51
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Zhou Y, Yuan S, Xiao F, Li H, Ye Z, Cheng T, Luo C, Tang K, Cai J, Situ J, Sridhar S, Chu WM, Tam AR, Chu H, Che CM, Jin L, Hung IFN, Lu L, Chan JFW, Sun H. Metal-coding assisted serological multi-omics profiling deciphers the role of selenium in COVID-19 immunity. Chem Sci 2023; 14:10570-10579. [PMID: 37799995 PMCID: PMC10548515 DOI: 10.1039/d3sc03345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023] Open
Abstract
Uncovering how host metal(loid)s mediate the immune response against invading pathogens is critical for better understanding the pathogenesis mechanism of infectious disease. Clinical data show that imbalance of host metal(loid)s is closely associated with the severity and mortality of COVID-19. However, it remains elusive how metal(loid)s, which are essential elements for all forms of life and closely associated with multiple diseases if dysregulated, are involved in COVID-19 pathophysiology and immunopathology. Herein, we built up a metal-coding assisted multiplexed serological metallome and immunoproteome profiling system to characterize the links of metallome with COVID-19 pathogenesis and immunity. We found distinct metallome features in COVID-19 patients compared with non-infected control subjects, which may serve as a biomarker for disease diagnosis. Moreover, we generated the first correlation network between the host metallome and immunity mediators, and unbiasedly uncovered a strong association of selenium with interleukin-10 (IL-10). Supplementation of selenium to immune cells resulted in enhanced IL-10 expression in B cells and reduced induction of proinflammatory cytokines in B and CD4+ T cells. The selenium-enhanced IL-10 production in B cells was confirmed to be attributable to the activation of ERK and Akt pathways. We further validated our cellular data in SARS-CoV-2-infected K18-hACE2 mice, and found that selenium supplementation alleviated SARS-CoV-2-induced lung damage characterized by decreased alveolar inflammatory infiltrates through restoration of virus-repressed selenoproteins to alleviate oxidative stress. Our approach can be readily extended to other diseases to understand how the host defends against invading pathogens through regulation of metallome.
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Affiliation(s)
- Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
| | - Fan Xiao
- Department of Pathology, Shenzhen Institute of Research and Innovation, The University of Hong Kong Hong Kong SAR China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Ziwei Ye
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Tianfan Cheng
- Faculty of Dentistry, The University of Hong Kong Pokfulam Hong Kong SAR Hong Kong China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Jianpiao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Jianwen Situ
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
- Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong SAR China
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Chi-Ming Che
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong Pokfulam Hong Kong SAR Hong Kong China
| | - Ivan Fan-Ngai Hung
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Liwei Lu
- Department of Pathology, Shenzhen Institute of Research and Innovation, The University of Hong Kong Hong Kong SAR China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
- Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong SAR China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong SAR China
- Guangzhou Laboratory Guangdong Province China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
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52
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Sarkar MMH, Naser SR, Chowdhury SF, Khan MS, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Nayem MR, Hassan MA, Khan MI, Rabbi MFA, Ahsan CR, Miah MI, Nessa A, Islam SMRU, Rahman MA, Shaikh MAA, Ahmed MS. M gene targeted qRT-PCR approach for SARS-CoV-2 virus detection. Sci Rep 2023; 13:16659. [PMID: 37789078 PMCID: PMC10547753 DOI: 10.1038/s41598-023-43204-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.
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Affiliation(s)
| | - Showti Raheel Naser
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | | | | | | | | | | | - Afzalun Nessa
- Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | | | | | - Md Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh.
- University of Dhaka, Dhaka, Bangladesh.
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53
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Lenhard S, Gerlich S, Khan A, Rödl S, Bökenkamp JE, Peker E, Zarges C, Faust J, Storchova Z, Räschle M, Riemer J, Herrmann JM. The Orf9b protein of SARS-CoV-2 modulates mitochondrial protein biogenesis. J Cell Biol 2023; 222:e202303002. [PMID: 37682539 PMCID: PMC10491932 DOI: 10.1083/jcb.202303002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses high amounts of the protein Orf9b to target the mitochondrial outer membrane protein Tom70. Tom70 serves as an import receptor for mitochondrial precursors and, independently of this function, is critical for the cellular antiviral response. Previous studies suggested that Orf9b interferes with Tom70-mediated antiviral signaling, but its implication for mitochondrial biogenesis is unknown. In this study, we expressed Orf9b in human HEK293 cells and observed an Orf9b-mediated depletion of mitochondrial proteins, particularly in respiring cells. To exclude that the observed depletion was caused by the antiviral response, we generated a yeast system in which the function of human Tom70 could be recapitulated. Upon expression of Orf9b in these cells, we again observed a specific decline of a subset of mitochondrial proteins and a general reduction of mitochondrial volume. Thus, the SARS-CoV-2 virus is able to modulate the mitochondrial proteome by a direct effect of Orf9b on mitochondrial Tom70-dependent protein import.
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Affiliation(s)
- Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sarah Gerlich
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Azkia Khan
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan-Eric Bökenkamp
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Esra Peker
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Christine Zarges
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Janina Faust
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchova
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
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54
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Chen R, Fulton KM, Tran A, Duque D, Kovalchik K, Caron E, Twine SM, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2-Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Mol Cell Proteomics 2023; 22:100645. [PMID: 37709257 PMCID: PMC10580047 DOI: 10.1016/j.mcpro.2023.100645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
We present an integrated immunopeptidomics and proteomics study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to comprehensively decipher the changes in host cells in response to viral infection. Immunopeptidomics analysis identified viral antigens presented by host cells through both class I and class II MHC system for recognition by the adaptive immune system. The host proteome changes were characterized by quantitative proteomics and glycoproteomics and from these data, the activation of toll-like receptor 3-interferon pathway was identified. Glycosylation analysis of human leukocyte antigen (HLA) proteins from the elution and flow-through of immunoprecipitation revealed that SARS-CoV-2 infection changed the glycosylation pattern of certain HLA alleles with different HLA alleles, showing distinct dynamic changes in relative abundance. The difference in the glycosylation and abundance of HLA alleles changed the number of strong binding antigens each allele presented, suggesting the impact of SARS-CoV-2 infection on antigen presentation is allele-specific. These results could be further exploited to explain the imbalanced response from innate and adaptive immune system in coronavirus disease 2019 cases, which would be helpful for the development of therapeutics and vaccine for coronavirus disease 2019 and preparation for future pandemic.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kevin Kovalchik
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Quebec, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
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55
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El-Derany MO, Hanna DMF, Youshia J, Elmowafy E, Farag MA, Azab SS. Metabolomics-directed nanotechnology in viral diseases management: COVID-19 a case study. Pharmacol Rep 2023; 75:1045-1065. [PMID: 37587394 PMCID: PMC10539420 DOI: 10.1007/s43440-023-00517-w] [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: 01/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently regarded as the twenty-first century's plague accounting for coronavirus disease 2019 (COVID-19). Besides its reported symptoms affecting the respiratory tract, it was found to alter several metabolic pathways inside the body. Nanoparticles proved to combat viral infections including COVID-19 to demonstrate great success in developing vaccines based on mRNA technology. However, various types of nanoparticles can affect the host metabolome. Considering the increasing proportion of nano-based vaccines, this review compiles and analyses how COVID-19 and nanoparticles affect lipids, amino acids, and carbohydrates metabolism. A search was conducted on PubMed, ScienceDirect, Web of Science for available information on the interrelationship between metabolomics and immunity in the context of SARS-CoV-2 infection and the effect of nanoparticles on metabolite levels. It was clear that SARS-CoV-2 disrupted several pathways to ensure a sufficient supply of its building blocks to facilitate its replication. Such information can help in developing treatment strategies against viral infections and COVID-19 based on interventions that overcome these metabolic changes. Furthermore, it showed that even drug-free nanoparticles can exert an influence on biological systems as evidenced by metabolomics.
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Affiliation(s)
- Marwa O El-Derany
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Diana M F Hanna
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt
| | - John Youshia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Enas Elmowafy
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr El-Aini St., P.B. 11562, Cairo, Egypt
| | - Samar S Azab
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt.
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56
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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57
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Adam L, Stanifer M, Springer F, Mathony J, Brune M, Di Ponzio C, Eils R, Boulant S, Niopek D, Kallenberger SM. Transcriptomics-inferred dynamics of SARS-CoV-2 interactions with host epithelial cells. Sci Signal 2023; 16:eabl8266. [PMID: 37751479 DOI: 10.1126/scisignal.abl8266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Virus-host interactions can reveal potentially effective and selective therapeutic targets for treating infection. Here, we performed an integrated analysis of the dynamics of virus replication and the host cell transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using human Caco-2 colon cancer cells as a model. Time-resolved RNA sequencing revealed that, upon infection, cells immediately transcriptionally activated genes associated with inflammatory pathways that mediate the antiviral response, which was followed by an increase in the expression of genes involved in ribosome and mitochondria function, thus suggesting rapid alterations in protein production and cellular energy supply. At later stages, between 24 and 48 hours after infection, the expression of genes involved in metabolic processes-in particular, those related to xenobiotic metabolism-was decreased. Mathematical modeling incorporating SARS-CoV-2 replication suggested that SARS-CoV-2 proteins inhibited the host antiviral response and that virus transcripts exceeded the translation capacity of the host cells. Targeting kinase-dependent pathways that exhibited increases in transcription in host cells was as effective as a virus-targeted inhibitor at repressing viral replication. Our findings in this model system delineate a sequence of SARS-CoV-2 virus-host interactions that may facilitate the identification of druggable host pathways to suppress infection.
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Affiliation(s)
- Lukas Adam
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Megan Stanifer
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg 69120, Germany
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Fabian Springer
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Jan Mathony
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- BZH Graduate School, Heidelberg University, Heidelberg 69120, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - Maik Brune
- Clinic of Endocrinology, Diabetology, Metabolism, and Clinical Chemistry, Central Laboratory, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Chiara Di Ponzio
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany
| | - Roland Eils
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg 69120, Germany
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
- Research Group "Cellular polarity and viral infection" (F140), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dominik Niopek
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - Stefan M Kallenberger
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- National Center for Tumor Diseases, Department of Medical Oncology, Heidelberg University Hospital, Heidelberg 69120, Germany
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58
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Schweizer L, Schaller T, Zwiebel M, Karayel Ö, Müller‐Reif JB, Zeng W, Dintner S, Nordmann TM, Hirschbühl K, Märkl B, Claus R, Mann M. Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation. EMBO Mol Med 2023; 15:e17459. [PMID: 37519267 PMCID: PMC10493576 DOI: 10.15252/emmm.202317459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
SARS-CoV-2 may directly and indirectly damage lung tissue and other host organs, but there are few system-wide, untargeted studies of these effects on the human body. Here, we developed a parallelized mass spectrometry (MS) proteomics workflow enabling the rapid, quantitative analysis of hundreds of virus-infected FFPE tissues. The first layer of response to SARS-CoV-2 in all tissues was dominated by circulating inflammatory molecules. Beyond systemic inflammation, we differentiated between systemic and true tissue-specific effects to reflect distinct COVID-19-associated damage patterns. Proteomic changes in the lungs resembled those of diffuse alveolar damage (DAD) in non-COVID-19 patients. Extensive organ-specific changes were also evident in the kidneys, liver, and lymphatic and vascular systems. Secondary inflammatory effects in the brain were related to rearrangements in neurotransmitter receptors and myelin degradation. These MS-proteomics-derived results contribute substantially to our understanding of COVID-19 pathomechanisms and suggest strategies for organ-specific therapeutic interventions.
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Affiliation(s)
- Lisa Schweizer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tina Schaller
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Özge Karayel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Department of Physiological ChemistryGenentechSouth San FranciscoUSA
| | | | - Wen‐Feng Zeng
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | - Thierry M Nordmann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Klaus Hirschbühl
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Bruno Märkl
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Rainer Claus
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
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59
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Cohen P, DeGrace EJ, Danziger O, Patel RS, Barrall EA, Bobrowski T, Kehrer T, Cupic A, Miorin L, García-Sastre A, Rosenberg BR. Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing. Microbiol Spectr 2023; 11:e0077623. [PMID: 37676044 PMCID: PMC10580996 DOI: 10.1128/spectrum.00776-23] [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: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 09/08/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). scRNA-Seq library preparation methods and data processing workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq library preparation methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We show that compared to 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') libraries or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5') libraries sequenced with standard read configurations, 10X 5' libraries sequenced with an extended length read 1 (R1) that covers both cell barcode and transcript sequence (termed "10X 5' with extended R1") increase the number of unambiguous reads spanning leader-sgmRNA junction sites. We further present a data processing workflow, single-cell coronavirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to viral sgmRNAs or viral genomic RNA (gRNA). We find that combining 10X 5' with extended R1 library preparation/sequencing and scCoVseq data processing maximizes the number of viral UMIs per cell quantified by scRNA-Seq. Corresponding sgmRNA expression levels are highly correlated with expression in matched bulk RNA-Seq data sets quantified with established tools for SARS-CoV-2 analysis. Using this scRNA-Seq approach, we find that SARS-CoV-2 gene expression is highly correlated across individual infected cells, which suggests that the proportion of viral sgmRNAs remains generally consistent throughout infection. Taken together, these results and corresponding data processing workflow enable robust quantification of coronavirus sgmRNA expression at single-cell resolution, thereby supporting high-resolution studies of viral RNA processes in individual cells. IMPORTANCE Single-cell RNA sequencing (scRNA-Seq) has emerged as a valuable tool to study host-virus interactions, especially for coronavirus disease 2019 (COVID-19). Here we compare the performance of different scRNA-Seq library preparation methods and sequencing strategies to detect SARS-CoV-2 RNAs and develop a data processing workflow to quantify unambiguous sequence reads derived from SARS-CoV-2 genomic RNA and subgenomic mRNAs. After establishing a workflow that maximizes the detection of SARS-CoV-2 subgenomic mRNAs, we explore patterns of SARS-CoV-2 gene expression across cells with variable levels of total viral RNA, assess host gene expression differences between infected and bystander cells, and identify non-canonical and lowly abundant SARS-CoV-2 RNAs. The sequencing and data processing strategies developed here can enhance studies of coronavirus RNA biology at single-cell resolution and thereby contribute to our understanding of viral pathogenesis.
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Affiliation(s)
- Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma J. DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roosheel S. Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erika A. Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tesia Bobrowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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60
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Antwi I, Watkins D, Pedawi A, Ghrayeb A, Van de Vuurst C, Cory TJ. Substances of abuse and their effect on SAR-CoV-2 pathogenesis. NEUROIMMUNE PHARMACOLOGY AND THERAPEUTICS 2023; 2:301-316. [PMID: 38013836 PMCID: PMC10474379 DOI: 10.1515/nipt-2023-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/19/2023] [Indexed: 11/29/2023]
Abstract
Following the emergence of SARS-CoV-2, various reports suggest that there has been a significant increase in substance abuse due to social distancing and related issues. Several reports have suggested the impact of chronic substance use on individuals' physiological and psychological health. Therefore, there is a need to know the impact of SARS-CoV-2 on persons with substance use disorders. Individuals with substance use disorders are the most vulnerable groups and are at a high risk of SARS-CoV-2 infection due to their already existing health issues associated with substance use. This review discusses some of the molecular and systemic/organic effects chronic substance use such as alcohol, nicotine, marijuana (cannabis), opioids, methamphetamine, and cocaine have on SARS-CoV-2 infectivity and its potential cause for worsened disease outcomes in persons with substance use disorder. This will provide healthcare providers, public health policies, and researchers with the needed knowledge to address some of the many challenges faced during the Covid-19 pandemic to facilitate treatment strategies for persons with substance use disorders.
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Affiliation(s)
- Ivy Antwi
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Destiny Watkins
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Alahn Pedawi
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Atheel Ghrayeb
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Christine Van de Vuurst
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Theodore J. Cory
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
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61
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Kaushik N, Patel P, Bhartiya P, Shin Y, Kim JH, Choi EH, Kaushik NK. Glycolytic stress deteriorates 229E virulence to improve host defense response. Microbes Infect 2023; 25:105150. [PMID: 37178787 PMCID: PMC10174727 DOI: 10.1016/j.micinf.2023.105150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Viral infection treatment is a difficult task due to its complex structure and metabolism. Additionally, viruses can alter the metabolism of host cells, mutate, and readily adjust to harsh environments. Coronavirus stimulates glycolysis, weakens mitochondrial activity, and impairs infected cells. In this study, we investigated the efficacy of 2-DG in inhibiting coronavirus-induced metabolic processes and antiviral host defense systems, which have not been explored so far. 2-Deoxy-d-glucose (2-DG), a molecule restricting substrate availability, has recently gained attention as a potential antiviral drug. The results revealed that 229E human coronavirus promoted glycolysis, producing a significant increase in the concentration of fluorescent 2-NBDG, a glucose analog, particularly in the infected host cells. The addition of 2-DG decreased its viral replication and suppressed infection-induced cell death and cytopathic effects, thereby improving the antiviral host defense response. It was also observed that administration of low doses of 2-DG inhibited glucose uptake, indicating that 2-DG consumption in virus-infected host cells was mediated by high-affinity glucose transporters, whose levels were amplified upon coronavirus infection. Our findings indicated that 2-DG could be a potential drug to improve the host defense system in coronavirus-infected cells.
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Affiliation(s)
- Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Paritosh Patel
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Pradeep Bhartiya
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Yungoh Shin
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - June Hyun Kim
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea.
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Annamalai A, Karuppaiya V, Ezhumalai D, Cheruparambath P, Balakrishnan K, Venkatesan A. Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness. J Drug Deliv Sci Technol 2023; 86:104567. [PMID: 37313114 PMCID: PMC10183109 DOI: 10.1016/j.jddst.2023.104567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.
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Affiliation(s)
- Asaikkutti Annamalai
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
| | - Vimala Karuppaiya
- Cancer Nanomedicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Dhineshkumar Ezhumalai
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | | | - Kaviarasu Balakrishnan
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | - Arul Venkatesan
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
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Higgins CA, Nilsson-Payant BE, Bonaventure B, Kurland AP, Ye C, Yaron TM, Johnson JL, Adhikary P, Golynker I, Panis M, Danziger O, Rosenberg BR, Cantley LC, Martínez-Sobrido L, tenOever B, Johnson JR. SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication. mBio 2023; 14:e0100723. [PMID: 37345956 PMCID: PMC10470746 DOI: 10.1128/mbio.01007-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, drastically modifies infected cells to optimize virus replication. One such modification is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammatory cytokine production, a hallmark of severe COVID-19. We previously demonstrated that inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduced both cytokine production and viral replication. Here, we combined quantitative genetic screening, genomics, proteomics, and phosphoproteomics to better understand mechanisms underlying the dependence of SARS-CoV-2 on the p38 pathway. We found that p38β is a critical host factor for SARS-CoV-2 replication in multiple relevant cell lines and that it functions at a step after viral mRNA expression. We identified putative host and viral p38β substrates in the context of SARS-CoV-2 infection and found that most host substrates have intrinsic antiviral activities. Taken together, this study reveals a unique proviral function for p38β and supports exploring p38β inhibitor development as a strategy toward creating a new class of COVID-19 therapies. IMPORTANCE SARS-CoV-2 is the causative agent of the COVID-19 pandemic that has claimed millions of lives since its emergence in 2019. SARS-CoV-2 infection of human cells requires the activity of several cellular pathways for successful replication. One such pathway, the p38 MAPK pathway, is required for virus replication and disease pathogenesis. Here, we applied systems biology approaches to understand how MAPK pathways benefit SARS-CoV-2 replication to inform the development of novel COVID-19 drug therapies.
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Affiliation(s)
- Christina A Higgins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Department of Microbiology, New York University Langone Health , New York, New York, USA
- Vilcek Graduate School for Biomedical Sciences, New York University Langone Health , New York, New York, USA
| | | | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute , San Antonio, Texas, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine Weill Cornell Medicine , New York, New York, USA
- Columbia University Vagelos College of Physicians and Surgeons , New York, New York, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | - Prithy Adhikary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Ilona Golynker
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Maryline Panis
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | | | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
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64
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Wei LH, Sun Y, Guo JU. Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting. Cell Rep 2023; 42:112987. [PMID: 37581984 DOI: 10.1016/j.celrep.2023.112987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Many positive-strand RNA viruses, including all known coronaviruses, employ programmed -1 ribosomal frameshifting (-1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate -1 PRF. Through a genome-wide CRISPR-Cas9 knockout screen, we have identified host factors that either suppress or enhance severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -1 PRF. Among them, eukaryotic translation initiation factor 2A (eIF2A) specifically and directly enhances -1 PRF independent of changes in initiation. Consistent with the crucial role of efficient -1 PRF in transcriptase/replicase expression, loss of eIF2A reduces SARS-CoV-2 replication in cells. Furthermore, transcriptome-wide analysis shows that eIF2A preferentially binds CG-rich RNA motifs, including a region within 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results indicate a role for eIF2A in modulating the translation of specific RNAs independent of its role during initiation.
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Affiliation(s)
- Lian-Huan Wei
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.
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65
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Shoraka S, Samarasinghe AE, Ghaemi A, Mohebbi SR. Host mitochondria: more than an organelle in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1228275. [PMID: 37692170 PMCID: PMC10485703 DOI: 10.3389/fcimb.2023.1228275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Since December 2019, the world has been facing viral pandemic called COVID-19 (Coronavirus disease 2019) caused by a new beta-coronavirus named severe acute respiratory syndrome coronavirus-2, or SARS-CoV-2. COVID-19 patients may present with a wide range of symptoms, from asymptomatic to requiring intensive care support. The severe form of COVID-19 is often marked by an altered immune response and cytokine storm. Advanced age, age-related and underlying diseases, including metabolic syndromes, appear to contribute to increased COVID-19 severity and mortality suggesting a role for mitochondria in disease pathogenesis. Furthermore, since the immune system is associated with mitochondria and its damage-related molecular patterns (mtDAMPs), the host mitochondrial system may play an important role during viral infections. Viruses have evolved to modulate the immune system and mitochondrial function for survival and proliferation, which in turn could lead to cellular stress and contribute to disease progression. Recent studies have focused on the possible roles of mitochondria in SARS-CoV-2 infection. It has been suggested that mitochondrial hijacking by SARS-CoV-2 could be a key factor in COVID-19 pathogenesis. In this review, we discuss the roles of mitochondria in viral infections including SARS-CoV-2 infection based on past and present knowledge. Paying attention to the role of mitochondria in SARS-CoV-2 infection will help to better understand the pathophysiology of COVID-19 and to achieve effective methods of prevention, diagnosis, and treatment.
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Affiliation(s)
- Shahrzad Shoraka
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Amali E. Samarasinghe
- Division of Pulmonology, Allergy and Immunology, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Memphis, TN, United States
| | - Amir Ghaemi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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66
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Staheli JP, Neal ML, Navare A, Mast FD, Aitchison JD. Predicting host-based, synthetic lethal antiviral targets from omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553430. [PMID: 37645861 PMCID: PMC10462099 DOI: 10.1101/2023.08.15.553430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Traditional antiviral therapies often have limited effectiveness due to toxicity and development of drug resistance. Host-based antivirals, while an alternative, may lead to non-specific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners of proteins disrupted by viral infection. Thus, we hypothesized that genes depleted in CRISPR KO screens of virus-infected cells may be enriched in SL partners of proteins altered by infection. To investigate this, we established a computational pipeline predicting SL drug targets of viral infections. First, we identified SARS-CoV-2-induced changes in gene products via a large compendium of omics data. Second, we identified SL partners for each altered gene product. Last, we screened CRISPR KO data for SL partners required for cell viability in infected cells. Despite differences in virus-induced alterations detected by various omics data, they share many predicted SL targets, with significant enrichment in CRISPR KO-depleted datasets. Comparing data from SARS-CoV-2 and influenza infections, we found possible broad-spectrum, host-based antiviral SL targets. This suggests that CRISPR KO data are replete with common antiviral targets due to their SL relationship with virus-altered states and that such targets can be revealed from analysis of omics datasets and SL predictions.
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Affiliation(s)
- Jeannette P. Staheli
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Arti Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
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67
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Soto Albrecht Y, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M Dybas
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S Kim
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Victoria K Baxter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily A Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
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68
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Huang T, Staniak M, da Veiga Leprevost F, Figueroa-Navedo AM, Ivanov AR, Nesvizhskii AI, Choi M, Vitek O. Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling. J Proteome Res 2023; 22:2641-2659. [PMID: 37467362 PMCID: PMC11090052 DOI: 10.1021/acs.jproteome.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly used in mass spectrometry-based proteomics. Such designs distinguish the biological variation within and between the subjects and increase the statistical power of detecting within-subject changes in protein abundance. Meanwhile, proteomics experiments increasingly incorporate tandem mass tag (TMT) labeling, a multiplexing strategy that gains both relative protein quantification accuracy and sample throughput. However, combining repeated measures and TMT multiplexing in a large-scale investigation presents statistical challenges due to unique interplays of between-mixture, within-mixture, between-subject, and within-subject variation. This manuscript proposes a family of linear mixed-effects models for differential analysis of proteomics experiments with repeated measures and TMT multiplexing. These models decompose the variation in the data into the contributions from its sources as appropriate for the specifics of each experiment, enable statistical inference of differential protein abundance, and recognize a difference in the uncertainty of between-subject versus within-subject comparisons. The proposed family of models is implemented in the R/Bioconductor package MSstatsTMT v2.2.0. Evaluations of four simulated datasets and four investigations answering diverse biological questions demonstrated the value of this approach as compared to the existing general-purpose approaches and implementations.
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Affiliation(s)
- Ting Huang
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Mateusz Staniak
- Institute of Mathematics, University of Wrocław, Wrocław, Poland
| | | | - Amanda M. Figueroa-Navedo
- Department of Chemistry and Chemical Biology, Barnett Institute of Biological and Chemical Analysis, Northeastern University, Boston, MA, USA
| | - Alexander R. Ivanov
- Department of Chemistry and Chemical Biology, Barnett Institute of Biological and Chemical Analysis, Northeastern University, Boston, MA, USA
| | | | - Meena Choi
- Departments of Microchemistry, Proteomics & Lipidomics, Genentech, South San Francisco, CA, USA
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
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69
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Jiao S, Miranda P, Li Y, Maric D, Holmgren M. Some aspects of the life of SARS-CoV-2 ORF3a protein in mammalian cells. Heliyon 2023; 9:e18754. [PMID: 37609425 PMCID: PMC10440475 DOI: 10.1016/j.heliyon.2023.e18754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
The accessory protein ORF3a, from SARS-CoV-2, plays a critical role in viral infection and pathogenesis. Here, we characterized ORF3a assembly, ion channel activity, subcellular localization, and interactome. At the plasma membrane, ORF3a exists mostly as monomers and dimers, which do not alter the native cell membrane conductance, suggesting that ORF3a does not function as a viroporin at the cell surface. As a membrane protein, ORF3a is synthesized at the ER and sorted via a canonical route. ORF3a overexpression induced an approximately 25% increase in cell death. By developing an APEX2-based proximity labeling assay, we uncovered proteins proximal to ORF3a, suggesting that ORF3a recruits some host proteins to weaken the cell. In addition, it exposed a set of mitochondria related proteins that triggered mitochondrial fission. Overall, this work can be an important instrument in understanding the role of ORF3a in the virus pathogenicity and searching for potential therapeutic treatments for COVID-19.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Pablo Miranda
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
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70
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Li J, Wang Y, Deng H, Li S, Qiu HJ. Cellular metabolism hijacked by viruses for immunoevasion: potential antiviral targets. Front Immunol 2023; 14:1228811. [PMID: 37559723 PMCID: PMC10409484 DOI: 10.3389/fimmu.2023.1228811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023] Open
Abstract
Cellular metabolism plays a central role in the regulation of both innate and adaptive immunity. Immune cells utilize metabolic pathways to modulate the cellular differentiation or death. The intricate interplay between metabolism and immune response is critical for maintaining homeostasis and effective antiviral activities. In recent years, immunometabolism induced by viral infections has been extensively investigated, and accumulating evidence has indicated that cellular metabolism can be hijacked to facilitate viral replication. Generally, virus-induced changes in cellular metabolism lead to the reprogramming of metabolites and metabolic enzymes in different pathways (glucose, lipid, and amino acid metabolism). Metabolic reprogramming affects the function of immune cells, regulates the expression of immune molecules and determines cell fate. Therefore, it is important to explore the effector molecules with immunomodulatory properties, including metabolites, metabolic enzymes, and other immunometabolism-related molecules as the antivirals. This review summarizes the relevant advances in the field of metabolic reprogramming induced by viral infections, providing novel insights for the development of antivirals.
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Affiliation(s)
| | | | | | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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71
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LaPorte M, Alverez C, Chatterley A, Kovaliov M, Carder EJ, Houghton MJ, Lim C, Miller ER, Samankumara LP, Liang M, Kerrigan K, Yue Z, Li S, Tomaino F, Wang F, Green N, Stott GM, Srivastava A, Chou TF, Wipf P, Huryn DM. Optimization of 1,2,4-Triazole-Based p97 Inhibitors for the Treatment of Cancer. ACS Med Chem Lett 2023; 14:977-985. [PMID: 37465292 PMCID: PMC10351062 DOI: 10.1021/acsmedchemlett.3c00163] [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: 04/25/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
The AAA+ ATPase p97 (valosin-containing protein, VCP) is a master regulator of protein homeostasis and therefore represents a novel target for cancer therapy. Starting from a known allosteric inhibitor, NMS-873, we systematically optimized this scaffold, in particular, by applying a benzene-to-acetylene isosteric replacement strategy, specific incorporation of F, and eutomer/distomer identification, which led to compounds that exhibited nanomolar biochemical and cell-based potency. In cellular pharmacodynamic assays, robust effects on biomarkers of p97 inhibition and apoptosis, including increased levels of ubiquitinated proteins, CHOP and cleaved caspase 3, were observed. Compound (R)-29 (UPCDC-30766) represents the most potent allosteric inhibitor of p97 reported to date.
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Affiliation(s)
- Matthew
G. LaPorte
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Celeste Alverez
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Chatterley
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marina Kovaliov
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Evan J. Carder
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael J. Houghton
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chaemin Lim
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Eric R. Miller
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lalith P. Samankumara
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mary Liang
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kaylan Kerrigan
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhizhou Yue
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shan Li
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Francesca Tomaino
- Leidos
Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Feng Wang
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Neal Green
- Leidos
Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Gordon M. Stott
- Leidos
Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Apurva Srivastava
- Leidos
Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Tsui-Fen Chou
- Division
of Biology and Biological Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Peter Wipf
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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72
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Ma P, Liu J, Pang S, Zhou W, Yu H, Wang M, Dong T, Wang Y, Wang Q, Liu A. Biopanning of specific peptide for SARS-CoV-2 nucleocapsid protein and enzyme-linked immunosorbent assay-based antigen assay. Anal Chim Acta 2023; 1264:341300. [PMID: 37230729 DOI: 10.1016/j.aca.2023.341300] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide which triggered serious public health issues. The search for rapid and accurate diagnosis, effective prevention, and treatment is urgent. The nucleocapsid protein (NP) of SARS-CoV-2 is one of the main structural proteins expressed and most abundant in the virus, and is considered a diagnostic marker for the accurate and sensitive detection of SARS-CoV-2. Herein, we report the screening of specific peptides from the pIII phage library that bind to SARS-CoV-2 NP. The phage monoclone expressing cyclic peptide N1 (peptide sequence, ACGTKPTKFC, with C&C bridged by disulfide bonding) specifically recognizes SARS-CoV-2 NP. Molecular docking studies reveal that the identified peptide is bound to the "pocket" region on the SARS-CoV-2 NP N-terminal domain mainly by forming a hydrogen bonding network and through hydrophobic interaction. Peptide N1 with the C-terminal linker was synthesized as the capture probe for SARS-CoV-2 NP in ELISA. The peptide-based ELISA was capable of assaying SARS-CoV-2 NP at concentrations as low as 61 pg/mL (∼1.2 pM). Furthermore, the as-proposed method could detect the SARS-CoV-2 virus at limits as low as 50 TCID50 (median tissue culture infective dose)/mL. This study demonstrates that selected peptides are powerful biomolecular tools for SARS-CoV-2 detection, providing a new and inexpensive method of rapidly screening infections as well as rapidly diagnosing coronavirus disease 2019 patients.
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Affiliation(s)
- Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Wenhao Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Yanbo Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Qiqin Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China.
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73
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Aviner R, Lidsky PV, Xiao Y, Tasseto M, Zhang L, McAlpine PL, Elias J, Frydman J, Andino R. SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547902. [PMID: 37461541 PMCID: PMC10350044 DOI: 10.1101/2023.07.05.547902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
A better mechanistic understanding of virus-host interactions can help reveal vulnerabilities and identify opportunities for therapeutic interventions. Of particular interest are essential interactions that enable production of viral proteins, as those could target an early step in the virus lifecycle. Here, we use subcellular proteomics, ribosome profiling analyses and reporter assays to detect changes in polysome composition and protein synthesis during SARS-CoV-2 (CoV2) infection. We identify specific translation factors and molecular chaperones whose inhibition impairs infectious particle production without major toxicity to the host. We find that CoV2 non-structural protein Nsp1 selectively enhances virus translation through functional interactions with initiation factor EIF1A. When EIF1A is depleted, more ribosomes initiate translation from an upstream CUG start codon, inhibiting translation of non-structural genes and reducing viral titers. Together, our work describes multiple dependencies of CoV2 on host biosynthetic networks and identifies druggable targets for potential antiviral development.
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Affiliation(s)
- Ranen Aviner
- These authors contributed equally
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Peter V Lidsky
- These authors contributed equally
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michel Tasseto
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lichao Zhang
- Chan Zuckerberg Biohub - San Francisco, Stanford, CA 94305, USA
| | | | - Joshua Elias
- Chan Zuckerberg Biohub - San Francisco, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raul Andino
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA
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74
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Zhang J, Zhang Y, Xia Y, Sun J. Microbiome and intestinal pathophysiology in post-acute sequelae of COVID-19. Genes Dis 2023; 11:S2352-3042(23)00223-4. [PMID: 37362775 PMCID: PMC10278891 DOI: 10.1016/j.gendis.2023.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 06/28/2023] Open
Abstract
Long COVID, also known for post-acute sequelae of COVID-19, describes the people who have the signs and symptoms that continue or develop after the acute COVID-19 phase. Long COVID patients suffer from an inflammation or host responses towards the virus approximately 4 weeks after initial infection with the SARS CoV-2 virus and continue for an uncharacterized duration. Anyone infected with COVID-19 before could experience long-COVID conditions, including the patients who were infected with SARS CoV-2 virus confirmed by tests and those who never knew they had an infection early. People with long COVID may experience health problems from different types and combinations of symptoms over time, such as fatigue, dyspnea, cognitive impairments, and gastrointestinal (GI) symptoms (e.g., nausea, vomiting, diarrhea, decreased or loss of appetite, abdominal pain, and dysgeusia). The critical role of the microbiome in these GI symptoms and long COVID were reported in clinical patients and experimental models. Here, we provide an overall view of the critical role of the GI tract and microbiome in the development of long COVID, including the clinical GI symptoms in patients, dysbiosis, viral-microbiome interactions, barrier function, and inflammatory bowel disease patients with long COVID. We highlight the potential mechanisms and possible treatment based on GI health and microbiome. Finally, we discuss challenges and future direction in the long COVID clinic and research.
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Affiliation(s)
- Jilei Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, IL 60612, USA
| | - Yongguo Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, IL 60612, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, IL 60612, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, IL 60612, USA
- UIC Cancer Center, Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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75
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Davies JP, Sivadas A, Keller KR, Wojcikiewicz RJ, Plate L. SARS-CoV-2 Nonstructural Proteins 3 and 4 tune the Unfolded Protein Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.22.537917. [PMID: 37162862 PMCID: PMC10168236 DOI: 10.1101/2023.04.22.537917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Coronaviruses (CoV), including SARS-CoV-2, modulate host proteostasis through activation of stress-responsive signaling pathways such as the Unfolded Protein Response (UPR), which remedies misfolded protein accumulation by attenuating translation and increasing protein folding capacity. While CoV nonstructural proteins (nsps) are essential for infection, little is known about the role of nsps in modulating the UPR. We characterized the impact of SARS-CoV-2 nsp4, a key driver of replication, on the UPR using quantitative proteomics to sensitively detect pathway-wide upregulation of effector proteins. We find nsp4 preferentially activates the ATF6 and PERK branches of the UPR. Previously, we found an N-terminal truncation of nsp3 (nsp3.1) can suppress pharmacological ATF6 activation. To determine how nsp3.1 and nsp4 tune the UPR, their co-expression demonstrated that nsp3.1 suppresses nsp4-mediated PERK, but not ATF6 activation. Re-analysis of SARS-CoV-2 infection proteomics data revealed time-dependent activation of PERK targets early in infection, which subsequently fades. This temporal regulation suggests a role for nsp3 and nsp4 in tuning the PERK pathway to attenuate host translation beneficial for viral replication while avoiding later apoptotic signaling caused by chronic activation. This work furthers our understanding of CoV-host proteostasis interactions and highlights the power of proteomic methods for systems-level analysis of the UPR.
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Affiliation(s)
| | - Athira Sivadas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | | | | | - Lars Plate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Department of Chemistry, Vanderbilt University, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
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76
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Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
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Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
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77
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Kelch MA, Vera-Guapi A, Beder T, Oswald M, Hiemisch A, Beil N, Wajda P, Ciesek S, Erfle H, Toptan T, Koenig R. Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral. Front Microbiol 2023; 14:1193320. [PMID: 37342561 PMCID: PMC10277617 DOI: 10.3389/fmicb.2023.1193320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus evolves under selection pressure which already led to the emergence of several drug resistant strains. Broad spectrum host-directed antivirals (HDA) are promising therapeutic options, however the robust identification of relevant host factors by CRISPR/Cas9 or RNA interference screens remains challenging due to low consistency in the resulting hits. To address this issue, we employed machine learning, based on experimental data from several knockout screens and a drug screen. We trained classifiers using genes essential for virus life cycle obtained from the knockout screens. The machines based their predictions on features describing cellular localization, protein domains, annotated gene sets from Gene Ontology, gene and protein sequences, and experimental data from proteomics, phospho-proteomics, protein interaction and transcriptomic profiles of SARS-CoV-2 infected cells. The models reached a remarkable performance suggesting patterns of intrinsic data consistency. The predicted HDF were enriched in sets of genes particularly encoding development, morphogenesis, and neural processes. Focusing on development and morphogenesis-associated gene sets, we found β-catenin to be central and selected PRI-724, a canonical β-catenin/CBP disruptor, as a potential HDA. PRI-724 limited infection with SARS-CoV-2 variants, SARS-CoV-1, MERS-CoV and IAV in different cell line models. We detected a concentration-dependent reduction in cytopathic effects, viral RNA replication, and infectious virus production in SARS-CoV-2 and SARS-CoV-1-infected cells. Independent of virus infection, PRI-724 treatment caused cell cycle deregulation which substantiates its potential as a broad spectrum antiviral. Our proposed machine learning concept supports focusing and accelerating the discovery of host dependency factors and identification of potential host-directed antivirals.
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Affiliation(s)
- Maximilian A. Kelch
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marcus Oswald
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Alicia Hiemisch
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Nina Beil
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Piotr Wajda
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility (ABSF), High-Content Analysis of the Cell (HiCell), BioQuant, Heidelberg University, Heidelberg, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Rainer Koenig
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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78
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Bhowal C, Ghosh S, Ghatak D, De R. Pathophysiological involvement of host mitochondria in SARS-CoV-2 infection that causes COVID-19: a comprehensive evidential insight. Mol Cell Biochem 2023; 478:1325-1343. [PMID: 36308668 PMCID: PMC9617539 DOI: 10.1007/s11010-022-04593-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a positive-strand RNA virus that infects humans through the nasopharyngeal and oral route causing COVID-19. Scientists left no stone unturned to explore a targetable key player in COVID-19 pathogenesis against which therapeutic interventions can be initiated. This article has attempted to review, coordinate and accumulate the most recent observations in support of the hypothesis predicting the altered state of mitochondria concerning mitochondrial redox homeostasis, inflammatory regulations, morphology, bioenergetics and antiviral signalling in SARS-CoV-2 infection. Mitochondria is extremely susceptible to physiological as well as pathological stimuli, including viral infections. Recent studies suggest that SARS-CoV-2 pathogeneses alter mitochondrial integrity, in turn mitochondria modulate cellular response against the infection. SARS-CoV-2 M protein inhibited mitochondrial antiviral signalling (MAVS) protein aggregation in turn hinders innate antiviral response. Viral open reading frames (ORFs) also play an instrumental role in altering mitochondrial regulation of immune response. Notably, ORF-9b and ORF-6 impair MAVS activation. In aged persons, the NLRP3 inflammasome is over-activated due to impaired mitochondrial function, increased mitochondrial reactive oxygen species (mtROS), and/or circulating free mitochondrial DNA, resulting in a hyper-response of classically activated macrophages. This article also tries to understand how mitochondrial fission-fusion dynamics is affected by the virus. This review comprehends the overall mitochondrial attribute in pathogenesis as well as prognosis in patients infected with COVID-19 taking into account pertinent in vitro, pre-clinical and clinical data encompassing subjects with a broad range of severity and morbidity. This endeavour may help in exploring novel non-canonical therapeutic strategies to COVID-19 disease and associated complications.
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Affiliation(s)
- Chandan Bhowal
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Sayak Ghosh
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, 700032, Kolkata, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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79
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Roesmann F, Jakobsche I, Pallas C, Wilhelm A, Raffel J, Kohmer N, Toptan T, Berger A, Goetsch U, Ciesek S, Widera M. Comparison of the Ct-values for genomic and subgenomic SARS-CoV-2 RNA reveals limited predictive value for the presence of replication competent virus. J Clin Virol 2023; 165:105499. [PMID: 37327554 DOI: 10.1016/j.jcv.2023.105499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/23/2023] [Accepted: 05/28/2023] [Indexed: 06/18/2023]
Abstract
SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19. In addition to the full length positive-sensed, single-stranded genomic RNA (gRNA), viral subgenomic RNAs (sgRNAs) that are required for expression of the 3' region of the genome are synthesized in virus-infected cells. However, whether these sgRNA-species might be used as a measure of active virus replication and to predict infectivity is still under debate. The commonly used methods to monitor and quantitate SARS-CoV-2 infections are based on RT-qPCR analysis and the detection of gRNA. The infectivity of a sample obtained from nasopharyngeal or throat swabs is associated with the viral load and inversely correlates with Ct-values, however, a cut-off value predicting the infectivity highly depends on the performance of the assay. Furthermore, gRNA derived Ct-values result from nucleic acid detection and do not necessarily correspond to active replicating virus. We established a multiplex RT-qPCR assay on the cobas 6800 omni utility channel concomitantly detecting SARS-CoV-2 gRNAOrf1a/b, sgRNAE,7a,N, and human RNaseP-mRNA used as human input control. We compared the target specific Ct-values with the viral culture frequency and performed ROC curve analysis to determine the assay sensitivity and specificity. We found no advantage in the prediction of viral culture when using sgRNA detection compared to gRNA only, since Ct-values for gRNA and sgRNA were highly correlated and gRNA offered a slightly more reliable predictive value. Single Ct-values alone only provide a very limited prediction for the presence of replication competent virus. Hence, careful consideration of the medical history including symptom onset has to be considered for risk stratification.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Irene Jakobsche
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Johanna Raffel
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Annemarie Berger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany
| | - Udo Goetsch
- Health Protection Authority, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany; German Center for Infection Research, DZIF, Braunschweig, Germany; Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Sandhofstr. 2-4, House 75, Room 1.207, Frankfurt am Main 60528, Germany.
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80
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Arieta CM, Xie YJ, Rothenberg DA, Diao H, Harjanto D, Meda S, Marquart K, Koenitzer B, Sciuto TE, Lobo A, Zuiani A, Krumm SA, Cadima Couto CI, Hein S, Heinen AP, Ziegenhals T, Liu-Lupo Y, Vogel AB, Srouji JR, Fesser S, Thanki K, Walzer K, Addona TA, Türeci Ö, Şahin U, Gaynor RB, Poran A. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Cell 2023; 186:2392-2409.e21. [PMID: 37164012 PMCID: PMC10099181 DOI: 10.1016/j.cell.2023.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/12/2023] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
T cell responses play an important role in protection against beta-coronavirus infections, including SARS-CoV-2, where they associate with decreased COVID-19 disease severity and duration. To enhance T cell immunity across epitopes infrequently altered in SARS-CoV-2 variants, we designed BNT162b4, an mRNA vaccine component that is intended to be combined with BNT162b2, the spike-protein-encoding vaccine. BNT162b4 encodes variant-conserved, immunogenic segments of the SARS-CoV-2 nucleocapsid, membrane, and ORF1ab proteins, targeting diverse HLA alleles. BNT162b4 elicits polyfunctional CD4+ and CD8+ T cell responses to diverse epitopes in animal models, alone or when co-administered with BNT162b2 while preserving spike-specific immunity. Importantly, we demonstrate that BNT162b4 protects hamsters from severe disease and reduces viral titers following challenge with viral variants. These data suggest that a combination of BNT162b2 and BNT162b4 could reduce COVID-19 disease severity and duration caused by circulating or future variants. BNT162b4 is currently being clinically evaluated in combination with the BA.4/BA.5 Omicron-updated bivalent BNT162b2 (NCT05541861).
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Affiliation(s)
| | - Yushu Joy Xie
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | - Huitian Diao
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Dewi Harjanto
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Shirisha Meda
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Adam Zuiani
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | - John R Srouji
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Özlem Türeci
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Uğur Şahin
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany
| | | | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA.
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Eser TM, Baranov O, Huth M, Ahmed MIM, Deák F, Held K, Lin L, Pekayvaz K, Leunig A, Nicolai L, Pollakis G, Buggert M, Price DA, Rubio-Acero R, Reich J, Falk P, Markgraf A, Puchinger K, Castelletti N, Olbrich L, Vanshylla K, Klein F, Wieser A, Hasenauer J, Kroidl I, Hoelscher M, Geldmacher C. Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion. Nat Commun 2023; 14:2952. [PMID: 37225706 DOI: 10.1038/s41467-023-38020-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 05/26/2023] Open
Abstract
Despite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19.
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Affiliation(s)
- Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Manuel Huth
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
| | - Mohammed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Luming Lin
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Alexander Leunig
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 81377, Munich, Germany
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE, UK
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, CF14 4XN, UK
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Jakob Reich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Philine Falk
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Alissa Markgraf
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Kerstin Puchinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
- Max von Pettenkofer Institute for Hygiene and Medical Microbiology, LMU Munich, 81377, Munich, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, 85748, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, 53113, Bonn, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, 81377, Munich, Germany.
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82
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Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540806. [PMID: 37293069 PMCID: PMC10245570 DOI: 10.1101/2023.05.15.540806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
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Affiliation(s)
- Isabella T. Whitworth
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Rachel A. Knoener
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53705, United States
| | - Sofia Romero
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - M’bark Baddouh
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53705, United States
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin, 53706, United States
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education, Madison, Wisconsin, 53706, United States
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83
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Cornet-Gomez A, Retana Moreira L, Kronenberger T, Osuna A. Extracellular vesicles of trypomastigotes of Trypanosoma cruzi induce changes in ubiquitin-related processes, cell-signaling pathways and apoptosis. Sci Rep 2023; 13:7618. [PMID: 37165081 PMCID: PMC10171165 DOI: 10.1038/s41598-023-34820-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. The disease has an acute and a chronic phase in which approximately 30% of the chronic patients suffer from heart disease and/or gastrointestinal symptoms. The pathogenesis of the disease is multifactorial and involves the virulence of the strains, immunological factors and extracellular vesicles (EV) shed by the parasite which participate in cell-cell communication and evasion of the immune response. In this work, we present a transcriptomic analysis of cells stimulated with EV of the trypomastigote stage of T. cruzi. Results after EV-cell incubation revealed 322 differentially expressed genes (168 were upregulated and 154 were downregulated). In this regard, the overexpression of genes related to ubiquitin-related processes (Ube2C, SUMO1 and SUMO2) is highlighted. Moreover, the expression of Rho-GTPases (RhoA, Rac1 and Cdc42) after the interaction was analyzed, revealing a downregulation of the analyzed genes after 4 h of interaction. Finally, a protective role of EV over apoptosis is suggested, as relative values of cells in early and late apoptosis were significantly lower in EV-treated cells, which also showed increased CSNK1G1 expression. These results contribute to a better understanding of the EV-cell interaction and support the role of EV as virulence factors.
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Affiliation(s)
- Alberto Cornet-Gomez
- Grupo de Bioquímica y Parasitología Molecular (CTS 183), Departamento de Parasitología, Instituto de Biotecnología, Universidad de Granada, Campus de Fuentenueva, 18071, Granada, Spain
| | - Lissette Retana Moreira
- Grupo de Bioquímica y Parasitología Molecular (CTS 183), Departamento de Parasitología, Instituto de Biotecnología, Universidad de Granada, Campus de Fuentenueva, 18071, Granada, Spain
- Departamento de Parasitología, Facultad de Microbiología, Universidad de Costa Rica, San José, 11501, Costa Rica
- Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, 11501, Costa Rica
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Antonio Osuna
- Grupo de Bioquímica y Parasitología Molecular (CTS 183), Departamento de Parasitología, Instituto de Biotecnología, Universidad de Granada, Campus de Fuentenueva, 18071, Granada, Spain.
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84
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Vodovotz Y. Towards systems immunology of critical illness at scale: from single cell 'omics to digital twins. Trends Immunol 2023; 44:345-355. [PMID: 36967340 PMCID: PMC10147586 DOI: 10.1016/j.it.2023.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023]
Abstract
Single-cell 'omics methodology has yielded unprecedented insights based largely on data-centric informatics for reducing, and thus interpreting, massive datasets. In parallel, parsimonious mathematical modeling based on abstractions of pathobiology has also yielded major insights into inflammation and immunity, with these models being extended to describe multi-organ disease pathophysiology as the basis of 'digital twins' and in silico clinical trials. The integration of these distinct methods at scale can drive both basic and translational advances, especially in the context of critical illness, including diseases such as COVID-19. Here, I explore achievements and argue the challenges that are inherent to the integration of data-driven and mechanistic modeling approaches, highlighting the potential of modeling-based strategies for rational immune system reprogramming.
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Affiliation(s)
- Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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85
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Chen TH, Chang CJ, Hung PH. Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder. Int J Mol Sci 2023; 24:8034. [PMID: 37175745 PMCID: PMC10179190 DOI: 10.3390/ijms24098034] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can alter the mitochondria responsible for energy production in cells. This alteration leads to mitochondrial dysfunction which, in turn, increases oxidative stress. Ultimately, this results in a loss of mitochondrial integrity and cell death. Moreover, viral proteins can bind to mitochondrial complexes, disrupting mitochondrial function and causing the immune cells to over-react. This over-reaction leads to inflammation and potentially long COVID symptoms. It is important to note that the roles of mitochondrial damage and inflammatory responses caused by SARS-CoV-2 in the development of long COVID are still being elucidated. Targeting mitochondrial function may provide promising new clinical approaches for long-COVID patients; however, further studies are needed to evaluate the safety and efficacy of such approaches.
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Affiliation(s)
- Tsung-Hsien Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
| | - Chia-Jung Chang
- Division of Critical Care Medicine, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
| | - Peir-Haur Hung
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
- Department of Life and Health Science, Chia-Nan University of Pharmacy and Science, Tainan 717301, Taiwan
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86
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Hessien M, Donia T, Tabll AA, Adly E, Abdelhafez TH, Attia A, Alkafaas SS, Kuna L, Glasnovic M, Cosic V, Smolic R, Smolic M. Mechanistic-Based Classification of Endocytosis-Related Inhibitors: Does It Aid in Assigning Drugs against SARS-CoV-2? Viruses 2023; 15:v15051040. [PMID: 37243127 DOI: 10.3390/v15051040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) canonically utilizes clathrin-mediated endocytosis (CME) and several other endocytic mechanisms to invade airway epithelial cells. Endocytic inhibitors, particularly those targeting CME-related proteins, have been identified as promising antiviral drugs. Currently, these inhibitors are ambiguously classified as chemical, pharmaceutical, or natural inhibitors. However, their varying mechanisms may suggest a more realistic classification system. Herein, we present a new mechanistic-based classification of endocytosis inhibitors, in which they are segregated among four distinct classes including: (i) inhibitors that disrupt endocytosis-related protein-protein interactions, and assembly or dissociation of complexes; (ii) inhibitors of large dynamin GTPase and/or kinase/phosphatase activities associated with endocytosis; (iii) inhibitors that modulate the structure of subcellular components, especially the plasma membrane, and actin; and (iv) inhibitors that cause physiological or metabolic alterations in the endocytosis niche. Excluding antiviral drugs designed to halt SARS-CoV-2 replication, other drugs, either FDA-approved or suggested through basic research, could be systematically assigned to one of these classes. We observed that many anti-SARS-CoV-2 drugs could be included either in class III or IV as they interfere with the structural or physiological integrity of subcellular components, respectively. This perspective may contribute to our understanding of the relative efficacy of endocytosis-related inhibitors and support the optimization of their individual or combined antiviral potential against SARS-CoV-2. However, their selectivity, combined effects, and possible interactions with non-endocytic cellular targets need more clarification.
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Affiliation(s)
- Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Thoria Donia
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Ashraf A Tabll
- National Research Centre, Microbial Biotechnology Department, Biotechnology Research Institute, Giza 12622, Egypt
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Eiman Adly
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Tawfeek H Abdelhafez
- National Research Centre, Microbial Biotechnology Department, Biotechnology Research Institute, Giza 12622, Egypt
| | - Amany Attia
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Lucija Kuna
- Department of Pharmacology and Biochemistry, Faculty of Dental Medicine and Health Osijek, University of J. J. Strossmayer Osijek, 31000 Osijek, Croatia
| | - Marija Glasnovic
- Department of Medicine, Family Medicine and History of Medicine, Faculty of Medicine Osijek, University of J. J. Strossmayer Osijek, 31000 Osijek, Croatia
| | - Vesna Cosic
- Department of Paediatrics and Gynaecology with Obstetrics, Faculty of Dental Medicine and Health Osijek, University of J. J. Strossmayer Osijek, 31000 Osijek, Croatia
| | - Robert Smolic
- Department of Pharmacology and Biochemistry, Faculty of Dental Medicine and Health Osijek, University of J. J. Strossmayer Osijek, 31000 Osijek, Croatia
| | - Martina Smolic
- Department of Pharmacology and Biochemistry, Faculty of Dental Medicine and Health Osijek, University of J. J. Strossmayer Osijek, 31000 Osijek, Croatia
- Department of Pharmacology, Faculty of Medicine Osijek, University of Osijek, 31000 Osijek, Croatia
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87
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Salgado BB, Jordão MF, de Morais TBDN, da Silva DSS, Pereira Filho IV, Salgado Sobrinho WB, Carvalho NO, Dos Santos RO, Forato J, Barbosa PP, Toledo-Teixeira DA, Pinto KR, Correia IS, Cordeiro IB, Souza Neto JND, Assunção END, Val FFA, Melo GC, Sampaio VDS, Monteiro WM, Granja F, Souza WMD, Astolfi Filho S, Proenca-Modena JL, Lalwani JDB, Lacerda MVGD, Nogueira PA, Lalwani P. Antigen-Specific Antibody Signature Is Associated with COVID-19 Outcome. Viruses 2023; 15:v15041018. [PMID: 37112998 PMCID: PMC10143282 DOI: 10.3390/v15041018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Numerous studies have focused on inflammation-related markers to understand COVID-19. In this study, we performed a comparative analysis of spike (S) and nucleocapsid (N) protein-specific IgA, total IgG and IgG subclass response in COVID-19 patients and compared this to their disease outcome. We observed that the SARS-CoV-2 infection elicits a robust IgA and IgG response against the N-terminal (N1) and C-terminal (N3) region of the N protein, whereas we failed to detect IgA antibodies and observed a weak IgG response against the disordered linker region (N2) in COVID-19 patients. N and S protein-specific IgG1, IgG2 and IgG3 response was significantly elevated in hospitalized patients with severe disease compared to outpatients with non-severe disease. IgA and total IgG antibody reactivity gradually increased after the first week of symptoms. Magnitude of RBD-ACE2 blocking antibodies identified in a competitive assay and neutralizing antibodies detected by PRNT assay correlated with disease severity. Generally, the IgA and total IgG response between the discharged and deceased COVID-19 patients was similar. However, significant differences in the ratio of IgG subclass antibodies were observed between discharged and deceased patients, especially towards the disordered linker region of the N protein. Overall, SARS-CoV-2 infection is linked to an elevated blood antibody response in severe patients compared to non-severe patients. Monitoring of antigen-specific serological response could be an important tool to accompany disease progression and improve outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Julia Forato
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Insititute of Biology, University of Campinas (UNICAMP), Campinas 13000-000, Brazil
| | - Priscilla Paschoal Barbosa
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Insititute of Biology, University of Campinas (UNICAMP), Campinas 13000-000, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Insititute of Biology, University of Campinas (UNICAMP), Campinas 13000-000, Brazil
| | - Kerollen Runa Pinto
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus 69000-000, Brazil
| | - Ingrid Silva Correia
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus 69000-000, Brazil
| | | | - Júlio Nino de Souza Neto
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus 69000-000, Brazil
| | | | | | - Gisely Cardoso Melo
- Fundação de Medicina Tropical, Doutor Heitor Vieira Dourado (FMT-HVD), Manaus 69000-000, Brazil
| | | | | | - Fabiana Granja
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima (UFRR), Boa Vista 69300-000, Brazil
| | - William M de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14000-000, Brazil
| | - Spartaco Astolfi Filho
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus 69000-000, Brazil
| | - Jose Luiz Proenca-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Insititute of Biology, University of Campinas (UNICAMP), Campinas 13000-000, Brazil
| | - Jaila Dias Borges Lalwani
- Faculdade de Ciências Farmacêuticas, Universidade Federal do Amazonas (UFAM), Manaus 69000-000, Brazil
| | - Marcus Vinícius Guimarães de Lacerda
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Manaus 69000-000, Brazil
- Fundação de Medicina Tropical, Doutor Heitor Vieira Dourado (FMT-HVD), Manaus 69000-000, Brazil
| | | | - Pritesh Lalwani
- Instituto Leônidas e Maria Deane (ILMD), Fiocruz Amazônia, Manaus 69000-000, Brazil
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88
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Altindiş M, Kahraman Kilbaş EP. Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081421. [PMID: 37189522 DOI: 10.3390/diagnostics13081421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.
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Affiliation(s)
- Mustafa Altindiş
- Medical Microbiology Department, Faculty of Medicine, Sakarya University, Sakarya 54050, Türkiye
| | - Elmas Pınar Kahraman Kilbaş
- Medical Laboratory Techniques, Vocational School of Health Services, Fenerbahce University, Istanbul 34758, Türkiye
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89
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Luo SY, Moussa EW, Lopez-Orozco J, Felix-Lopez A, Ishida R, Fayad N, Gomez-Cardona E, Wang H, Wilson JA, Kumar A, Hobman TC, Julien O. Identification of Human Host Substrates of the SARS-CoV-2 M pro and PL pro Using Subtiligase N-Terminomics. ACS Infect Dis 2023; 9:749-761. [PMID: 37011043 PMCID: PMC10081575 DOI: 10.1021/acsinfecdis.2c00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Indexed: 04/04/2023]
Abstract
The recent emergence of SARS-CoV-2 in the human population has caused a global pandemic. The virus encodes two proteases, Mpro and PLpro, that are thought to play key roles in the suppression of host protein synthesis and immune response evasion during infection. To identify the specific host cell substrates of these proteases, active recombinant SARS-CoV-2 Mpro and PLpro were added to A549 and Jurkat human cell lysates, and subtiligase-mediated N-terminomics was used to capture and enrich protease substrate fragments. The precise location of each cleavage site was identified using mass spectrometry. Here, we report the identification of over 200 human host proteins that are potential substrates for SARS-CoV-2 Mpro and PLpro and provide a global mapping of proteolysis for these two viral proteases in vitro. Modulating proteolysis of these substrates will increase our understanding of SARS-CoV-2 pathobiology and COVID-19.
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Affiliation(s)
- Shu Y. Luo
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joaquin Lopez-Orozco
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Alberto Felix-Lopez
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ray Ishida
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nawell Fayad
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Henry Wang
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joyce A. Wilson
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Anil Kumar
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Tom C. Hobman
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
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90
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Wang M, Yan L, Jia J, Lai J, Zhou H, Yu B. DE-MHAIPs: Identification of SARS-CoV-2 phosphorylation sites based on differential evolution multi-feature learning and multi-head attention mechanism. Comput Biol Med 2023; 160:106935. [PMID: 37120990 PMCID: PMC10140648 DOI: 10.1016/j.compbiomed.2023.106935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 05/02/2023]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) around the world affects the normal lives of people all over the world. The computational methods can be used to accurately identify SARS-CoV-2 phosphorylation sites. In this paper, a new prediction model of SARS-CoV-2 phosphorylation sites, called DE-MHAIPs, is proposed. First, we use six feature extraction methods to extract protein sequence information from different perspectives. For the first time, we use a differential evolution (DE) algorithm to learn individual feature weights and fuse multi-information in a weighted combination. Next, Group LASSO is used to select a subset of good features. Then, the important protein information is given higher weight through multi-head attention. After that, the processed data is fed into long short-term memory network (LSTM) to further enhance model's ability to learn features. Finally, the data from LSTM are input into fully connected neural network (FCN) to predict SARS-CoV-2 phosphorylation sites. The AUC values of the S/T and Y datasets under 5-fold cross-validation reach 91.98% and 98.32%, respectively. The AUC values of the two datasets on the independent test set reach 91.72% and 97.78%, respectively. The experimental results show that the DE-MHAIPs method exhibits excellent predictive ability compared with other methods.
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Affiliation(s)
- Minghui Wang
- College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China
| | - Lu Yan
- College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China
| | - Jihua Jia
- College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China
| | - Jiali Lai
- College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China
| | - Hongyan Zhou
- College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China.
| | - Bin Yu
- College of Information Science and Technology, School of Data Science, Qingdao University of Science and Technology, Qingdao, 266061, China; School of Data Science, University of Science and Technology of China, Hefei, 230027, China.
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91
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Singh A, Pandey KK, Agrawal SK, Srivastava RK, Bhattacharyya S, Verma B. The SARS-CoV-2 UTR’s Intrudes Host RBP’s and Modulates Cellular Splicing. Adv Virol 2023; 2023:2995443. [PMID: 37065904 PMCID: PMC10098413 DOI: 10.1155/2023/2995443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5′ and 3′UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5′ and 3’UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5′ and 3′UTRs, using in-silico approaches. Our results suggest that 5′ and 3′UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.
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Affiliation(s)
- Anjali Singh
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- Nebraska Center for Virology and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln 68583, NE, USA
| | - Shubham Kumar Agrawal
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rupesh K. Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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92
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Maity S, Mayer MG, Shu Q, Linh H, Bao D, Blair RV, He Y, Lyon CJ, Hu TY, Fischer T, Fan J. Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates. Mol Cell Proteomics 2023; 22:100523. [PMID: 36870567 PMCID: PMC9981268 DOI: 10.1016/j.mcpro.2023.100523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/18/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Neurologic manifestations are among the most frequently reported complications of COVID-19. However, given the paucity of tissue samples and the highly infectious nature of the etiologic agent of COVID-19, we have limited information to understand the neuropathogenesis of COVID-19. Therefore, to better understand the impact of COVID-19 on the brain, we used mass-spectrometry-based proteomics with a data-independent acquisition mode to investigate cerebrospinal fluid (CSF) proteins collected from two different nonhuman primates, Rhesus Macaque and African Green Monkeys, for the neurologic effects of the infection. These monkeys exhibited minimal to mild pulmonary pathology but moderate to severe central nervous system (CNS) pathology. Our results indicated that CSF proteome changes after infection resolution corresponded with bronchial virus abundance during early infection and revealed substantial differences between the infected nonhuman primates and their age-matched uninfected controls, suggesting these differences could reflect altered secretion of CNS factors in response to SARS-CoV-2-induced neuropathology. We also observed the infected animals exhibited highly scattered data distributions compared to their corresponding controls indicating the heterogeneity of the CSF proteome change and the host response to the viral infection. Dysregulated CSF proteins were preferentially enriched in functional pathways associated with progressive neurodegenerative disorders, hemostasis, and innate immune responses that could influence neuroinflammatory responses following COVID-19. Mapping these dysregulated proteins to the Human Brain Protein Atlas found that they tended to be enriched in brain regions that exhibit more frequent injury following COVID-19. It, therefore, appears reasonable to speculate that such CSF protein changes could serve as signatures for neurologic injury, identify important regulatory pathways in this process, and potentially reveal therapeutic targets to prevent or attenuate the development of neurologic injuries following COVID-19.
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Affiliation(s)
- Sudipa Maity
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Meredith G Mayer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Hellmers Linh
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Robert V Blair
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Yanlin He
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tracy Fischer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA.
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93
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Chen SC, Xu CT, Chang CF, Chao TY, Lin CC, Fu PW, Yu CH. Optimization of 5'UTR to evade SARS-CoV-2 Nonstructural protein 1-directed inhibition of protein synthesis in cells. Appl Microbiol Biotechnol 2023; 107:2451-2468. [PMID: 36843199 PMCID: PMC9968647 DOI: 10.1007/s00253-023-12442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Maximizing the expression level of therapeutic proteins in cells is the general goal for DNA/mRNA therapies. It is particularly challenging to achieve efficient protein expression in the cellular contexts with inhibited translation machineries, such as in the presence of cellular Nonstructural protein 1 (Nsp1) of coronaviruses (CoVs) that has been reported to inhibit overall protein synthesis of host genes and exogenously delivered mRNAs/DNAs. In this study, we thoroughly examined the sequence and structure contexts of viral and non-viral 5'UTRs that determine the protein expression levels of exogenously delivered DNAs and mRNAs in cells expressing SARS-CoV-2 Nsp1. It was found that high 5'-proximal A/U content promotes an escape from Nsp1-directed inhibition of protein synthesis and results in selective protein expression. Furthermore, 5'-proximal Cs were found to significantly enhance the protein expression in an Nsp1-dependent manner, while Gs located at a specific window close to the 5'-end counteract such enhancement. The distinct protein expression levels resulted from different 5'UTRs were found correlated to Nsp1-induced mRNA degradations. These findings ultimately enabled rational designs for optimized 5'UTRs that lead to strong expression of exogenous proteins regardless of the translationally repressive Nsp1. On the other hand, we have also identified several 5'-proximal sequences derived from host genes that are capable of mediating the escapes. These results provided novel perspectives to the optimizations of 5'UTRs for DNA/mRNA therapies and/or vaccinations, as well as shedding light on the potential host escapees from Nsp1-directed translational shutoffs. KEY POINTS: • The 5'-proximal SL1 and 5a/b derived from SARS-CoV-2 genomic RNA promote exogenous protein synthesis in cells expressing Nsp1 comparing with non-specific 5'UTRs. • Specific 5'-proximal sequence contexts are the key determinants of the escapes from Nsp1-directed translational repression and thereby enhance protein expressions. • Systematic mutagenesis identified optimized 5'UTRs that strongly enhance protein expression and promote resistance to Nsp1-induced translational repression and RNA degradation.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, New Taipei, Taiwan
| | - Cui-Ting Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan-Fu Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Chao
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Wen Fu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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94
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Tang N, Chen P, Zhao C, Liu P, Tan L, Song C, Qiu X, Liao Y, Liu X, Luo T, Sun Y, Ding C. Newcastle Disease Virus Manipulates Mitochondrial MTHFD2-Mediated Nucleotide Metabolism for Virus Replication. J Virol 2023; 97:e0001623. [PMID: 36794935 PMCID: PMC10062132 DOI: 10.1128/jvi.00016-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/22/2023] [Indexed: 02/17/2023] Open
Abstract
Viruses require host cell metabolic reprogramming to satisfy their replication demands; however, the mechanism by which the Newcastle disease virus (NDV) remodels nucleotide metabolism to support self-replication remains unknown. In this study, we demonstrate that NDV relies on the oxidative pentose phosphate pathway (oxPPP) and the folate-mediated one-carbon metabolic pathway to support replication. In concert with [1,2-13C2] glucose metabolic flow, NDV used oxPPP to promote pentose phosphate synthesis and to increase antioxidant NADPH production. Metabolic flux experiments using [2,3,3-2H] serine revealed that NDV increased one-carbon (1C) unit synthesis flux through the mitochondrial 1C pathway. Interestingly, methylenetetrahydrofolate dehydrogenase (MTHFD2) was upregulated as a compensatory mechanism for insufficient serine availability. Unexpectedly, direct knockdown of enzymes in the one-carbon metabolic pathway, except for cytosolic MTHFD1, significantly inhibited NDV replication. Specific complementation rescue experiments on small interfering RNA (siRNA)-mediated knockdown further revealed that only a knockdown of MTHFD2 strongly restrained NDV replication and was rescued by formate and extracellular nucleotides. These findings indicated that NDV replication relies on MTHFD2 to maintain nucleotide availability. Notably, nuclear MTHFD2 expression was increased during NDV infection and could represent a pathway by which NDV steals nucleotides from the nucleus. Collectively, these data reveal that NDV replication is regulated by the c-Myc-mediated 1C metabolic pathway and that the mechanism of nucleotide synthesis for viral replication is regulated by MTHFD2. IMPORTANCE Newcastle disease virus (NDV) is a dominant vector for vaccine and gene therapy that accommodates foreign genes well but can only infect mammalian cells that have undergone cancerous transformation. Understanding the remodeling of nucleotide metabolic pathways in host cells by NDV proliferation provides a new perspective for the precise use of NDV as a vector or in antiviral research. In this study, we demonstrated that NDV replication is strictly dependent on pathways involved in redox homeostasis in the nucleotide synthesis pathway, including the oxPPP and the mitochondrial one-carbon pathway. Further investigation revealed the potential involvement of NDV replication-dependent nucleotide availability in promoting MTHFD2 nuclear localization. Our findings highlight the differential dependence of NDV on enzymes for one-carbon metabolism, and the unique mechanism of action of MTHFD2 in viral replication, thereby providing a novel target for antiviral or oncolytic virus therapy.
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Affiliation(s)
- Ning Tang
- Laboratory of Veterinary Microbiology and Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Pingyi Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, P. R. China
| | - Changrun Zhao
- Laboratory of Veterinary Microbiology and Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
| | - Panrao Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
| | - Lei Tan
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Cuiping Song
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Xusheng Qiu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Ying Liao
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Xiufan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
| | - Tingrong Luo
- Laboratory of Veterinary Microbiology and Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
| | - Chan Ding
- Laboratory of Veterinary Microbiology and Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, P. R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
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95
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Talukder P, Saha A, Roy S, Ghosh G, Roy DD, Barua S. Drugs for COVID-19 Treatment: A New Challenge. Appl Biochem Biotechnol 2023; 195:3653-3670. [PMID: 36961509 PMCID: PMC10037400 DOI: 10.1007/s12010-023-04439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
COVID-19 infection is a new disease and our knowledge is limited; day in and day out more and more interesting yet diverse observations are reported by the different research groups from different corners of the world. So, there is an urgent requirement of the invention of some effective and efficient drugs that can carry out the end of the deadly viral infection. Throughout the world, there have been many efforts carried out in different labs to invent such a drug and also identifying any pre-existing drugs which can carry out the killing of the virus. In this review, an effort has been made to understand the potential drugs which can be used against the SARS-CoV-2 viral infection. Again, the strategies on the current and the future drug discovery mechanisms against the SARS-CoV-2 are also mentioned. The different drugs made and the drugs re-used and also the drugs which are in the making process in different research laboratories across the world are also mentioned. To combat this unexpected crisis, we still need some more efforts from the different scientific communities around the world for finding a cure against this viral infection and this is needed to be done for the prevention of more loss of human life.
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Affiliation(s)
- Pratik Talukder
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India.
| | - Arunima Saha
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Sohini Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Gargi Ghosh
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Debshikha Dutta Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Snejuti Barua
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
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96
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Mancini M, Natoli S, Gardoni F, Di Luca M, Pisani A. Dopamine Transmission Imbalance in Neuroinflammation: Perspectives on Long-Term COVID-19. Int J Mol Sci 2023; 24:ijms24065618. [PMID: 36982693 PMCID: PMC10056044 DOI: 10.3390/ijms24065618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Dopamine (DA) is a key neurotransmitter in the basal ganglia, implicated in the control of movement and motivation. Alteration of DA levels is central in Parkinson’s disease (PD), a common neurodegenerative disorder characterized by motor and non-motor manifestations and deposition of alpha-synuclein (α-syn) aggregates. Previous studies have hypothesized a link between PD and viral infections. Indeed, different cases of parkinsonism have been reported following COVID-19. However, whether SARS-CoV-2 may trigger a neurodegenerative process is still a matter of debate. Interestingly, evidence of brain inflammation has been described in postmortem samples of patients infected by SARS-CoV-2, which suggests immune-mediated mechanisms triggering the neurological sequelae. In this review, we discuss the role of proinflammatory molecules such as cytokines, chemokines, and oxygen reactive species in modulating DA homeostasis. Moreover, we review the existing literature on the possible mechanistic interplay between SARS-CoV-2-mediated neuroinflammation and nigrostriatal DAergic impairment, and the cross-talk with aberrant α-syn metabolism.
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Affiliation(s)
- Maria Mancini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Silvia Natoli
- Department of Clinical Science and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- IRCCS Maugeri Pavia, 27100 Pavia, Italy
| | - Fabrizio Gardoni
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, University of Milan, 20133 Milan, Italy; (F.G.); (M.D.L.)
| | - Monica Di Luca
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, University of Milan, 20133 Milan, Italy; (F.G.); (M.D.L.)
| | - Antonio Pisani
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- IRCCS Mondino Foundation, 27100 Pavia, Italy
- Correspondence: ; Tel.: +39-0382-380-247
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97
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Singh R, Gupta V, Kumar A, Singh K. 2-Deoxy-D-Glucose: A Novel Pharmacological Agent for Killing Hypoxic Tumor Cells, Oxygen Dependence-Lowering in Covid-19, and Other Pharmacological Activities. Adv Pharmacol Pharm Sci 2023; 2023:9993386. [PMID: 36911357 PMCID: PMC9998157 DOI: 10.1155/2023/9993386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/02/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The nonmetabolizable glucose analog 2-deoxy-D-glucose (2-DG) has shown promising pharmacological activities, including inhibition of cancerous cell growth and N-glycosylation. It has been used as a glycolysis inhibitor and as a potential energy restriction mimetic agent, inhibiting pathogen-associated molecular patterns. Radioisotope derivatives of 2-DG have applications as tracers. Recently, 2-DG has been used as an anti-COVID-19 drug to lower the need for supplemental oxygen. In the present review, various pharmaceutical properties of 2-DG are discussed.
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Affiliation(s)
- Raman Singh
- Division Chemistry & Toxicology, WTL-Clean and Renewable Energy Pvt. Ltd., New Delhi, India
| | - Vidushi Gupta
- Department of Chemistry, Indian Institute of Science Education and Research, Mohali, Punjab, India
| | - Antresh Kumar
- Department of Biochemistry, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana 123031, India
| | - Kuldeep Singh
- Department of Applied Chemistry, Amity University Madhya Pradesh, Gwalior, MP 474005, India
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98
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Pan J, Gao Y, Han H, Pan T, Guo J, Li S, Xu J, Li Y. Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19. Comput Biol Med 2023; 155:106651. [PMID: 36805221 PMCID: PMC9916187 DOI: 10.1016/j.compbiomed.2023.106651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The COVID-19 has led to a devastating global health crisis, which emphasizes the urgent need to deepen our understanding of the molecular mechanism and identifying potential antiviral drugs. Here, we comprehensively analyzed the transcriptomic and proteomic profiles of 178 COVID-19 patients, ranging from asymptomatic to critically ill. Our analyses found that the RNA binding proteins (RBPs) were likely to be perturbed in infection. Interactome analysis revealed that RBPs interact with virus proteins and the viral interacting RBPs were likely to locate in central regions of human protein-protein interaction network. Functional enrichment analysis revealed that the viral interacting RBPs were likely to be enriched in RNA transport, apoptosis and viral genome replication-related pathways. Based on network proximity analyses of 299 human complex-disease genes and COVID-19-related RBPs in the human interactome, we revealed the significant associations between complex diseases and COVID-19. Network analysis also implicated potential antiviral drugs for treatment of COVID-19. In summary, our integrative characterization of COVID-19 patients may thus help providing evidence regarding pathophysiology and potential therapeutic strategies for COVID-19.
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Affiliation(s)
- Jiwei Pan
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Yueying Gao
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Huirui Han
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Tao Pan
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Jing Guo
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Si Li
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yongsheng Li
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China.
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99
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Berber E, Sumbria D, Kokkaya S. A metabolic blueprint of COVID-19 and long-term vaccine efficacy. Drug Metab Pers Ther 2023; 38:15-29. [PMID: 36166711 DOI: 10.1515/dmpt-2022-0148] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Viruses are obligatory protein-coated units and often utilize the metabolic functions of the cells they infect. Viruses hijack cellular metabolic functions and cause consequences that can range from minor to devastating, as we have all witnessed during the COVID-19 pandemic. For understanding the virus-driven pathogenesis and its implications on the host, the cellular metabolism needs to be elucidated. How SARS-CoV-2 triggers metabolic functions and rewires the metabolism remains unidentified but the implications of the metabolic patterns are under investigation by several researchers. In this review, we have described the SARS-CoV-2-mediated metabolic alterations from in vitro studies to metabolic changes reported in victims of COVID-19. We have also discussed potential therapeutic targets to diminish the viral infection and suppress the inflammatory response, with respect to evidenced studies based on COVID-19 research. Finally, we aimed to explain how we could extend vaccine-induced immunity in people by targeting the immunometabolism.
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Affiliation(s)
- Engin Berber
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN, USA
| | - Deepak Sumbria
- College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Rampura Phul, Bathinda, India
| | - Serkan Kokkaya
- Faculty of Veterinary Medicine, Bozok University, Yozgat, Turkey
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100
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Maria NI, Rapicavoli RV, Alaimo S, Bischof E, Stasuzzo A, Broek JA, Pulvirenti A, Mishra B, Duits AJ, Ferro A. Application of the PHENotype SIMulator for rapid identification of potential candidates in effective COVID-19 drug repurposing. Heliyon 2023; 9:e14115. [PMID: 36911878 PMCID: PMC9986505 DOI: 10.1016/j.heliyon.2023.e14115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
The current, rapidly diversifying pandemic has accelerated the need for efficient and effective identification of potential drug candidates for COVID-19. Knowledge on host-immune response to SARS-CoV-2 infection, however, remains limited with few drugs approved to date. Viable strategies and tools are rapidly arising to address this, especially with repurposing of existing drugs offering significant promise. Here we introduce a systems biology tool, the PHENotype SIMulator, which -by leveraging available transcriptomic and proteomic databases-allows modeling of SARS-CoV-2 infection in host cells in silico to i) determine with high sensitivity and specificity (both>96%) the viral effects on cellular host-immune response, resulting in specific cellular SARS-CoV-2 signatures and ii) utilize these cell-specific signatures to identify promising repurposable therapeutics. Powered by this tool, coupled with domain expertise, we identify several potential COVID-19 drugs including methylprednisolone and metformin, and further discern key cellular SARS-CoV-2-affected pathways as potential druggable targets in COVID-19 pathogenesis.
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Key Words
- 2DG, 2-Deoxy-Glucose
- ACE2, Angiotensin-converting enzyme 2
- COVID-19
- COVID-19, Coronavirus disease 2019
- Caco-2, Human colon epithelial carcinoma cell line
- Calu-3, Epithelial cell line
- Cellular SARS-CoV-2 signatures
- Cellular host-immune response
- Cellular simulation models
- DEGs, Differentially Expressed Genes
- DEPs, Differentially expressed proteins
- Drug repurposing
- HCQ-CQ, (Hydroxy)chloroquine
- IFN, Interferon
- ISGs, IFN-stimulated genes
- MITHrIL, Mirna enrIched paTHway Impact anaLysis
- MOI, Multiplicity of infection
- MP, Methylprednisolone
- NHBE, Normal human bronchial epithelial cells
- PHENSIM, PHENotype SIMulator
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- Systems biology
- TLR, Toll-like Receptor
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Affiliation(s)
- Naomi I. Maria
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra, Northwell Health, Manhasset, NY, USA
- Red Cross Blood Bank Foundation Curaçao, Willemstad, Curaçao
- Department of Medical Microbiology and Immunology, St. Antonius Ziekenhuis, Niewegein, the Netherlands
- Corresponding author. Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA.
| | - Rosaria Valentina Rapicavoli
- Department of Physics and Astronomy, University of Catania, Italy
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Salvatore Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Evelyne Bischof
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Via Pansini, Naples, Italy
- School of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Pudong, Shanghai, China
- Insilico Medicine, Hong Kong Special Administrative Region, China
| | | | - Jantine A.C. Broek
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Bud Mishra
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
- Simon Center for Quantitative Biology, Cold Spring Harbor Lab, Long Island, USA
- Corresponding author. Courant Institute of Mathematical Sciences, Room 405, 251 Mercer Street, NY, USA.
| | - Ashley J. Duits
- Red Cross Blood Bank Foundation Curaçao, Willemstad, Curaçao
- Curaçao Biomedical Health Research Institute, Willemstad, Curaçao
- Institute for Medical Education, University Medical Center Groningen, Groningen, the Netherlands
| | - Alfredo Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
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