (miRNAs) as potent regulators of immune responses have gained much attention in this regard. Recent studies have shown aberrant expression of miRNAs in COVID-19 in association with disease course. Differentially expressed miRNAs have been enriched in pathways related with inflammation and antiviral immune response. miRNAs have also been regarded as potential therapeutic targets in COVID-19, particularly for management of pathological consequences of COVID-19. In the current review, we summarize the data about dysregulation of miRNAs in COVID-19.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- ARDS, Acute respiratory distress syndrome
- COVID-19
- COVID-19, Coronavirus disease 2019
- HDAC, Histone deacetylate
- HMVEC, Human Lung Microvascular Endothelial Cells
- ORF, Open reading frame
- ROC, Receiver operating characteristic
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- TLR, Toll-like receptor
- TMPRSS2, Transmembrane protease serine 2
- UTR, Untranslated region
- hBMEC, Human brain microvascular endothelial cells
- miRNA
- miRNAs, microRNAs
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Affiliation(s)
| | - Romina Hemmati
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Sepideh Kadkhoda
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Serum microRNAs targeting ACE2 and RAB14 genes distinguish asymptomatic from critical COVID-19 patients. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:76-87. [PMID: 35721225 PMCID: PMC9188110 DOI: 10.1016/j.omtn.2022.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/05/2022] [Indexed: 01/08/2023]
Abstract
Despite the extraordinary advances achieved to beat COVID-19 disease, many questions remain unsolved, including the mechanisms of action of SARS-CoV-2 and which factors determine why individuals respond so differently to the viral infection. Herein, we performed an in silico analysis to identify host microRNA targeting ACE2, TMPRSS2, and/or RAB14, all genes known to participate in viral entry and replication. Next, the levels of six microRNA candidates previously linked to viral and respiratory-related pathologies were measured in the serum of COVID-19-negative controls (n = 16), IgG-positive COVID-19 asymptomatic individuals (n = 16), and critical COVID-19 patients (n = 17). Four of the peripheral microRNAs analyzed (hsa-miR-32-5p, hsa-miR-98-3p, hsa-miR-423-3p, and hsa-miR-1246) were upregulated in COVID-19 critical patients compared with COVID-19-negative controls. Moreover, hsa-miR-32-5p and hsa-miR-1246 levels were also altered in critical versus asymptomatic individuals. Furthermore, these microRNA target genes were related to viral infection, inflammatory response, and coagulation-related processes. In conclusion, SARS-CoV-2 promotes the alteration of microRNAs targeting the expression of key proteins for viral entry and replication, and these changes are associated with disease severity. The microRNAs identified could be taken as potential biomarkers of COVID-19 progression as well as candidates for future therapeutic approaches against this disease.
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Moatar AI, Chis AR, Marian C, Sirbu IO. Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease. Int J Mol Sci 2022; 23:ijms23169239. [PMID: 36012503 PMCID: PMC9409149 DOI: 10.3390/ijms23169239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 02/07/2023] Open
Abstract
According to the World Health Organization (WHO), as of June 2022, over 536 million confirmed COVID-19 disease cases and over 6.3 million deaths had been globally reported. COVID-19 is a multiorgan disease involving multiple intricated pathological mechanisms translated into clinical, biochemical, and molecular changes, including microRNAs. MicroRNAs are essential post-transcriptional regulators of gene expression, being involved in the modulation of most biological processes. In this study, we characterized the biological impact of SARS-CoV-2 interacting microRNAs differentially expressed in COVID-19 disease by analyzing their impact on five distinct tissue transcriptomes. To this end, we identified the microRNAs’ predicted targets within the list of differentially expressed genes (DEGs) in tissues affected by high loads of SARS-CoV-2 virus. Next, we submitted the tissue-specific lists of the predicted microRNA-targeted DEGs to gene network functional enrichment analysis. Our data show that the upregulated microRNAs control processes such as mitochondrial respiration and cytokine and cell surface receptor signaling pathways in the heart, lymph node, and kidneys. In contrast, downregulated microRNAs are primarily involved in processes related to the mitotic cell cycle in the heart, lung, and kidneys. Our study provides the first exploratory, systematic look into the biological impact of the microRNAs associated with COVID-19, providing a new perspective for understanding its multiorgan physiopathology.
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Affiliation(s)
- Alexandra Ioana Moatar
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Doctoral School, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
| | - Aimee Rodica Chis
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
| | - Ioan-Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy “Victor Babes”, E. Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: ; Tel.: +40-756-136-272
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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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59
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Understanding the Pivotal Role of the Vagus Nerve in Health from Pandemics. Bioengineering (Basel) 2022; 9:bioengineering9080352. [PMID: 36004877 PMCID: PMC9405360 DOI: 10.3390/bioengineering9080352] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
The COVID-19 pandemic seems endless with the regular emergence of new variants. Is the SARS-CoV-2 virus particularly evasive to the immune system, or is it merely disrupting communication between the body and the brain, thus pre-empting homeostasis? Retrospective analysis of the COVID-19 and AIDS pandemics, as well as prion disease, emphasizes the pivotal but little-known role of the 10th cranial nerve in health. Considering neuroimmunometabolism from the point of view of the vagus nerve, non-invasive bioengineering solutions aiming at monitoring and stimulating the vagal tone are subsequently discussed as the next optimal and global preventive treatments, far beyond pandemics.
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60
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Li X, Wang Y, Zhou Q, Pan J, Xu J. Potential Predictive Value of miR-125b-5p, miR-155-5p and Their Target Genes in the Course of COVID-19. Infect Drug Resist 2022; 15:4079-4091. [PMID: 35937783 PMCID: PMC9346419 DOI: 10.2147/idr.s372420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to provide new biomarkers for predicting the disease course of COVID-19 by analyzing the dynamic changes of microRNA (miRNA) and its target gene expression in the serum of COVID-19 patients at different stages. Methods Serum samples were collected from all COVID-19 patients at three time points: the acute stage, the turn-negative stage, and the recovery stage. The expression level of miRNA and the target mRNA was measured by Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR). The classification tree model was established to predict the disease course, and the prediction efficiency of independent variables in the model was analyzed using the receiver operating characteristic (ROC) curve. Results The expression of miR-125b-5p and miR-155-5p was significantly up-regulated in the acute stage and gradually decreased in the turn-negative and recovery stages. The expression of the target genes CDH5, STAT3, and TRIM32 gradually down-regulated in the acute, turn-negative, and recovery stages. MiR-125b-5p, miR-155-5p, STAT3, and TRIM32 constituted a classification tree model with 100% accuracy of prediction and AUC >0.7 for identification and prediction in all stages. Conclusion MiR-125b-5p, miR-155-5p, STAT3, and TRIM32 could be useful biomarkers to predict the time nodes of the acute, turn-negative, and recovery stages of COVID-19.
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Affiliation(s)
- Xuewen Li
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, People’s Republic of China
| | - Yiting Wang
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, People’s Republic of China
| | - Qi Zhou
- Department of Pediatrics, First Hospital of Jilin University, Changchun, People’s Republic of China
| | - Junqi Pan
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Jiancheng Xu
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, People’s Republic of China
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Li W, Wang H, Zheng SJ. Roles of RNA Sensors in Host Innate Response to Influenza Virus and Coronavirus Infections. Int J Mol Sci 2022; 23:8285. [PMID: 35955436 PMCID: PMC9368391 DOI: 10.3390/ijms23158285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Influenza virus and coronavirus are two important respiratory viruses, which often cause serious respiratory diseases in humans and animals after infection. In recent years, highly pathogenic avian influenza virus (HPAIV) and SARS-CoV-2 have become major pathogens causing respiratory diseases in humans. Thus, an in-depth understanding of the relationship between viral infection and host innate immunity is particularly important to the stipulation of effective control strategies. As the first line of defense against pathogens infection, innate immunity not only acts as a natural physiological barrier, but also eliminates pathogens through the production of interferon (IFN), the formation of inflammasomes, and the production of pro-inflammatory cytokines. In this process, the recognition of viral pathogen-associated molecular patterns (PAMPs) by host pattern recognition receptors (PRRs) is the initiation and the most important part of the innate immune response. In this review, we summarize the roles of RNA sensors in the host innate immune response to influenza virus and coronavirus infections in different species, with a particular focus on innate immune recognition of viral nucleic acids in host cells, which will help to develop an effective strategy for the control of respiratory infectious diseases.
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Affiliation(s)
- Wei Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hongnuan Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shijun J. Zheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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MicroRNAs as Potential Tools for Predicting Cancer Patients’ Susceptibility to SARS-CoV-2 Infection and Vaccination Response. Cells 2022; 11:cells11152279. [PMID: 35892576 PMCID: PMC9332853 DOI: 10.3390/cells11152279] [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: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease that is caused by a highly contagious and severe acute respiratory syndrome—coronavirus 2 (SARS-CoV-2). This infection started to spread across the world in 2019 and rapidly turned into a global pandemic, causing an urgent necessity for treatment strategies development. The mRNA vaccines against SARS-CoV-2 can trigger an immune response, providing genetic information that allows the production of spike glycoproteins. MiRNAs play a crucial role in diverse key cellular processes, including antiviral defense. Several miRNAs are described as key factors in SARS-CoV-2 human infection through the regulation of ACE2 levels and by the inhibition of SARS-CoV-2 replication and spike expression. Consequently, these molecules have been considered as highly promising biomarkers. In numerous human malignancies, it has been recognized that miRNAs expression is dysregulated. Since miRNAs can target SARS-CoV-2-associated mRNAs, in cancer patients, the deregulation of these molecules can impair the immune response to the vaccines. Therefore, in this review, we propose a miRNA profile of seven SARS-CoV-2-related miRNAs, namely miR-214, miR-98-5p, miR-7-5p, miR-24-3p, miR-145-5p, miR-223-3p and miR-15b-5p, that are deregulated in a high number of cancers and have the potential to be used as prognostic biomarkers to stratify cancer patients.
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63
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Samy A, Maher MA, Abdelsalam NA, Badr E. SARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis. Sci Rep 2022; 12:11934. [PMID: 35831333 PMCID: PMC9279364 DOI: 10.1038/s41598-022-15898-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
COVID-19 is a global pandemic impacting the daily living of millions. As variants of the virus evolve, a complete comprehension of the disease and drug targets becomes a decisive duty. The Omicron variant, for example, has a notably high transmission rate verified in 155 countries. We performed integrative transcriptomic and network analyses to identify drug targets and diagnostic biomarkers and repurpose FDA-approved drugs for SARS-CoV-2. Upon the enrichment of 464 differentially expressed genes, pathways regulating the host cell cycle were significant. Regulatory and interaction networks featured hsa-mir-93-5p and hsa-mir-17-5p as blood biomarkers while hsa-mir-15b-5p as an antiviral agent. MYB, RRM2, ERG, CENPF, CIT, and TOP2A are potential drug targets for treatment. HMOX1 is suggested as a prognostic biomarker. Enhancing HMOX1 expression by neem plant extract might be a therapeutic alternative. We constructed a drug-gene network for FDA-approved drugs to be repurposed against the infection. The key drugs retrieved were members of anthracyclines, mitotic inhibitors, anti-tumor antibiotics, and CDK1 inhibitors. Additionally, hydroxyquinone and digitoxin are potent TOP2A inhibitors. Hydroxyurea, cytarabine, gemcitabine, sotalol, and amiodarone can also be redirected against COVID-19. The analysis enforced the repositioning of fluorouracil and doxorubicin, especially that they have multiple drug targets, hence less probability of resistance.
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Affiliation(s)
- Asmaa Samy
- University of Science and Technology, Zewail City, Giza, 12578, Egypt
| | - Mohamed A Maher
- University of Science and Technology, Zewail City, Giza, 12578, Egypt
| | - Nehal Adel Abdelsalam
- University of Science and Technology, Zewail City, Giza, 12578, Egypt.,Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City, Giza, 12578, Egypt. .,Faculty of Computers and Artificial Intelligence, Cairo University, Giza, 12613, Egypt.
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64
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Circulating microRNA profiling is altered in the acute respiratory distress syndrome related to SARS-CoV-2 infection. Sci Rep 2022; 12:6929. [PMID: 35484171 PMCID: PMC9047579 DOI: 10.1038/s41598-022-10738-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/07/2022] [Indexed: 12/23/2022] Open
Abstract
One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome and acute respiratory distress syndrome (ARDS). Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Circulating miRNAs in patients who underwent ARDS and needed mechanical ventilation (MV+; n = 15) were analyzed by next generation sequencing in comparison with patients who had COVID-19 poor symptoms but without intensive care unit requirement (MV−; n = 13). A comprehensive in silico analysis by integration with public gene expression dataset and pathway enrichment was performed. Whole miRNA sequencing identified 170 differentially expressed miRNAs between patient groups. After the validation step by qPCR in an independent sample set (MV+ = 10 vs. MV− = 10), the miR-369-3p was found significantly decreased in MV+ patients (Fold change − 2.7). After integrating with gene expression results from COVID-19 patients, the most significant GO enriched pathways were acute inflammatory response, regulation of transmembrane receptor protein Ser/Thr, fat cell differentiation, and regulation of biomineralization and ossification. In conclusion, miR-369-3p was altered in patients with mechanical ventilation requirement in comparison with COVID-19 patients without this requirement. This miRNA is involved in inflammatory response which it can be considered as a prognosis factor for ARDS in COVID-19 patients.
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65
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Yang X, Rutkovsky AC, Zhou J, Zhong Y, Reese J, Schnell T, Albrecht H, Owens WB, Nagarkatti PS, Nagarkatti M. Characterization of Altered Gene Expression and Histone Methylation in Peripheral Blood Mononuclear Cells Regulating Inflammation in COVID-19 Patients. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1968-1977. [PMID: 35379747 PMCID: PMC9012677 DOI: 10.4049/jimmunol.2101099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022]
Abstract
The pandemic of COVID-19 has caused >5 million deaths in the world. One of the leading causes of the severe form of COVID-19 is the production of massive amounts of proinflammatory cytokines. Epigenetic mechanisms, such as histone/DNA methylation, miRNA, and long noncoding RNA, are known to play important roles in the regulation of inflammation. In this study, we investigated if hospitalized COVID-19 patients exhibit alterations in epigenetic pathways in their PBMCs. We also compared gene expression profiles between healthy controls and COVID-19 patients. Despite individual variations, the expressions of many inflammation-related genes, such as arginase 1 and IL-1 receptor 2, were significantly upregulated in COVID-19 patients. We also found the expressions of coagulation-related genes Von Willebrand factor and protein S were altered in COVID-19 patients. The expression patterns of some genes, such as IL-1 receptor 2, correlated with their histone methylation marks. Pathway analysis indicated that most of those dysregulated genes were in the TGF-β, IL-1b, IL-6, and IL-17 pathways. A targeting pathway revealed that the majority of those altered genes were targets of dexamethasone, which is an approved drug for COVID-19 treatment. We also found that the expression of bone marrow kinase on chromosome X, a member of TEC family kinases, was increased in the PBMCs of COVID-19 patients. Interestingly, some inhibitors of TEC family kinases have been used to treat COVID-19. Overall, this study provides important information toward identifying potential biomarkers and therapeutic targets for COVID-19 disease.
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Affiliation(s)
- Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
| | - Alex C Rutkovsky
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
| | - Juhua Zhou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
| | - Yin Zhong
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
| | - Julian Reese
- Prisma Health Richland Hospital, School of Medicine, University of South Carolina, Columbia, SC
| | - Timothy Schnell
- Prisma Health Richland Hospital, School of Medicine, University of South Carolina, Columbia, SC
| | - Helmut Albrecht
- Prisma Health Richland Hospital, School of Medicine, University of South Carolina, Columbia, SC
| | - William B Owens
- Prisma Health Richland Hospital, School of Medicine, University of South Carolina, Columbia, SC
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC; and
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66
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Yeh YC, Doan LH, Huang ZY, Chu LW, Shi TH, Lee YR, Wu CT, Lin CH, Chiang ST, Liu HK, Chuang TH, Ping YH, Liu HS, Huang CYF. Honeysuckle ( Lonicera japonica) and Huangqi ( Astragalus membranaceus) Suppress SARS-CoV-2 Entry and COVID-19 Related Cytokine Storm in Vitro. Front Pharmacol 2022; 12:765553. [PMID: 35401158 PMCID: PMC8990830 DOI: 10.3389/fphar.2021.765553] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
COVID-19 is threatening human health worldwide but no effective treatment currently exists for this disease. Current therapeutic strategies focus on the inhibition of viral replication or using anti-inflammatory/immunomodulatory compounds to improve host immunity, but not both. Traditional Chinese medicine (TCM) compounds could be promising candidates due to their safety and minimal toxicity. In this study, we have developed a novel in silico bioinformatics workflow that integrates multiple databases to predict the use of honeysuckle (Lonicera japonica) and Huangqi (Astragalus membranaceus) as potential anti-SARS-CoV-2 agents. Using extracts from honeysuckle and Huangqi, these two herbs upregulated a group of microRNAs including let-7a, miR-148b, and miR-146a, which are critical to reduce the pathogenesis of SARS-CoV-2. Moreover, these herbs suppressed pro-inflammatory cytokines including IL-6 or TNF-α, which were both identified in the cytokine storm of acute respiratory distress syndrome, a major cause of COVID-19 death. Furthermore, both herbs partially inhibited the fusion of SARS-CoV-2 spike protein-transfected BHK-21 cells with the human lung cancer cell line Calu-3 that was expressing ACE2 receptors. These herbs inhibited SARS-CoV-2 Mpro activity, thereby alleviating viral entry as well as replication. In conclusion, our findings demonstrate that honeysuckle and Huangqi have the potential to be used as an inhibitor of SARS-CoV-2 virus entry that warrants further in vivo analysis and functional assessment of miRNAs to confirm their clinical importance. This fast-screening platform can also be applied to other drug discovery studies for other infectious diseases.
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Affiliation(s)
- Yuan-Chieh Yeh
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.,Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ly Hien Doan
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Zi-Yi Huang
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,ASUS Intelligent Cloud Services, Taipei, Taiwan
| | - Li-Wei Chu
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzu-Hau Shi
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ying-Ray Lee
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan.,Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Tao Wu
- Division of Big Data, Phalanx Biotech Group, Hsinchu, Taiwan
| | - Chao-Hsiung Lin
- Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Tuan Chiang
- Chuang Song Zong Pharmaceutical Co., Ltd. Ligang Plant, Pingtung, Taiwan
| | - Hui-Kang Liu
- National Research Institute of Chinese Medicine (NRICM), Ministry of Health and Welfare, Taipei, Taiwan.,Ph. D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Miaoli, Taiwan.,Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yueh-Hsin Ping
- Department and Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biophotonics, College of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiao-Sheng Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center for Cancer Research, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,M.Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chi-Ying F Huang
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung, Taipei, Taiwan.,Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung, Taipei, Taiwan.,Department of Biochemistry, School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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67
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Zhang L, Chen D, Song D, Liu X, Zhang Y, Xu X, Wang X. Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther 2022; 7:111. [PMID: 35365599 PMCID: PMC8972902 DOI: 10.1038/s41392-022-00960-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal molecular medicine. The present article overviews the development of ST and aims to evaluate clinical and translational values for understanding molecular pathogenesis and uncovering disease-specific biomarkers. We compare the advantages and disadvantages of sequencing- and imaging-based technologies and highlight opportunities and challenges of ST. We also describe the bioinformatics tools necessary on dissecting spatial patterns of gene expression and cellular interactions and the potential applications of ST in human diseases for clinical practice as one of important issues in clinical and translational medicine, including neurology, embryo development, oncology, and inflammation. Thus, clear clinical objectives, designs, optimizations of sampling procedure and protocol, repeatability of ST, as well as simplifications of analysis and interpretation are the key to translate ST from bench to clinic.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Dongsheng Chen
- Suzhou Institute of Systems Medicine, Suzhou, 215123, Jiangsu, China
| | - Dongli Song
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Xiaoxia Liu
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China
| | - Yanan Zhang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, 518055, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiangdong Wang
- Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, 200000, China.
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68
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had an enormous impact on the world, affecting people's lifestyle, economy, and livelihood. Recently, with the development of vaccines, the number of infected cases has decreased. Many case reports have revealed that COVID-19 may induce other serious comorbidities such as anti-N-methyl-d-aspartate (anti-NMDA) receptor encephalitis. Anti-NMDA receptor encephalitis is an acute autoimmune disease that occurs more commonly in women than in men. To explore the association between COVID-19 and anti-NMDA receptor encephalitis, the microRNA (miRNA) biomarkers of COVID-19, anti-NMDA receptor encephalitis, and other related diseases from the literature are reviewed; then on the basis of these miRNA biomarkers, the relationship between COVID-19 and anti-NMDA receptor encephalitis is discussed. miRNAs are small non-coding RNAs that play important roles in cell differentiation, development, cell-cycle regulation, and apoptosis. miRNAs have been used as biological biomarkers for many diseases. The results in this study reveal that the relationship between anti-NMDA receptor encephalitis and COVID-19 infection or COVID-19 vaccination cannot be excluded; however, the risk that COVID-19 triggers the anti-NMDA receptor encephalitis is not high.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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69
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Azhar A, Khan WH, Al-Hosaini K, Kamal MA. miRNAs in SARS-CoV-2 Infection: An Update. Curr Drug Metab 2022; 23:283-298. [PMID: 35319361 DOI: 10.2174/1389200223666220321102824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 02/08/2023]
Abstract
Coronavirus disease-2019 (COVID-19) is a highly infectious disease caused by newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the inception of SARS-CoV-2 from Wuhan, China, the virus has traveled to more than 200 countries globally. The role of SARS-CoV-2 in COVID-19 has been thoroughly investigated and reviewed in the last 22 months or so; however, a comprehensive outline of miRNAs in SARS-CoV-2 infection is still missing. The genetic material of SARS-CoV-2 is a single-stranded RNA molecule nearly 29 kb in size. RNA is composed of numerous sub-constituents, including microRNAs (miRNAs). miRNAs play an essential role in biological processes like apoptosis, cellular metabolism, cell death, cell movement, oncogenesis, intracellular signaling, immunity, and infection. Lately, miRNAs have been involved in SARS-CoV-2 infection, though the clear demonstration of miRNAs in the SARS-CoV-2 infection is not fully elucidated. The present review article summarizes recent findings of miRNAs associated with SARS-CoV-2 infection. We presented various facets of miRNAs such as miRNAs as the protagonist in viral infection, the occurrence of miRNA in cellular receptors, expression of miRNAs in multiple diseases, miRNA as a biomarker, and miRNA as a therapeutic tool discussed in detail. We also presented the vaccine status available in various countries.
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Affiliation(s)
- Asim Azhar
- Aligarh College of Education, Aligarh, UP, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Khaled Al-Hosaini
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Post Box 2457, Riyadh 11451, Kingdom of Saudi Arabia
| | - Mohammad Amjad Kamal
- West China School of Nursing / Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah 21589, Saudi Arabia
- Enzymoics, NSW; Novel Global Community Educational Foundation, Australia
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70
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Nicoletti ADS, Visacri MB, da Ronda CRDSC, Vasconcelos PEDNS, Quintanilha JCF, de Souza RN, Ventura DDS, Eguti A, Silva LFDS, Perroud Junior MW, Catharino RR, Reis LO, Dos Santos LA, Durán N, Fávaro WJ, Lancellotti M, da Costa JL, Moriel P, Pincinato EDC. Differentially expressed plasmatic microRNAs in Brazilian patients with Coronavirus disease 2019 (COVID-19): preliminary results. Mol Biol Rep 2022; 49:6931-6943. [PMID: 35301654 PMCID: PMC8929466 DOI: 10.1007/s11033-022-07338-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is known that host microRNAs (miRNAs) can be modulated to favor viral infection or to protect the host. Herein, we report preliminary results of a study aiming at identifying differentially expressed plasmatic miRNAs in Brazilian patients with COVID-19. Methods and results miRNAs were extracted from the plasma of eight patients with COVID-19 (four patients with mild COVID-19 and four patients with severe/critical COVID-19) and four healthy controls. Patients and controls were matched for sex and age. miRNA expression levels were detected using high-throughput sequencing. Differential miRNA expression and enrichment analyses were further evaluated. A total of 18 miRNAs were differentially expressed between patients with COVID-19 and controls. miR-4433b-5p, miR-6780b-3p, miR-6883-3p, miR-320b, miR-7111-3p, miR-4755-3p, miR-320c, and miR-6511a-3p were the most important miRNAs significantly involved in the PI3K/AKT, Wnt/β-catenin, and STAT3 signaling pathways. Moreover, 42 miRNAs were differentially expressed between severe/critical and mild patients with COVID-19. miR-451a, miR-101-3p, miR-185-5p, miR-30d-5p, miR-25-3p, miR-342-3p, miR-30e-5p, miR-150-5p, miR-15b-5p, and miR-29c-3p were the most important miRNAs significantly involved in the Wnt/β-catenin, NF-κβ, and STAT3 signaling pathways. Conclusions If validated by quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) in a larger number of participants, the miRNAs identified in this study might be used as possible biomarkers for the diagnosis and severity of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07338-9.
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Affiliation(s)
| | | | - Carla Regina da Silva Correa da Ronda
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | | | | | | | | | - Adriana Eguti
- Hospital Estadual Sumaré Dr. Leandro Francheschini, Sumaré, SP, Brazil
| | | | - Mauricio Wesley Perroud Junior
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil.,Hospital Estadual Sumaré Dr. Leandro Francheschini, Sumaré, SP, Brazil
| | - Rodrigo Ramos Catharino
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil.,Innovare Biomarkers Laboratory, University of Campinas, Campinas, SP, Brazil
| | | | | | - Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, SP, Brazil
| | - Wagner José Fávaro
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, SP, Brazil
| | - Marcelo Lancellotti
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | - José Luiz da Costa
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil
| | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Cândido Portinari Street, 200, Cidade Universitária Zeferino Vaz-Barão Geraldo, Campinas, SP, 13083-871, Brazil.
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71
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Li J, Yang Y, Xiong B, Lu J, Zhou Y, Li C, Hu X. The immunomodulatory effects of Qushi Jianpi Hewei Decoction (QJHD) for patients with COVID-19 by metagenomics and transcriptomic sequencing. PHARMACOLOGICAL RESEARCH - MODERN CHINESE MEDICINE 2022. [PMCID: PMC8759103 DOI: 10.1016/j.prmcm.2022.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ethnopharmacological relevance Several studies have confirmed that intestinal microflora dysbiosis correlates with the severity of COVID-19 patients. Clinical meta-analysis and our data show that the circulating miRNAs like miRNA-146 and the levels of serum cytokines in the peripheral blood are closely related to mild to moderate COVID-19 patients. Despite the widespread use of traditional herbal medicine for COVID-19 in China, the mechanisms remain largely uncovered. Aim of the study We conducted an observational case-control study to verify the efficacy and safety of traditional Chinese herbal medicine Qushi Jianpi Hewei Decoction (QJHD) for mild to moderate COVID-19 patients, and investigated the potential biomolecular mechanisms through metagenomics and transcriptomic sequencing methods. Materials and methods QJHD was given orally twice a day individually for 14 to 28 days. A total of 10 patients were enrolled in the study and given QJHD. We observed advantages in clinical cure time rate, and the relief of gastrointestinal symptoms as compared with reports in the literature. The metagenomics sequencing data of fecal microflora and transcriptomic sequencing data of blood cell in patients with SARS-Cov-2 infection patients were selected compared to the healthy control donors. Results No serious adverse events were reported. Meanwhile, the transcriptome analysis showed a decrease of the hsa-miR-21-5p expression in peripheral blood without QJHD. The species composition analysis showed an increase in the expression of Faecalibacterium prausnitzii in the intestinal tract; The interleukin-10 (IL-10) expression also in COVID-19 patient decreased in peripheral blood compared with healthy control donors. And we found an improvement in these parameters in patients taking QJHD. Conclusions Our findings show that QJHD could improve clinical outcomes of mild to moderate COVID-19 patients, probably through beneficial immunomodulatory effects by regulating Faecalibacterium prausnitzii in the intestinal tract and hsa-miR-21 and IL-10 expression in peripheral blood. (chictr.org.cn, ChiCTR2000030305)
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72
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Pinacchio C, Scordio M, Santinelli L, Frasca F, Sorrentino L, Bitossi C, Oliveto G, Viscido A, Ceci FM, Celani L, Ceccarelli G, Antonelli G, Mastroianni CM, d’Ettorre G, Scagnolari C. Analysis of serum microRNAs and rs2910164 GC single-nucleotide polymorphism of miRNA-146a in COVID-19 patients. J Immunoassay Immunochem 2022; 43:347-364. [DOI: 10.1080/15321819.2022.2035394] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Claudia Pinacchio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mirko Scordio
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Letizia Santinelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Frasca
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Leonardo Sorrentino
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Camilla Bitossi
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Giuseppe Oliveto
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Agnese Viscido
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
| | - Flavio Maria Ceci
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luigi Celani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
- Microbiology and Virology Unit, Sapienza University, Hospital Policlinico Umberto I, Rome, Italy
- Department of Molecular Medicine, Pasteur Institute Italy, Cenci Bolognetti Foundation, Rome, Italy
| | | | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carolina Scagnolari
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University, Rome, Italy
- Department of Molecular Medicine, Pasteur Institute Italy, Cenci Bolognetti Foundation, Rome, Italy
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73
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Maranini B, Ciancio G, Ferracin M, Cultrera R, Negrini M, Sabbioni S, Govoni M. microRNAs and Inflammatory Immune Response in SARS-CoV-2 Infection: A Narrative Review. Life (Basel) 2022; 12:life12020288. [PMID: 35207576 PMCID: PMC8879390 DOI: 10.3390/life12020288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
The current SARS-CoV-2 pandemic has emerged as an international challenge with strong medical and socioeconomic impact. The spectrum of clinical manifestations of SARS-CoV-2 is wide, covering asymptomatic or mild cases up to severe and life-threatening complications. Critical courses of SARS-CoV-2 infection are thought to be driven by the so-called “cytokine storm”, derived from an excessive immune response that induces the release of proinflammatory cytokines and chemokines. In recent years, non-coding RNAs (ncRNAs) emerged as potential diagnostic and therapeutic biomarkers in both inflammatory and infectious diseases. Therefore, the identification of SARS-CoV-2 miRNAs and host miRNAs is an important research topic, investigating the host–virus crosstalk in COVID-19 infection, trying to answer the pressing question of whether miRNA-based therapeutics can be employed to tackle SARS-CoV-2 complications. In this review, we aimed to directly address ncRNA role in SARS-CoV-2-immune system crosstalk upon COVID-19 infection, particularly focusing on inflammatory pathways and cytokine storm syndromes.
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Affiliation(s)
- Beatrice Maranini
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
- Correspondence:
| | - Giovanni Ciancio
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy;
| | - Rosario Cultrera
- Infectious Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Massimo Negrini
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnologies, University of Ferrara, 44121 Ferrara, Italy;
| | - Marcello Govoni
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
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74
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Martínez-Fleta P, Vera-Tomé P, Jiménez-Fernández M, Requena S, Roy-Vallejo E, Sanz-García A, Lozano-Prieto M, López-Sanz C, Vara A, Lancho-Sánchez Á, Martín-Gayo E, Muñoz-Calleja C, Alfranca A, González-Álvaro I, Galván-Román JM, Aspa J, de la Fuente H, Sánchez-Madrid F. A Differential Signature of Circulating miRNAs and Cytokines Between COVID-19 and Community-Acquired Pneumonia Uncovers Novel Physiopathological Mechanisms of COVID-19. Front Immunol 2022; 12:815651. [PMID: 35087533 PMCID: PMC8787267 DOI: 10.3389/fimmu.2021.815651] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) pneumonia is a life-threatening infectious disease, especially for elderly patients with multiple comorbidities. Despite enormous efforts to understand its underlying etiopathogenic mechanisms, most of them remain elusive. In this study, we compared differential plasma miRNAs and cytokines profiles between COVID-19 and other community-acquired pneumonias (CAP). A first screening and subsequent validation assays in an independent cohort of patients revealed a signature of 15 dysregulated miRNAs between COVID-19 and CAP patients. Additionally, multivariate analysis displayed a combination of 4 miRNAs (miR-106b-5p, miR-221-3p, miR-25-3p and miR-30a-5p) that significantly discriminated between both pathologies. Search for targets of these miRNAs, combined with plasma protein measurements, identified a differential cytokine signature between COVID-19 and CAP that included EGFR, CXCL12 and IL-10. Significant differences were also detected in plasma levels of CXCL12, IL-17, TIMP-2 and IL-21R between mild and severe COVID-19 patients. These findings provide new insights into the etiopathological mechanisms underlying COVID-19.
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Affiliation(s)
- Pedro Martínez-Fleta
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Paula Vera-Tomé
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - María Jiménez-Fernández
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Silvia Requena
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Emilia Roy-Vallejo
- Department of Internal Medicine, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Ancor Sanz-García
- Data Analysis Unit, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Marta Lozano-Prieto
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Celia López-Sanz
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Alicia Vara
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Ángel Lancho-Sánchez
- Biobank, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Enrique Martín-Gayo
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Department of Medicine, Universidad Autónoma de Madrid (IIS-IP), Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Department of Medicine, Universidad Autónoma de Madrid (IIS-IP), Madrid, Spain
| | - Arantzazu Alfranca
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Isidoro González-Álvaro
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Department of Rheumatology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - José María Galván-Román
- Department of Internal Medicine, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Javier Aspa
- Department of Pneumology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain
| | - Hortensia de la Fuente
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Francisco Sánchez-Madrid
- Department of Immunology, Hospital Universitario de La Princesa IIS-IP (Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa), Madrid, Spain.,Department of Medicine, Universidad Autónoma de Madrid (IIS-IP), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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75
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Molinero M, Benítez ID, González J, Gort-Paniello C, Moncusí-Moix A, Rodríguez-Jara F, García-Hidalgo MC, Torres G, Vengoechea JJ, Gómez S, Cabo R, Caballero J, Bermejo-Martin JF, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Bronchial Aspirate-Based Profiling Identifies MicroRNA Signatures Associated With COVID-19 and Fatal Disease in Critically Ill Patients. Front Med (Lausanne) 2022; 8:756517. [PMID: 35186962 PMCID: PMC8850692 DOI: 10.3389/fmed.2021.756517] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
Background The pathophysiology of COVID-19-related critical illness is not completely understood. Here, we analyzed the microRNA (miRNA) profile of bronchial aspirate (BAS) samples from COVID-19 and non-COVID-19 patients admitted to the ICU to identify prognostic biomarkers of fatal outcomes and to define molecular pathways involved in the disease and adverse events. Methods Two patient populations were included (n = 89): (i) a study population composed of critically ill COVID-19 and non-COVID-19 patients; (ii) a prospective study cohort composed of COVID-19 survivors and non-survivors among patients assisted by invasive mechanical ventilation (IMV). BAS samples were obtained by bronchoaspiration during the ICU stay. The miRNA profile was analyzed using RT-qPCR. Detailed biomarker and bioinformatics analyses were performed. Results The deregulation in five miRNA ratios (miR-122-5p/miR-199a-5p, miR-125a-5p/miR-133a-3p, miR-155-5p/miR-486-5p, miR-214-3p/miR-222-3p, and miR-221-3p/miR-27a-3p) was observed when COVID-19 and non-COVID-19 patients were compared. In addition, five miRNA ratios segregated between ICU survivors and nonsurvivors (miR-1-3p/miR-124-3p, miR-125b-5p/miR-34a-5p, miR-126-3p/miR-16-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). Through multivariable analysis, we constructed a miRNA ratio-based prediction model for ICU mortality that optimized the best combination of miRNA ratios (miR-125b-5p/miR-34a-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). The model (AUC 0.85) and the miR-199a-5p/miR-9-5p ratio (AUC 0.80) showed an optimal discrimination value and outperformed the best clinical predictor for ICU mortality (days from first symptoms to IMV initiation, AUC 0.73). The survival analysis confirmed the usefulness of the miRNA ratio model and the individual ratio to identify patients at high risk of fatal outcomes following IMV initiation. Functional enrichment analyses identified pathological mechanisms implicated in fibrosis, coagulation, viral infections, immune responses and inflammation. Conclusions COVID-19 induces a specific miRNA signature in BAS from critically ill patients. In addition, specific miRNA ratios in BAS samples hold individual and collective potential to improve risk-based patient stratification following IMV initiation in COVID-19-related critical illness. The biological role of the host miRNA profiles may allow a better understanding of the different pathological axes of the disease.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, 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
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, 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
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- 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
| | - 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
| | - J. J. Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Silvia Gómez
- 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
| | - Ramón Cabo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, 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
- *Correspondence: David de Gonzalo-Calvo
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76
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Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Brief Bioinform 2022; 23:bbab397. [PMID: 34585235 PMCID: PMC8500159 DOI: 10.1093/bib/bbab397] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/11/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Some studies reported that genomic RNA of SARS-CoV-2 can absorb a few host miRNAs that regulate immune-related genes and then deprive their function. In this perspective, we conjecture that the absorption of the SARS-CoV-2 genome to host miRNAs is not a coincidence, which may be an indispensable approach leading to viral survival and development in host. In our study, we collected five datasets of miRNAs that were predicted to interact with the genome of SARS-CoV-2. The targets of these miRNAs in the five groups were consistently enriched immune-related pathways and virus-infectious diseases. Interestingly, the five datasets shared no one miRNA but their targets shared 168 genes. The signaling pathway enrichment of 168 shared targets implied an unbalanced immune response that the most of interleukin signaling pathways and none of the interferon signaling pathways were significantly different. Protein-protein interaction (PPI) network using the shared targets showed that PPI pairs, including IL6-IL6R, were related to the process of SARS-CoV-2 infection and pathogenesis. In addition, we found that SARS-CoV-2 absorption to host miRNA could benefit two popular mutant strains for more infectivity and pathogenicity. Conclusively, our results suggest that genomic RNA absorption to host miRNAs may be a vital approach by which SARS-CoV-2 disturbs the host immune system and infects host cells.
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Affiliation(s)
- Song Zhang
- College of Pharmaceutical Sciences in Zhejiang University, and the First Affiliated Hospital of Zhejiang University School of Medicine, China
| | | | - Chenyang Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Yunqing Qiu
- First Affiliated Hospital in Zhejiang University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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77
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Huang K, Wang C, Vagts C, Raguveer V, Finn PW, Perkins DL. Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single-cell analysis. PLoS One 2022; 17:e0261242. [PMID: 35007307 PMCID: PMC8746747 DOI: 10.1371/journal.pone.0261242] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/25/2021] [Indexed: 01/08/2023] Open
Abstract
Hyperactive and damaging inflammation is a hallmark of severe rather than mild Coronavirus disease 2019 (COVID-19). To uncover key inflammatory differentiators between severe and mild COVID-19, we applied an unbiased single-cell transcriptomic analysis. We integrated two single-cell RNA-seq datasets with COVID-19 patient samples, one that sequenced bronchoalveolar lavage (BAL) cells and one that sequenced peripheral blood mononuclear cells (PBMCs). The combined cell population was then analyzed with a focus on genes associated with disease severity. The immunomodulatory long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 were highly differentially expressed between mild and severe patients in multiple cell types. Within those same cell types, the concurrent detection of other severity-associated genes involved in cellular stress response and apoptosis regulation suggests that the pro-inflammatory functions of these lncRNAs may foster cell stress and damage. Thus, NEAT1 and MALAT1 are potential components of immune dysregulation in COVID-19 that may provide targets for severity related diagnostic measures or therapy.
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Affiliation(s)
- Kai Huang
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Catherine Wang
- College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Christen Vagts
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Vanitha Raguveer
- College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Patricia W. Finn
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - David L. Perkins
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Surgery, University of Illinois at Chicago, Chicago, Illinois, United States of America
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78
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Evaluation of potential sponge effects of SARS genomes in human. Noncoding RNA Res 2022; 7:48-53. [PMID: 35075440 PMCID: PMC8769905 DOI: 10.1016/j.ncrna.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/15/2022] [Accepted: 01/15/2022] [Indexed: 12/15/2022] Open
Abstract
To date the coronavirus family is composed of seven different viruses which were commonly known as cold viruses until the appearance of the severe acute respiratory coronavirus (SARS-CoV) in 2002, the middle east respiratory syndrome coronavirus (MERS) in 2012 and the severe acute respiratory coronavirus 2 (SARS-CoV-2) which caused the COVID-19 global pandemic in 2019. Using bioinformatic approaches we tested the potential interactions of human miRNAs, expressed in pulmonary epithelial cells, with the available coronavirus genomes. Putative miRNA binding sites were then compared between pathogenic and non pathogenic virus groups. The pathogenic group shares 6 miRNA binding sites that can be potentially involved in the sequestration of miRNAs already known to be associated with deep vein thrombosis. We then analysed ∼100k SARS-CoV-2 variant genomes for their potential interaction with human miRNAs and this study highlighted a group of 97 miRNA binding sites which is present in all the analysed genomes. Among these, we identified 6 miRNA binding sites specific for SARS-CoV-2 and the other two pathogenic viruses whose down-regulation has been seen associated with deep vein thrombosis and cardiovascular diseases. Interestingly, one of these miRNAs, namely miR-20a-5p, whose expression decreases with advancing age, is involved in cytokine signaling, cell differentiation and/or proliferation. We hypothesize that depletion of poorly expressed miRNA could be related with disease severity.
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79
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Bautista-Becerril B, Pérez-Dimas G, Sommerhalder-Nava PC, Hanono A, Martínez-Cisneros JA, Zarate-Maldonado B, Muñoz-Soria E, Aquino-Gálvez A, Castillejos-López M, Juárez-Cisneros A, Lopez-Gonzalez JS, Camarena A. miRNAs, from Evolutionary Junk to Possible Prognostic Markers and Therapeutic Targets in COVID-19. Viruses 2021; 14:41. [PMID: 35062245 PMCID: PMC8781105 DOI: 10.3390/v14010041] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has been a public health issue around the world in the last few years. Currently, there is no specific antiviral treatment to fight the disease. Thus, it is essential to highlight possible prognostic predictors that could identify patients with a high risk of developing complications. Within this framework, miRNA biomolecules play a vital role in the genetic regulation of various genes, principally, those related to the pathophysiology of the disease. Here, we review the interaction of host and viral microRNAs with molecular and cellular elements that could potentiate the main pulmonary, cardiac, renal, circulatory, and neuronal complications in COVID-19 patients. miR-26a, miR-29b, miR-21, miR-372, and miR-2392, among others, have been associated with exacerbation of the inflammatory process, increasing the risk of a cytokine storm. In addition, increased expression of miR-15b, -199a, and -491 are related to the prognosis of the disease, and miR-192 and miR-323a were identified as clinical predictors of mortality in patients admitted to the intensive care unit. Finally, we address miR-29, miR-122, miR-155, and miR-200, among others, as possible therapeutic targets. However, more studies are required to confirm these findings.
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Affiliation(s)
- Brandon Bautista-Becerril
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Guillermo Pérez-Dimas
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Paola C. Sommerhalder-Nava
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | - Alejandro Hanono
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | | | - Bárbara Zarate-Maldonado
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | - Evangelina Muñoz-Soria
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Arnoldo Aquino-Gálvez
- Laboratorio de Biología Molecular, Departamento de Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Manuel Castillejos-López
- Departamento de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Armida Juárez-Cisneros
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
| | - Jose S. Lopez-Gonzalez
- Laboratorio de Cáncer Pulmonar, Departamento de Enfermedades Crónico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Angel Camarena
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
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80
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Hasankhani A, Bahrami A, Sheybani N, Aria B, Hemati B, Fatehi F, Ghaem Maghami Farahani H, Javanmard G, Rezaee M, Kastelic JP, Barkema HW. Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic. Front Immunol 2021; 12:789317. [PMID: 34975885 PMCID: PMC8714803 DOI: 10.3389/fimmu.2021.789317] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 01/08/2023] Open
Abstract
Background The recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches. Methods RNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules. Results Based on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19's main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis. Conclusion This study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Behzad Aria
- Department of Physical Education and Sports Science, School of Psychology and Educational Sciences, Yazd University, Yazd, Iran
| | - Behzad Hemati
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Farhang Fatehi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mahsa Rezaee
- Department of Medical Mycology, School of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - John P. Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Fang H, Zeng Y, Zhang L, Chen C, Powell CA, Wang X. Can single cell RNA sequencing reshape the clinical biochemistry of hematology: New clusters of circulating blood cells. Clin Transl Med 2021; 11:e671. [PMID: 34898038 PMCID: PMC8666581 DOI: 10.1002/ctm2.671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 12/16/2022] Open
Abstract
scRNA‐seq is on track for use as a routine measurement of clinical biochemistry and to assist in clinical decision‐making and guide the performance of molecular medicine, but there are still a large number of challenges to be overcome. In conclusion, scRNA‐seq‐based clusters and differentiation of circulating blood cells have been examined and informative in patients with various diseases, although the information generated from scRNA‐seq varies between different conditions, technologies, and diseases. Most of the clinical studies published have focused on the landscape of circulating immune cells, disease‐specific patterns of new clusters, understanding of potential mechanisms, and potential correlation between cell clusters, differentiations, cell interactions, and circulating and migrated cells. It is clear that the information from scRNA‐seq advances the understanding of the disease, identifies disease‐specific target panels, and suggests new therapeutic strategies. The adaptation of scRNA‐seq as a routine clinical measurement will require standardization and normalization of scRNA‐seq‐based comprehensive information and validation in a large population of healthy and diseased patients. The integration of public databases on human circulating cell clusters and differentiations with an application of artificial intelligence and computational science will accelerate the application of scRNA‐seq for clinical practice. Thus, we call special attention from scientists and clinicians to the clinical and translational discovery, validation, and medicine opportunities of scRNA‐seq development.
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Affiliation(s)
- Hao Fang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Anesthesiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Molecular Diagnosis and Therapy, Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, China
| | - Lianzhong Zhang
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, Zhejiang, China
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Fudan University Shanghai Medical College, Shanghai, China
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Rodrigues AC, Adamoski D, Genelhould G, Zhen F, Yamaguto GE, Araujo‐Souza PS, Nogueira MB, Raboni SM, Bonatto AC, Gradia DF, Carvalho de Oliveira J. NEAT1 and MALAT1 are highly expressed in saliva and nasopharyngeal swab samples of COVID-19 patients. Mol Oral Microbiol 2021; 36:291-294. [PMID: 34463043 PMCID: PMC8661855 DOI: 10.1111/omi.12351] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
COVID-19, caused by the SARS-CoV-2 virus, has become a significant global public health problem, with a wide variety of clinical manifestations and disease progression outcomes. LncRNAs are key regulators of the immune response and have been associated with COVID-19 risk infection. Previous studies focused mainly on in-silico analysis of lncRNA expression in the lungs or peripheral blood cells. We evaluated the expression of lncRNAs NEAT1, MALAT1, and MIR3142 in saliva and nasopharyngeal swab from SARS-CoV-2 positive (n = 34) and negative patients (n = 46). A higher expression of the lncRNAs NEAT1 and MALAT1 (p < 0.05) were found in positive samples. NEAT1 had a higher expression mainly in saliva samples (p < 0.001), and MALAT1 was upregulated in nasopharyngeal samples (p < 0.05). Area under the ROC curve for NEAT1 in saliva was 0.8067. This study was the first to investigate the expression of lncRNAs in saliva and nasopharyngeal samples of COVID-19 patients, which gives new insights into the initial response to infection and infectivity and may provide new biomarkers for severity and targets for therapy.
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Affiliation(s)
- Ana Carolina Rodrigues
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)Sao PauloBrazil
| | - Gustavo Genelhould
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Felipe Zhen
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Guilherme Eiji Yamaguto
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Patrícia Savio Araujo‐Souza
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Meri Bordignon Nogueira
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Sonia Mara Raboni
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Ana Claudia Bonatto
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Daniela Fiori Gradia
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Jaqueline Carvalho de Oliveira
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
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Wang X, Powell CA. How to translate the knowledge of COVID-19 into the prevention of Omicron variants. Clin Transl Med 2021; 11:e680. [PMID: 34898050 PMCID: PMC8666580 DOI: 10.1002/ctm2.680] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022] Open
Abstract
Omicron variants are part of the "Coronavirus disease 2019 [COVID-19] Variants of Concerns" and has the potential to spread around the world rapidly and can harm human life. We can anticipate that the endemic state of COVID-19 will be characterized by the development of new strains with surges that will predominate in unvaccinated and immunodeficient populations. Thus, there will be an important role in promoting vaccinations, boosters and accessible testing to prevent disease transmission and to rapidly detect surges. There is an urgent need to explore the virology and biology of Omicron variants, define clinical phenomes and therapies, monitor dynamics of genetic changes, and translate the knowledge of COVID-19 into new variants. Clinical and translational medicine will be impactful in addressing these challenges by providing new insights for understanding and predicting new variants-associated transmissibility, disease severity, immune escape, diagnostic or therapeutic failure.
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Affiliation(s)
- Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan HospitalShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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Visacri MB, Nicoletti ADS, Pincinato EDC, Loren P, Saavedra N, Saavedra K, Salazar LA, Moriel P. Role of miRNAs as biomarkers of COVID-19: a scoping review of the status and future directions for research in this field. Biomark Med 2021; 15:1785-1795. [PMID: 34784802 PMCID: PMC8601154 DOI: 10.2217/bmm-2021-0348] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Aim: miRNAs are potential biomarkers of several diseases. This review aimed to identify the miRNAs that could serve as biomarkers of COVID-19. Materials & methods: A literature search of nine databases was carried out for studies published before 13 June 2021 that described dysregulated miRNAs in cells or animals infected by SARS-CoV-2 or in patients with COVID-19. Two independent reviewers selected the studies and extracted data; disagreements were resolved by a third reviewer. Results: Twenty studies were included in this scoping review; results suggested that miR-21-5p, miR-146a, miR-126-3p, miR-144 and miR-155 are the most important dysregulated miRNAs that could serve as biomarkers for diagnosing and indicating the severity of COVID-19. miRNAs appear to play key roles in viral replication, proliferation of infected cells, immune response, inflammation and cardiovascular dysfunction. Conclusion: This review provides insights into the role of miRNAs as biomarkers in COVID-19 and the current status and future directions for research in this field.
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Affiliation(s)
- Marília B Visacri
- Department of Pharmacology, School of Medical Sciences, University of Campinas, Campinas, 13083-887, Brazil
| | - Aline de S Nicoletti
- Department of Pharmacology, School of Medical Sciences, University of Campinas, Campinas, 13083-887, Brazil
| | - Eder de C Pincinato
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Campinas, 13083-887, Brazil
| | - Pía Loren
- Center of Molecular Biology & Pharmacogenetics, Scientific & Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, 4811230, Chile
| | - Nicolás Saavedra
- Center of Molecular Biology & Pharmacogenetics, Scientific & Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, 4811230, Chile
| | - Kathleen Saavedra
- Center of Molecular Biology & Pharmacogenetics, Scientific & Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, 4811230, Chile
| | - Luis A Salazar
- Center of Molecular Biology & Pharmacogenetics, Scientific & Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, 4811230, Chile
| | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, 13083-871, Brazil
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Aminu AJ, Petkova M, Atkinson AJ, Yanni J, Morris AD, Simms RT, Chen W, Yin Z, Kuniewicz M, Holda MK, Kuzmin VS, Perde F, Molenaar P, Dobrzynski H. Further insights into the molecular complexity of the human sinus node - The role of 'novel' transcription factors and microRNAs. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 166:86-104. [PMID: 34004232 DOI: 10.1016/j.pbiomolbio.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023]
Abstract
RESEARCH PURPOSE The sinus node (SN) is the heart's primary pacemaker. Key ion channels (mainly the funny channel, HCN4) and Ca2+-handling proteins in the SN are responsible for its function. Transcription factors (TFs) regulate gene expression through inhibition or activation and microRNAs (miRs) do this through inhibition. There is high expression of macrophages and mast cells within the SN connective tissue. 'Novel'/unexplored TFs and miRs in the regulation of ion channels and immune cells in the SN are not well understood. Using RNAseq and bioinformatics, the expression profile and predicted interaction of key TFs and cell markers with key miRs in the adult human SN vs. right atrial tissue (RA) were determined. PRINCIPAL RESULTS 68 and 60 TFs significantly more or less expressed in the SN vs. RA respectively. Among those more expressed were ISL1 and TBX3 (involved in embryonic development of the SN) and 'novel' RUNX1-2, CEBPA, GLI1-2 and SOX2. These TFs were predicted to regulate HCN4 expression in the SN. Markers for different cells: fibroblasts (COL1A1), fat (FABP4), macrophages (CSF1R and CD209), natural killer (GZMA) and mast (TPSAB1) were significantly more expressed in the SN vs. RA. Interestingly, RUNX1-3, CEBPA and GLI1 also regulate expression of these cells. MiR-486-3p inhibits HCN4 and markers involved in immune response. MAJOR CONCLUSIONS In conclusion, RUNX1-2, CSF1R, TPSAB1, COL1A1 and HCN4 are highly expressed in the SN but not miR-486-3p. Their complex interactions can be used to treat SN dysfunction such as bradycardia. Interestingly, another research group recently reported miR-486-3p is upregulated in blood samples from severe COVID-19 patients who suffer from bradycardia.
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Affiliation(s)
- Abimbola J Aminu
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Maria Petkova
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Andrew J Atkinson
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Joseph Yanni
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Alex D Morris
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Robert T Simms
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Weixuan Chen
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Zeyuan Yin
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Marcin Kuniewicz
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland
| | - Mateusz K Holda
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland
| | - Vladislav S Kuzmin
- Department of Human and Animal Physiology, Lomonosov Moscow State University, Moscow, Russia
| | - Filip Perde
- National Institute of Legal Medicine, Bucharest, Romania
| | - Peter Molenaar
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Cardiovascular Molecular & Therapeutics Translational Research Group, University of Queensland, The Prince Charles Hospital, Brisbane, Australia
| | - Halina Dobrzynski
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland.
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McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler JC, Mason CE, Chatterjee A, Meller R, Beheshti A. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Rep 2021; 37:109839. [PMID: 34624208 PMCID: PMC8481092 DOI: 10.1016/j.celrep.2021.109839] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/13/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.
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Affiliation(s)
- J Tyson McDonald
- COVID-19 International Research Team; Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Francisco J Enguita
- COVID-19 International Research Team; Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Deanne Taylor
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Griffin
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Waldemar Priebe
- COVID-19 International Research Team; University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team; University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Anthony D Harris
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean Clement
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph M Dybas
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Joseph W Guarnieri
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Grabham
- COVID-19 International Research Team; Columbia University, New York, NY 10032, USA
| | - Stephen B Baylin
- COVID-19 International Research Team; Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Aliza Yousey
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | - Peter M Corry
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team; Logyx LLC, Mountain View, CA 94043, USA; NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sadhana Sharma
- University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA; Quantum Biology Inc., Boulder, CO 80301, USA
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Bianca Cerqueira
- COVID-19 International Research Team; KBR Space & Science, San Antonio, TX 78235, USA; United States Air Force School of Aerospace Medicine, Lackland AFB, San Antonio, TX 78236, USA
| | - Viktorija Zaksas
- COVID-19 International Research Team; University of Chicago, Chicago, IL 60615, USA
| | - Urminder Singh
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | | | | | - Diego Galeano
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Alberto Paccanaro
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; University of London, Egham Hill, Egham, UK
| | - Suzanne L Meinig
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert S Hagan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie M Bowman
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Selin Altinok
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | - Douglas C Wallace
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- COVID-19 International Research Team; Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY, USA
| | - Anushree Chatterjee
- COVID-19 International Research Team; University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA
| | - Robert Meller
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Afshin Beheshti
- COVID-19 International Research Team; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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de Gonzalo-Calvo D, Benítez ID, Pinilla L, Carratalá A, Moncusí-Moix A, Gort-Paniello C, Molinero M, González J, Torres G, Bernal M, Pico S, Almansa R, Jorge N, Ortega A, Bustamante-Munguira E, Gómez JM, González-Rivera M, Micheloud D, Ryan P, Martinez A, Tamayo L, Aldecoa C, Ferrer R, Ceccato A, Fernández-Barat L, Motos A, Riera J, Menéndez R, Garcia-Gasulla D, Peñuelas O, Torres A, Bermejo-Martin JF, Barbé F. Circulating microRNA profiles predict the severity of COVID-19 in hospitalized patients. Transl Res 2021; 236:147-159. [PMID: 34048985 PMCID: PMC8149473 DOI: 10.1016/j.trsl.2021.05.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
We aimed to examine the circulating microRNA (miRNA) profile of hospitalized COVID-19 patients and evaluate its potential as a source of biomarkers for the management of the disease. This was an observational and multicenter study that included 84 patients with a positive nasopharyngeal swab Polymerase chain reaction (PCR) test for SARS-CoV-2 recruited during the first pandemic wave in Spain (March-June 2020). Patients were stratified according to disease severity: hospitalized patients admitted to the clinical wards without requiring critical care and patients admitted to the intensive care unit (ICU). An additional study was completed including ICU nonsurvivors and survivors. Plasma miRNA profiling was performed using reverse transcription polymerase quantitative chain reaction (RT-qPCR). Predictive models were constructed using least absolute shrinkage and selection operator (LASSO) regression. Ten circulating miRNAs were dysregulated in ICU patients compared to ward patients. LASSO analysis identified a signature of three miRNAs (miR-148a-3p, miR-451a and miR-486-5p) that distinguishes between ICU and ward patients [AUC (95% CI) = 0.89 (0.81-0.97)]. Among critically ill patients, six miRNAs were downregulated between nonsurvivors and survivors. A signature based on two miRNAs (miR-192-5p and miR-323a-3p) differentiated ICU nonsurvivors from survivors [AUC (95% CI) = 0.80 (0.64-0.96)]. The discriminatory potential of the signature was higher than that observed for laboratory parameters such as leukocyte counts, C-reactive protein (CRP) or D-dimer [maximum AUC (95% CI) for these variables = 0.73 (0.55-0.92)]. miRNA levels were correlated with the duration of ICU stay. Specific circulating miRNA profiles are associated with the severity of COVID-19. Plasma miRNA signatures emerge as a novel tool to assist in the early prediction of vital status deterioration among ICU patients.
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, 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, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Amara Carratalá
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, 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, 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, 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, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María Bernal
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Silvia Pico
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Noelia Jorge
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Alicia Ortega
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | | | | | | | | | - Pablo Ryan
- Hospital Universitario Infanta Leonor, Madrid, Spain
| | | | - Luis Tamayo
- Hospital Universitario Río Hortega, Valladolid, Spain
| | - César Aldecoa
- Hospital Universitario Río Hortega, Valladolid, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | | | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario de Getafe, Madrid, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Servei de Pneumologia, Hospital Clinic. Universitat de Barcelona. IDIBAPS, Barcelona, Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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88
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Duecker RP, Adam EH, Wirtz S, Gronau L, Khodamoradi Y, Eberhardt FJ, Donath H, Gutmann D, Vehreschild MJGT, Zacharowski K, Kreyenberg H, Chiocchetti AG, Zielen S, Schubert R. The MiR-320 Family Is Strongly Downregulated in Patients with COVID-19 Induced Severe Respiratory Failure. Int J Mol Sci 2021; 22:ijms221910351. [PMID: 34638691 PMCID: PMC8508658 DOI: 10.3390/ijms221910351] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023] Open
Abstract
A high incidence of thromboembolic events associated with high mortality has been reported in severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infections with respiratory failure. The present study characterized post-transcriptional gene regulation by global microRNA (miRNA) expression in relation to activated coagulation and inflammation in 21 critically ill SARS-CoV-2 patients. The cohort consisted of patients with moderate respiratory failure (n = 11) and severe respiratory failure (n = 10) at an acute stage (day 0-3) and in the later course of the disease (>7 days). All patients needed supplemental oxygen and severe patients were defined by the requirement of positive pressure ventilation (intubation). Levels of D-dimers, activated partial thromboplastin time (aPTT), C-reactive protein (CRP), and interleukin (IL)-6 were significantly higher in patients with severe compared with moderate respiratory failure. Concurrently, next generation sequencing (NGS) analysis demonstrated increased dysregulation of miRNA expression with progression of disease severity connected to extreme downregulation of miR-320a, miR-320b and miR-320c. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed involvement in the Hippo signaling pathway, the transforming growth factor (TGF)-β signaling pathway and in the regulation of adherens junctions. The expression of all miR-320 family members was significantly correlated with CRP, IL-6, and D-dimer levels. In conclusion, our analysis underlines the importance of thromboembolic processes in patients with respiratory failure and emphasizes miRNA-320s as potential biomarkers for severe progressive SARS-CoV-2 infection.
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Affiliation(s)
- Ruth P. Duecker
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
- Correspondence:
| | - Elisabeth H. Adam
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy 2, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (E.H.A.); (K.Z.)
| | - Sarah Wirtz
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
| | - Lucia Gronau
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
- Department of Food Technology, University of Applied Sciences Fulda, 36037 Fulda, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (Y.K.); (F.J.E.); (M.J.G.T.V.)
| | - Fabian J. Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (Y.K.); (F.J.E.); (M.J.G.T.V.)
| | - Helena Donath
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
| | - Desiree Gutmann
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (Y.K.); (F.J.E.); (M.J.G.T.V.)
| | - Kai Zacharowski
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy 2, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (E.H.A.); (K.Z.)
| | - Hermann Kreyenberg
- Division for Stem Cell Transplantation and Immunology, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany;
| | - Andreas G. Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany;
| | - Stefan Zielen
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
| | - Ralf Schubert
- Division for Allergy, Pneumology and Cystic Fibrosis, Department for Children and Adolescence, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (S.W.); (L.G.); (H.D.); (D.G.); (S.Z.); (R.S.)
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89
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SnoRNAs and miRNAs Networks Underlying COVID-19 Disease Severity. Vaccines (Basel) 2021; 9:vaccines9101056. [PMID: 34696164 PMCID: PMC8538251 DOI: 10.3390/vaccines9101056] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 12/18/2022] Open
Abstract
There is a lack of predictive markers for early and rapid identification of disease progression in COVID-19 patients. Our study aims at identifying microRNAs (miRNAs)/small nucleolar RNAs (snoRNAs) as potential biomarkers of COVID-19 severity. Using differential expression analysis of microarray data (n = 29), we identified hsa-miR-1246, ACA40, hsa-miR-4532, hsa-miR-145-5p, and ACA18 as the top five differentially expressed transcripts in severe versus asymptomatic, and ACA40, hsa-miR-3609, ENSG00000212378 (SNORD78), hsa-miR-1231, hsa-miR-885-3p as the most significant five in severe versus mild cases. Moreover, we found that white blood cell (WBC) count, absolute neutrophil count (ANC), neutrophil (%), lymphocyte (%), red blood cell (RBC) count, hemoglobin, hematocrit, D-Dimer, and albumin are significantly correlated with the identified differentially expressed miRNAs and snoRNAs. We report a unique miRNA and snoRNA profile that is associated with a higher risk of severity in a cohort of SARS-CoV-2 infected patients. Altogether, we present a differential expression analysis of COVID-19-associated microRNA (miRNA)/small nucleolar RNA (snoRNA) signature, highlighting their importance in SARS-CoV-2 infection.
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90
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Wang S, Tan Y, Yang T, Liu C, Li R. Pulmonary AngII promotes LPS-induced lung inflammation by regulating microRNA-143. Cytotechnology 2021; 73:745-754. [PMID: 34493899 PMCID: PMC8414951 DOI: 10.1007/s10616-021-00493-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Angiotensin converting enzyme 2 (ACE2) is a terminal carboxypeptidase, which cleaves single terminal residues from several bioactive peptides such as Angiotensin II (AngII). Many investigations indicated that ACE2 functions in angiotensin system and plays a crucial role in inflammatory lung diseases. However, the mechanism behind the involvement of ACE2 in inflammatory lung disease has not been fully elucidated. In this study, BEAS-2B cells were treated with gradient concentration of AngII and lipopolysaccharide (LPS) to induce inflammatory condition. Quantitative RT-PCR was performed to detect the level of ACE2 and miR-143-3p. Western blotting and immunofluorescence assays were performed to measure the expression of related proteins. The levels of inflammatory cytokines and cell viability were respectively measured by ELISA and CCK-8 kits. And ACE2 activity was detected by corresponding commercial kits. Bioinformatics methods were employed to predict the potential microRNA targeting ACE2, which was then confirmed by dual luciferase reporter assay. The results showed that ACE2 expression and activity were time-dependently decreased in LPS group for the first 12 h, after which this tendency was reversed. AngII addition enhanced these effects, compared with LPS group. Additionally, the lowest ACE2 activity level was found in both LPS and AngII + LPS groups at 6 h. The number of nuclei and the ACE2 expression were decreased in LPS groups at 6 h and further reduced by addition of AngII, detected by immunofluorescence. Moreover, ACE2 was validated to be a direct target of miR-143-3p. Pretreatment of AngII and LPS regulated the activity of ACE2, increased the expression of proinflammatory cytokines and cell apoptosis and regulated the expression of Bax, Bcl-2 and cleaved caspase-3 in BEAS-2B cells, which could be reversed by transfecting miR-143-3p inhibitor. The results collectively suggest that AngII promotes LPS-induced inflammation by regulating miR-143-3p in BEAS-2B cells. Therefore, miR-143-3p is considered a potential molecular target for the treatment of lung inflammation.
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Affiliation(s)
- Shenglan Wang
- Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China.,The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China
| | - Yan Tan
- Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China.,The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China
| | - Tingting Yang
- Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China.,The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China
| | - Chen Liu
- Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China.,The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China
| | - Rufang Li
- Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China.,The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Xishan District, Kunming, 650032 Yunnan China
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91
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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92
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Narożna M, Rubiś B. Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy. Int J Mol Sci 2021; 22:8663. [PMID: 34445368 PMCID: PMC8395427 DOI: 10.3390/ijms22168663] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, we have experienced a serious pandemic. Despite significant technological advances in molecular technologies, it is very challenging to slow down the infection spread. It appeared that due to globalization, SARS-CoV-2 spread easily and adapted to new environments or geographical or weather zones. Additionally, new variants are emerging that show different infection potential and clinical outcomes. On the other hand, we have some experience with other pandemics and some solutions in virus elimination that could be adapted. This is of high importance since, as the latest reports demonstrate, vaccine technology might not follow the new, mutated virus outbreaks. Thus, identification of novel strategies and markers or diagnostic methods is highly necessary. For this reason, we present some of the latest views on SARS-CoV-2/COVID-19 therapeutic strategies and raise a solution based on miRNA. We believe that in the face of the rapidly increasing global situation and based on analogical studies of other viruses, the possibility of using the biological potential of miRNA technology is very promising. It could be used as a promising diagnostic and prognostic factor, as well as a therapeutic target and tool.
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Affiliation(s)
- Maria Narożna
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4 Święcickiego St., 60-781 Poznan, Poland;
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, 49 Przybyszewskiego St., 60-355 Poznan, Poland
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93
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Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19. Viruses 2021; 13:v13081593. [PMID: 34452458 PMCID: PMC8402885 DOI: 10.3390/v13081593] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3′-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.
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94
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Saulle I, Garziano M, Fenizia C, Cappelletti G, Parisi F, Clerici M, Cetin I, Savasi V, Biasin M. MiRNA Profiling in Plasma and Placenta of SARS-CoV-2-Infected Pregnant Women. Cells 2021; 10:1788. [PMID: 34359957 PMCID: PMC8305278 DOI: 10.3390/cells10071788] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs are gene expression regulators associated with several human pathologies, including those generated by viral infections. Their role in SARS-CoV-2 infection and COVID-19 has been investigated and reviewed in many informative studies; however, a thorough miRNA outline in SARS-CoV-2-infected pregnant women (SIPW), at both systemic and placental levels, is missing. To fill this gap, blood and placenta biopsies collected at delivery from 15 asymptomatic SIPW were immediately analysed for: miRNA expression (n = 84) (QPCR array), antiviral/immune mRNA target expression (n = 74) (QGene) and cytokine/chemokines production (n = 27) (Multiplex ELISA). By comparing these results with those obtained from six uninfected pregnant women (UPW), we observed that, following SARS-CoV-2 infection, the transcriptomic profile of pregnant women is significantly altered in different anatomical districts, even in the absence of clinical symptoms and vertical transmission. This characteristic combination of miRNA and antiviral/immune factors seems to control both the infection and the dysfunctional immune reaction, thus representing a positive correlate of protection and a potential therapeutic target against SARS-CoV-2.
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Affiliation(s)
- Irma Saulle
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
| | - Micaela Garziano
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
| | - Claudio Fenizia
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
| | - Gioia Cappelletti
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
| | - Francesca Parisi
- Unit of Obstetrics and Gynecology, ASST Fatebenefratelli-Sacco, Department of Biological and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (F.P.)
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
- IRCCS Fondazione Don Carlo Gnocchi, 20148 Milan, Italy
| | - Irene Cetin
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
- Department of Woman, Mother and Neonate Buzzi Children’s Hospital, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy
| | - Valeria Savasi
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
- Unit of Obstetrics and Gynecology, ASST Fatebenefratelli-Sacco, Department of Biological and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (F.P.)
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, 20157 Milan, Italy; (I.S.); (M.G.); (C.F.); (G.C.); (I.C.); (V.S.)
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95
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Kesheh MM, Mahmoudvand S, Shokri S. Long noncoding RNAs in respiratory viruses: A review. Rev Med Virol 2021; 32:e2275. [PMID: 34252234 PMCID: PMC8420315 DOI: 10.1002/rmv.2275] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as RNA molecules longer than 200 nucleotides that can regulate gene expression at the transcriptional or post‐transcriptional levels. Both human lncRNAs and lncRNAs encoded by viruses can modulate the expression of host genes which are critical for viral replication, latency, activation of signalling pathways, cytokine and chemokine production, RNAi processing, expression of interferons (IFNs) and interferon‐stimulated genes (ISGs). Studies on lncRNAs as key regulators of host‐virus interactions may give new insights into therapeutic strategies for the treatment of related diseases. This current review focuses on the role of lncRNAs, and their interactions with respiratory viruses including influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2).
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahab Mahmoudvand
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Somayeh Shokri
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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96
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Regulation of sinus node pacemaking and atrioventricular node conduction by HCN channels in health and disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 166:61-85. [PMID: 34197836 DOI: 10.1016/j.pbiomolbio.2021.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/02/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022]
Abstract
The funny current, If, was first recorded in the heart 40 or more years ago by Dario DiFrancesco and others. Since then, we have learnt that If plays an important role in pacemaking in the sinus node, the innate pacemaker of the heart, and more recently evidence has accumulated to show that If may play an important role in action potential conduction through the atrioventricular (AV) node. Evidence has also accumulated to show that regulation of the transcription and translation of the underlying Hcn genes plays an important role in the regulation of sinus node pacemaking and AV node conduction under normal physiological conditions - in athletes, during the circadian rhythm, in pregnancy, and during postnatal development - as well as pathological states - ageing, heart failure, pulmonary hypertension, diabetes and atrial fibrillation. There may be yet more pathological conditions involving changes in the expression of the Hcn genes. Here, we review the role of If and the underlying HCN channels in physiological and pathological changes of the sinus and AV nodes and we begin to explore the signalling pathways (microRNAs, transcription factors, GIRK4, the autonomic nervous system and inflammation) involved in this regulation. This review is dedicated to Dario DiFrancesco on his retirement.
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97
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Feng J, Bian Q, He X, Zhang H, He J. A LncRNA-miRNA-mRNA ceRNA regulatory network based tuberculosis prediction model. Microb Pathog 2021; 158:105069. [PMID: 34175436 DOI: 10.1016/j.micpath.2021.105069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022]
Abstract
The high incidence of tuberculosis (TB) has brought serious social burdens and it is urgent to explore the mechanism of TB development. This study was conducted to analyze the role of lncRNA-miRNA-mRNA regulatory network and its contained nodes involved in TB to identify crucial biomarkers for early diagnosis of TB. Long-noncoding RNAs (lncRNAs), messenger RNA (mRNAs) and microRNAs (miRNAs) expression profiles of TB patients and healthy individuals were downloaded from the GSE34608 dataset. Weighted gene co-expression network analysis (WGCNA) was performed to identified the key modules related to TB and the highly related mRNA-lncRNA pair in the module. Based on highly related mRNAs and lncRNAs in greenyellow module, lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network was constructed. The DE-mRNAs in the network were functionally enriched with Gene ontology (GO) and Gene set enrichment analysis (GSEA). Least absolute shrinkage and selection operator (LASSO) algorithm and receiver operating characteristic curve (ROC) were used to construct and evaluate the prediction model of TB. We identified 3267 DE-mRNAs, 484 DE-lncRNAs and 69 DE-miRNAs between the TB and healthy subjects, from which 8 DE-mRNAs, 14 DE-lncRNAs and 3 DE-miRNAs were used to construct the ceRNA network. The genes contained in the ceRNA network were mainly enriched in neutrophil mediated immune response, including neutrophil activation, degradation and signal transduction. ROC analysis revealed that has-miR-140-5p, has-miR-142-3p and the LASSO cox prediction model based on HMGA1 and CAPN1 have potential value for forecasting TB (AUC > 0.7). Hence, our study provides a new perspective from the lncRNA-miRNA-mRNA ceRNA regulatory network for TB diagnosis and treatment.
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Affiliation(s)
- Jinfang Feng
- Clinical Laboratory Department, Guangyuan Central Hospital, Guangyuan, 628000, China
| | - Qin Bian
- Clinical Laboratory Department, Guangyuan Central Hospital, Guangyuan, 628000, China.
| | - Xianwei He
- Clinical Laboratory Department, Guangyuan Central Hospital, Guangyuan, 628000, China
| | - Han Zhang
- Clinical Laboratory Department, Guangyuan Central Hospital, Guangyuan, 628000, China
| | - Jiujiang He
- Clinical Laboratory Department, Guangyuan Central Hospital, Guangyuan, 628000, China
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98
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Hu S, Hu Z, Qin J, Lin C, Jiang X. In silico analysis identifies neuropilin-1 as a potential therapeutic target for SARS-Cov-2 infected lung cancer patients. Aging (Albany NY) 2021; 13:15770-15784. [PMID: 34168096 PMCID: PMC8266340 DOI: 10.18632/aging.203159] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), and is highly contagious and pathogenic. TMPRSS2 and Neuropilin-1, the key components that facilitate SARS-CoV-2 infection, are potential targets for treatment of COVID-19. Here we performed a comprehensive analysis on NRP1 and TMPRSS2 in lung to provide information for treating comorbidity of COVID-19 with lung cancer. NRP1 is widely expressed across all the human tissues while TMPRSS2 is expressed in a restricted pattern. High level of NRP1 associates with worse prognosis in multiple cancers, while high level of TMPRSS2 is associated with better survival of Lung Adenocarcinoma (LUAD). Moreover, NRP1 positively correlates with the oncogenic Cancer Associated Fibroblast (CAF), macrophage and endothelial cells infiltration, negatively correlates with infiltration of CD8+ T cell, the tumor killer cell in Lung Squamous cell carcinoma (LUSC). TMPRSS2 shows negative correlation with the oncogenic events in LUAD. RNA-seq data show that NRP1 level is slightly decreased in peripheral blood of ICU admitted COVID-19 patients, unaltered in lung, while TMPRSS2 level is significantly decreased in lung of COVID-19 patients. Our analysis suggests NRP1 as a potential therapeutic target, while sets an alert on targeting TMPRSS2 for treating comorbidity of COVID-19 and lung cancers.
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Affiliation(s)
- Song Hu
- Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
| | - Zheyu Hu
- Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
| | - Jiajia Qin
- Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
| | - Chuwen Lin
- Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
| | - Xuan Jiang
- Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, Guangdong, China
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99
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A single transcript for the prognosis of disease severity in COVID-19 patients. Sci Rep 2021; 11:12174. [PMID: 34108608 PMCID: PMC8190311 DOI: 10.1038/s41598-021-91754-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
With many countries strapped for medical resources due to the COVID-19 pandemic, it is highly desirable to allocate the precious resources to those who need them the most. Several markers have been found to be associated with the disease severity in COVID-19 patients. However, the established markers only display modest prognostic power individually and better markers are urgently needed. The aim of this study is to investigate the potential of S100A12, a prominent marker gene for bacterial infection, in the prognosis of disease severity in COVID-19 patients. To ensure the robustness of the association, a total of 1695 samples from 14 independent transcriptome datasets on sepsis, influenza infection and COVID-19 infection were examined. First, it was demonstrated that S100A12 was a marker for sepsis and severity of sepsis. Then, S100A12 was found to be a marker for severe influenza infection, and there was an upward trend of S100A12 expression as the severity level of influenza infection increased. As for COVID-19 infection, it was found that S100A12 expression was elevated in patients with severe and critical COVID-19 infection. More importantly, S100A12 expression at hospital admission was robustly correlated with future quantitative indexes of disease severity and outcome in COVID-19 patients, superior to established prognostic markers including CRP, PCT, d-dimer, ferritin, LDH and fibrinogen. Thus, S100A12 is a valuable novel prognostic marker for COVID-19 severity and deserves more attention.
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100
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Siniscalchi C, Di Palo A, Russo A, Potenza N. Human MicroRNAs Interacting With SARS-CoV-2 RNA Sequences: Computational Analysis and Experimental Target Validation. Front Genet 2021; 12:678994. [PMID: 34163530 PMCID: PMC8215607 DOI: 10.3389/fgene.2021.678994] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel RNA virus affecting humans, causing a form of acute pulmonary respiratory disorder named COVID-19, declared a pandemic by the World Health Organization. MicroRNAs (miRNA) play an emerging and important role in the interplay between viruses and host cells. Although the impact of host miRNAs on SARS-CoV-2 infection has been predicted, experimental data are still missing. This study started by a bioinformatics prediction of cellular miRNAs potentially targeting viral RNAs; then, a number of criteria also based on experimental evidence and virus biology were applied, giving rise to eight promising binding miRNAs. Their interaction with viral sequences was experimentally validated by transfecting luciferase-based reporter plasmids carrying viral target sequences or their inverted sequences into the lung A549 cell line. Transfection of the reporter plasmids resulted in a reduction of luciferase activity for five out of the eight potential binding sites, suggesting responsiveness to endogenously expressed miRNAs. Co-transfection of the reporter plasmids along with miRNA mimics led to a further and strong reduction of luciferase activity, validating the interaction between miR-219a-2-3p, miR-30c-5p, miR-378d, miR-29a-3p, miR-15b-5p, and viral sequences. miR-15b was also able to repress plasmid-driven Spike expression. Intriguingly, the viral target sequences are fully conserved in more recent variants such as United Kingdom variant B.1.1.7 and South Africa 501Y.V2. Overall, this study provides a first experimental evidence of the interaction between specific cellular miRNAs and SARS-CoV-2 sequences, thus contributing to understanding the molecular mechanisms underlying virus infection and pathogenesis to envisage innovative therapeutic interventions and diagnostic tools.
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Affiliation(s)
- Chiara Siniscalchi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Armando Di Palo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Aniello Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
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