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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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Gilyazova I, Timasheva Y, Karunas A, Kazantseva A, Sufianov A, Mashkin A, Korytina G, Wang Y, Gareev I, Khusnutdinova E. COVID-19: Mechanisms, risk factors, genetics, non-coding RNAs and neurologic impairments. Noncoding RNA Res 2023; 8:240-254. [PMID: 36852336 PMCID: PMC9946734 DOI: 10.1016/j.ncrna.2023.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
The novel coronavirus infection (COVID-19) causes a severe acute illness with the development of respiratory distress syndrome in some cases. COVID-19 is a global problem of mankind to this day. Among its most important aspects that require in-depth study are pathogenesis and molecular changes in severe forms of the disease. A lot of literature data is devoted to the pathogenetic mechanisms of COVID-19. Without dwelling in detail on some paths of pathogenesis discussed, we note that at present there are many factors of development and progression. Among them, this is the direct role of both viral non-coding RNAs (ncRNAs) and host ncRNAs. One such class of ncRNAs that has been extensively studied in COVID-19 is microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Moreover, Initially, it was believed that this COVID-19 was limited to damage to the respiratory system. It has now become clear that COVID-19 affects not only the liver and kidneys, but also the nervous system. In this review, we summarized the current knowledge of mechanisms, risk factors, genetics and neurologic impairments in COVID-19. In addition, we discuss and evaluate evidence demonstrating the involvement of miRNAs and lnRNAs in COVID-19 and use this information to propose hypotheses for future research directions.
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Affiliation(s)
- Irina Gilyazova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
- Bashkir State Medical University, 450008, Ufa, Russia
| | - Yanina Timasheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
| | - Alexandra Karunas
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
- Federal State Educational Institution of Higher Education, Ufa University of Science and Technology, 450076, Ufa, Russia
| | - Anastasiya Kazantseva
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
- Federal State Educational Institution of Higher Education, Ufa University of Science and Technology, 450076, Ufa, Russia
| | - Albert Sufianov
- Рeoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow, 117198, Russia
- Department of Neurosurgery, Sechenov First Moscow State Medical University (Sechenov University), 119435, Moscow, Russia
| | - Andrey Mashkin
- Рeoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow, 117198, Russia
| | - Gulnaz Korytina
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
| | - Yaolou Wang
- Harbin Medical University, 157 Baojian Rd, Nangang, Harbin, Heilongjiang, 150088, China
| | - Ilgiz Gareev
- Bashkir State Medical University, 450008, Ufa, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054, Ufa, Russia
- Federal State Educational Institution of Higher Education, Ufa University of Science and Technology, 450076, Ufa, Russia
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Xu Y, Ma Q, Ren J, Chen L, Guo W, Feng K, Zeng Z, Huang T, Cai Y. Using Machine Learning Methods in Identifying Genes Associated with COVID-19 in Cardiomyocytes and Cardiac Vascular Endothelial Cells. Life (Basel) 2023; 13:life13041011. [PMID: 37109540 PMCID: PMC10146712 DOI: 10.3390/life13041011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) not only causes respiratory system damage, but also imposes strain on the cardiovascular system. Vascular endothelial cells and cardiomyocytes play an important role in cardiac function. The aberrant expression of genes in vascular endothelial cells and cardiomyocytes can lead to cardiovascular diseases. In this study, we sought to explain the influence of respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gene expression levels of vascular endothelial cells and cardiomyocytes. We designed an advanced machine learning-based workflow to analyze the gene expression profile data of vascular endothelial cells and cardiomyocytes from patients with COVID-19 and healthy controls. An incremental feature selection method with a decision tree was used in building efficient classifiers and summarizing quantitative classification genes and rules. Some key genes, such as MALAT1, MT-CO1, and CD36, were extracted, which exert important effects on cardiac function, from the gene expression matrix of 104,182 cardiomyocytes, including 12,007 cells from patients with COVID-19 and 92,175 cells from healthy controls, and 22,438 vascular endothelial cells, including 10,812 cells from patients with COVID-19 and 11,626 cells from healthy controls. The findings reported in this study may provide insights into the effect of COVID-19 on cardiac cells and further explain the pathogenesis of COVID-19, and they may facilitate the identification of potential therapeutic targets.
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Affiliation(s)
- Yaochen Xu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
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Gambardella J, Kansakar U, Sardu C, Messina V, Jankauskas SS, Marfella R, Maggi P, Wang X, Mone P, Paolisso G, Sorriento D, Santulli G. Exosomal miR-145 and miR-885 Regulate Thrombosis in COVID-19. J Pharmacol Exp Ther 2023; 384:109-115. [PMID: 35772782 PMCID: PMC9827505 DOI: 10.1124/jpet.122.001209] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 01/13/2023] Open
Abstract
We hypothesized that exosomal microRNAs could be implied in the pathogenesis of thromboembolic complications in coronavirus disease 2019 (COVID-19). We isolated circulating exosomes from patients with COVID-19, and then we divided our population in two arms based on the D-dimer level on hospital admission. We observed that exosomal miR-145 and miR-885 significantly correlate with D-dimer levels. Moreover, we demonstrate that human endothelial cells express the main cofactors needed for the internalization of the "Severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2), including angiotensin converting enzyme 2, transmembrane protease serine 2, and CD-147. Interestingly, human endothelial cells treated with serum from COVID-19 patients release significantly less miR-145 and miR-885, exhibit increased apoptosis, and display significantly impaired angiogenetic properties compared with cells treated with non-COVID-19 serum. Taken together, our data indicate that exosomal miR-145 and miR-885 are essential in modulating thromboembolic events in COVID-19. SIGNIFICANCE STATEMENT: This work demonstrates for the first time that two specific microRNAs (namely miR-145 and miR-885) contained in circulating exosomes are functionally involved in thromboembolic events in COVID-19. These findings are especially relevant to the general audience when considering the emerging prominence of post-acute sequelae of COVID-19 systemic manifestations known as Long COVID.
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Affiliation(s)
- Jessica Gambardella
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Urna Kansakar
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Celestino Sardu
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Vincenzo Messina
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Stanislovas S Jankauskas
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Raffaele Marfella
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Paolo Maggi
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Xujun Wang
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Pasquale Mone
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Giuseppe Paolisso
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Daniela Sorriento
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
| | - Gaetano Santulli
- Department of Medicine, Wilf Family Cardiovascular Research Institute (J.G., U.K., S.S.J., X.W., P.Mo.) and Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Institute for Neuroimmunology and Inflammation (INI), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Aging Research (G.S.), Albert Einstein College of Medicine, New York City, New York; Department of Advanced Biomedical Sciences, International Translational Research and Medical Education (ITME) Consortium, "Federico II" University, Naples, Italy (J.G., D.S., G.S.); Department of Advanced Medical and Surgical Sciences (C.S., R.M., P. Ma., G.P.), and Department of Mental and Physical Health and Preventive Medicine (P.Ma.) University of Campania, Naples, Italy; Infectious Disease Unit, "Sant'Anna and San Sebastiano" Hospital, Caserta, Italy (V.M.)
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