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Guo S, Yan Y, Zhang J, Yang Z, Tu L, Wang C, Kong Z, Wang S, Wang B, Qin D, Zhou J, Wang W, Hao Y, Guo S. Serum lipidome reveals lipid metabolic dysregulation in severe fever with thrombocytopenia syndrome. BMC Med 2024; 22:458. [PMID: 39396989 PMCID: PMC11472499 DOI: 10.1186/s12916-024-03672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/30/2024] [Indexed: 10/15/2024] Open
Abstract
BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is a rapidly progressing infectious disease with a high fatality rate caused by a novel bunyavirus (SFTSV). The role of lipids in viral infections is well-documented; however, the specific alterations in lipid metabolism during SFTSV infection remain elusive. This study aims to elucidate the lipid metabolic dysregulations in the early stages of SFTS patients. METHODS This study prospectively collected peripheral blood sera from 11 critical SFTS patients, 37 mild SFTS patients, and 23 healthy controls during the early stages of infection for lipidomics analysis. A systematic bioinformatics analysis was conducted from three aspects integrating lipid differential expressions, lipid differential correlations, and lipid-clinical indices correlations to reveal the serum lipid metabolic dysregulation in SFTSV-infected individuals. RESULTS Our findings reveal significant lipid metabolic dysregulation in SFTS patients. Specifically, compared to healthy controls, SFTS patients exhibited three distinct modes of lipid differential expression: increased levels of lipids including phosphatidylserine (PS), hexosylceramide (HexCer), and triglycerides (TG); decreased levels of lipids including lysophosphatidylcholine (LPC), acylcarnitine (AcCa), and cholesterol esters (ChE); and lipids showing "dual changes" including phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Finally, based on lipid metabolic pathways and literature analysis, we systematically elucidated the potential mechanisms underlying lipid metabolic dysregulation in the early stage of SFTSV infection. CONCLUSIONS Our study presents the first global serum lipidome profile and reveals the lipid metabolic dysregulation patterns in the early stage of SFTSV infection. These findings provide a new basis for the diagnosis, treatment, and further investigation of the disease.
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Affiliation(s)
- Shuai Guo
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
| | - Yunjun Yan
- Jinan Dian Medical Laboratory CO., LTD, Shandong, China
| | - Jingyao Zhang
- Department of Infectious Diseases, Shandong Provincial Public Health Clinical Center, Jinan, China
| | - Zhangong Yang
- Calibra Lab at DIAN Diagnostics, Hangzhou, 310030, China
| | - Lirui Tu
- Department of Infectious Diseases, Shandong Provincial Public Health Clinical Center, Jinan, China
| | - Chunjuan Wang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
| | - Ziqing Kong
- Calibra Lab at DIAN Diagnostics, Hangzhou, 310030, China
| | - Shuhua Wang
- Center of Health Management, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
| | - Baojie Wang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Neurology, Shandong Second Provincial General Hospital, Jinan, China
| | - Danqing Qin
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
| | - Jie Zhou
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
- Department of Neurology, The Fifth People's Hospital of Jinan, Jinan, China
| | - Wenjin Wang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China
| | - Yumei Hao
- Institute of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group, Hangzhou, China.
| | - Shougang Guo
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, China.
- Department of Neurology, Shandong Provincial HospitalAffiliated to, Shandong First Medical University , Jinan, China.
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Loeb K, Lemaille C, Frederick C, Wallace HL, Kindrachuk J. Harnessing high-throughput OMICS in emerging zoonotic virus preparedness and response activities. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167337. [PMID: 38986821 DOI: 10.1016/j.bbadis.2024.167337] [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: 05/06/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Emerging and re-emerging viruses pose unpredictable and significant challenges to global health. Emerging zoonotic infectious diseases, which are transmitted between humans and non-human animals, have been estimated to be responsible for nearly two-thirds of emerging infectious disease events and emergence events attributed to these pathogens have been increasing in frequency with the potential for high global health and economic burdens. In this review we will focus on the application of highthroughput OMICS approaches to emerging zoonotic virus investigtations. We highlight the key contributions of transcriptome and proteome investigations to emerging zoonotic virus preparedness and response activities with a focus on SARS-CoV-2, avian influenza virus subtype H5N1, and Orthoebolavirus investigations.
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Affiliation(s)
- Kristi Loeb
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Candice Lemaille
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Christina Frederick
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Hannah L Wallace
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Manitoba Centre for Proteomics and Systems Biology, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada.
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Stubbs DB, Ruzicka JA, Taylor EW. Modular Polymerase Synthesis and Internal Protein Domain Swapping via Dual Opposed Frameshifts in the Ebola Virus L Gene. Pathogens 2024; 13:829. [PMID: 39452701 PMCID: PMC11510084 DOI: 10.3390/pathogens13100829] [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: 08/07/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/26/2024] Open
Abstract
Sequence analysis of the Zaire ebolavirus (EBOV) polymerase (L gene) mRNA, using online tools, identified a highly ranked -1 programmed ribosomal frameshift (FS) signal including an ideal slippery sequence heptamer (UUUAAAA), with an overlapping coding region featuring two tandem UGA codons, immediately followed by an RNA region that is the inverse complement (antisense) to a region of the mRNA of the selenoprotein iodothyronine deiodinase II (DIO2). This antisense interaction was confirmed in vitro via electrophoretic gel shift assay, using cDNAs at the EBOV and DIO2 segments. The formation of a duplex between the two mRNAs could trigger the ribosomal frameshift, by mimicking the enhancing role of a pseudoknot structure, while providing access to the selenocysteine insertion sequence (SECIS) element contained in the DIO2 mRNA. This process would allow the -1 frame UGA codons to be recoded as selenocysteine, forming part of a C-terminal module in a low abundance truncated isoform of the viral polymerase, potentially functioning in a redox role. Remarkably, 90 bases downstream of the -1 FS site, an active +1 FS site can be demonstrated, which, via a return to the zero frame, would enable the attachment of the entire C-terminal of the polymerase protein. Using a construct with upstream and downstream reporter genes, spanning a wildtype or mutated viral insert, we show significant +1 ribosomal frameshifting at this site. Acting singly or together, frameshifting at these sites (both of which are highly conserved in EBOV strains) could enable the expression of several modified isoforms of the polymerase. The 3D modeling of the predicted EBOV polymerase FS variants using the AI tool, AlphaFold, reveals a peroxiredoxin-like active site with arginine and threonine residues adjacent to a putative UGA-encoded selenocysteine, located on the back of the polymerase "hand". This module could serve to protect the viral RNA from peroxidative damage.
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Affiliation(s)
| | | | - Ethan W. Taylor
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, NC 27402-6170, USA; (D.B.S.); (J.A.R.)
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4
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Fletcher P, Clancy CS, O’Donnell KL, Doratt BM, Malherbe DC, Rhoderick JF, Feldmann F, Hanley PW, Takada A, Messaoudi I, Marzi A. Pathogenic differences of cynomolgus macaques after Taï Forest virus infection depend on the viral stock propagation. PLoS Pathog 2024; 20:e1012290. [PMID: 38861571 PMCID: PMC11195944 DOI: 10.1371/journal.ppat.1012290] [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: 01/29/2024] [Revised: 06/24/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Taï Forest virus (TAFV) is a negative-sense RNA virus in the Filoviridae family. TAFV has caused only a single human infection, but several disease outbreaks in chimpanzees have been linked to this virus. Limited research has been done on this human-pathogenic virus. We sought to establish an animal model to assess TAFV disease progression and pathogenicity at our facility. We had access to two different viral stock preparations from different institutions, both originating from the single human case. Type I interferon receptor knockout mice were inoculated with TAFV stock 1 or stock 2 by the intraperitoneal route. Inoculation resulted in 100% survival with no disease regardless of viral stock preparation or infectious dose. Next, cynomolgus macaques were inoculated with TAFV stock 1 or stock 2. Inoculation with TAFV stock 1 resulted in 100% survival and robust TAFV glycoprotein-specific IgG responses including neutralizing antibodies. In contrast, macaques infected with TAFV stock 2 developed disease and were euthanized 8-11 days after infection exhibiting viremia, thrombocytopenia, and increased inflammatory mediators identified by transcriptional analysis. Histopathologic analysis of tissue samples collected at necropsy confirmed classic filovirus disease in numerous organs. Genomic differences in both stock preparations were mapped to several viral genes which may have contributed to disease severity. Taken together, we demonstrate that infection with the two TAFV stocks resulted in no disease in mice and opposing disease phenotypes in cynomolgus macaques, highlighting the impact of viral stock propagation on pathogenicity in animal models.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chad S. Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kyle L. O’Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brianna M. Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Joseph F. Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Patrick W. Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
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5
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McDermott JE, Jacobs JM, Merrill NJ, Mitchell HD, Arshad OA, McClure R, Teeguarden J, Gajula RP, Porter KI, Satterfield BC, Lundholm KR, Skene DJ, Gaddameedhi S, Dongen HPAV. Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment. J Proteome Res 2024; 23:1547-1558. [PMID: 38619923 DOI: 10.1021/acs.jproteome.3c00418] [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] [Indexed: 04/17/2024]
Abstract
Circadian misalignment due to night work has been associated with an elevated risk for chronic diseases. We investigated the effects of circadian misalignment using shotgun protein profiling of peripheral blood mononuclear cells taken from healthy humans during a constant routine protocol, which was conducted immediately after participants had been subjected to a 3-day simulated night shift schedule or a 3-day simulated day shift schedule. By comparing proteomic profiles between the simulated shift conditions, we identified proteins and pathways that are associated with the effects of circadian misalignment and observed that insulin regulation pathways and inflammation-related proteins displayed markedly different temporal patterns after simulated night shift. Further, by integrating the proteomic profiles with previously assessed metabolomic profiles in a network-based approach, we found key associations between circadian dysregulation of protein-level pathways and metabolites of interest in the context of chronic metabolic diseases. Endogenous circadian rhythms in circulating glucose and insulin differed between the simulated shift conditions. Overall, our results suggest that circadian misalignment is associated with a tug of war between central clock mechanisms controlling insulin secretion and peripheral clock mechanisms regulating insulin sensitivity, which may lead to adverse long-term outcomes such as diabetes and obesity. Our study provides a molecular-level mechanism linking circadian misalignment and adverse long-term health consequences of night work.
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Affiliation(s)
- Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Jon M Jacobs
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nathaniel J Merrill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Justin Teeguarden
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Rajendra P Gajula
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Kenneth I Porter
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Brieann C Satterfield
- Sleep and Performance Research Center, Washington State University, Spokane, Washington 99202, United States
- Department of Translational Medicine and Physiology, Washington State University, Spokane, Washington 99202, United States
| | - Kirsie R Lundholm
- Sleep and Performance Research Center, Washington State University, Spokane, Washington 99202, United States
- Department of Translational Medicine and Physiology, Washington State University, Spokane, Washington 99202, United States
| | - Debra J Skene
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Shobhan Gaddameedhi
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hans P A Van Dongen
- Sleep and Performance Research Center, Washington State University, Spokane, Washington 99202, United States
- Department of Translational Medicine and Physiology, Washington State University, Spokane, Washington 99202, United States
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6
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Eisfeld AJ, Anderson LN, Fan S, Walters KB, Halfmann PJ, Westhoff Smith D, Thackray LB, Tan Q, Sims AC, Menachery VD, Schäfer A, Sheahan TP, Cockrell AS, Stratton KG, Webb-Robertson BJM, Kyle JE, Burnum-Johnson KE, Kim YM, Nicora CD, Peralta Z, N'jai AU, Sahr F, van Bakel H, Diamond MS, Baric RS, Metz TO, Smith RD, Kawaoka Y, Waters KM. A compendium of multi-omics data illuminating host responses to lethal human virus infections. Sci Data 2024; 11:328. [PMID: 38565538 PMCID: PMC10987564 DOI: 10.1038/s41597-024-03124-3] [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: 12/04/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.
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Affiliation(s)
- Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Lindsey N Anderson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Shufang Fan
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Coronavirus and Other Respiratory Viruses Laboratory Branch (CRVLB), Coronavirus and Other Respiratory Viruses Division (CORVD), National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30329, USA
| | - Kevin B Walters
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Danielle Westhoff Smith
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Qing Tan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Amy C Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Nuclear, Chemistry, and Biosciences Division; National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam S Cockrell
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Solid Biosciences, Charlston, MA, 02139, USA
| | - Kelly G Stratton
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Partillion Bioscience, Los Angeles, CA, 90064, USA
| | - Alhaji U N'jai
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biological Sciences, Fourah Bay College, Freetown, Sierra Leone
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Department of Medical Education, California University of Science and Medicine, Colton, CA, 92324, USA
| | - Foday Sahr
- Department of Microbiology, College of Medicine and Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 108-8639, Japan
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Kralova K, Vrtelka O, Fouskova M, Smirnova TA, Michalkova L, Hribek P, Urbanek P, Kuckova S, Setnicka V. Comprehensive spectroscopic, metabolomic, and proteomic liquid biopsy in the diagnostics of hepatocellular carcinoma. Talanta 2024; 270:125527. [PMID: 38134814 DOI: 10.1016/j.talanta.2023.125527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Liquid biopsy is a very topical issue in clinical diagnostics research nowadays. In this study, we explored and compared various analytical approaches to blood plasma analysis. Finally, we proposed a comprehensive procedure, which, thanks to the utilization of multiple analytical techniques, allowed the targeting of various biomolecules in blood plasma reflecting diverse biological processes underlying disease development. The potential of such an approach, combining proteomics, metabolomics, and vibrational spectroscopy along with preceding blood plasma fractionation, was demonstrated on blood plasma samples of patients suffering from hepatocellular carcinoma in cirrhotic terrain (n = 20) and control subjects with liver cirrhosis (n = 20) as well as healthy subjects (n = 20). Most of the applied methods allowed the classification of the samples with an accuracy exceeding 80.0 % and therefore have the potential to be used as a stand-alone method in clinical diagnostics. Moreover, a final panel of 48 variables obtained by a combination of the utilized analytical methods enabled the discrimination of the hepatocellular carcinoma samples from cirrhosis with 94.3 % cross-validated accuracy. Thus, this study, although limited by the cohort size, clearly demonstrated the benefit of the multimethod approach in clinical diagnosis.
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Affiliation(s)
- Katerina Kralova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Ondrej Vrtelka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Marketa Fouskova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Tatiana Anatolievna Smirnova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Lenka Michalkova
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic; Department of Analytical Chemistry, Institute of Chemical Process Fundamentals of the CAS, Rozvojova 135, 165 02, Prague 6, Czech Republic
| | - Petr Hribek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic; Department of Internal Medicine, Faculty of Military Health Sciences in Hradec Kralove, University of Defense, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Petr Urbanek
- Military University Hospital Prague, Department of Medicine 1st Faculty of Medicine Charles University and Military University Hospital Prague, U Vojenske Nemocnice 1200, 169 02, Prague 6, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic
| | - Vladimir Setnicka
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technicka 5, 166 28, Prague 6, Czech Republic.
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8
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Wang X, Ding D, Liu Y, Zhao H, Sun J, Li Y, Cao J, Hou S, Zhang Y. Plasma lipidome reveals susceptibility and resistance of Pekin ducks to DHAV-3. Int J Biol Macromol 2023; 253:127095. [PMID: 37758112 DOI: 10.1016/j.ijbiomac.2023.127095] [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: 01/14/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Duck hepatitis A virus genotype 3 (DHAV-3) is the most popular pathogen of duck viral hepatitis (DVH) and has led to a huge economic threat to the Asian duck industry. In this work, we investigated the differences in the LC-MS/MS-based dynamic lipid profiles between susceptible and resistant Pekin duck lines with DHAV-3 infection. We found that the plasma lipidome of the two duck lines was characterized differently in expression levels of lipids during the infection, such as decreased levels of glycerolipids and increased levels of cholesteryl esters and glycerophospholipids in susceptible ducks compared with resistant ducks. By integrating lipidomics and transcriptomics analysis, we showed that the altered homeostasis of lipids was potentially regulated by a variety of differentially expressed genes including CHPT1, PI4K2A, and OSBP2 between the two duck lines, which could account for liver dysfunction, apoptosis, and illness upon DHAV-3 infection. Using the least absolute shrinkage and selection operator (LASSO) approach, we determined a total of 25 infection-related lipids that were able to distinguish between the infection states of susceptible and resistant ducks. This study provides molecular clues for elucidating the pathogenesis and therapeutic strategies of DHAV-3 infection in ducklings, which has implication for the development of resistance breeding.
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Affiliation(s)
- Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Dingbang Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ying Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haonan Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianfeng Sun
- Botnar Research Centre, University of Oxford, OX3 7LD Oxford, United Kingdom
| | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junting Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunsheng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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9
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Marzi A, Feldmann F, O’Donnell KL, Hanley PW, Messaoudi I, Feldmann H. Preexisting Immunity Does Not Prevent Efficacy of Vesicular Stomatitis Virus-Based Filovirus Vaccines in Nonhuman Primates. J Infect Dis 2023; 228:S671-S676. [PMID: 37290042 PMCID: PMC10651194 DOI: 10.1093/infdis/jiad208] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023] Open
Abstract
Ebola virus (EBOV) and Marburg virus (MARV) made headlines in the past decade, causing outbreaks of human disease in previously nonendemic yet overlapping areas. While EBOV outbreaks can be mitigated with licensed vaccines and treatments, there is not yet a licensed countermeasure for MARV. Here, we used nonhuman primates (NHPs) previously vaccinated with vesicular stomatitis virus (VSV)-MARV and protected against lethal MARV challenge. After a resting period of 9 months, these NHPs were revaccinated with VSV-EBOV and challenged with EBOV, resulting in 75% survival. Surviving NHPs developed EBOV glycoprotein (GP)-specific antibody titers and no viremia or clinical signs of disease. The single vaccinated NHP succumbing to challenge showed the lowest EBOV GP-specific antibody response after challenge, supporting previous findings with VSV-EBOV that antigen-specific antibodies are critical in mediating protection. This study again demonstrates that VSVΔG-based filovirus vaccine can be successfully used in individuals with preexisting VSV vector immunity, highlighting the platform's applicability for consecutive outbreak response.
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Affiliation(s)
- Andrea Marzi
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Kyle L O’Donnell
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Heinz Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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10
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Kuroda M, Halfmann PJ, Kawaoka Y. Ebola Virus Infection Induces HCAR2 Expression Leading to Cell Death. J Infect Dis 2023; 228:S508-S513. [PMID: 37578011 PMCID: PMC10651187 DOI: 10.1093/infdis/jiad344] [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: 04/17/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023] Open
Abstract
Ebola virus (EBOV) induces cell death not only in infected permissive cells but also in nonpermissive, bystander cells by employing different mechanisms. Hydroxycarboxylic acid receptor 2 (HCAR2) has been reported to be involved in apoptotic cell death. We previously reported an increase in the expression of HCAR2-specific mRNA in EBOV-infected individuals with fatal outcomes. Here, we report that infection with an EBOV lacking the VP30 gene (EBOVΔVP30) results in the upregulation of HCAR2 mRNA expression in human hepatocyte Huh7.0 cells stably expressing VP30. Transient overexpression of HCAR2 reduced the viability of Huh7.0 cells and human embryonic kidney cells. Phosphatidylserine externalization and cell membrane permeabilization by HCAR2 overexpression was also observed. Interestingly, coexpression of HCAR2 with EBOV VP40 further reduced cell viability in transfected cells compared to HCAR2 coexpression with other viral proteins. Our data suggest that HCAR2 may contribute to EBOV-induced cell death.
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Affiliation(s)
- Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection, and Advanced Research Center, University of Tokyo, Tokyo, Japan
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11
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Figueirêdo Leite GG, Colo Brunialti MK, Peçanha-Pietrobom PM, Abrão Ferreira PR, Ota-Arakaki JS, Cunha-Neto E, Ferreira BL, Ronsein GE, Tashima AK, Salomão R. Understanding COVID-19 progression with longitudinal peripheral blood mononuclear cell proteomics: Changes in the cellular proteome over time. iScience 2023; 26:107824. [PMID: 37736053 PMCID: PMC10509719 DOI: 10.1016/j.isci.2023.107824] [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: 04/11/2023] [Revised: 07/16/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023] Open
Abstract
The clinical presentation of COVID-19 is highly variable, and understanding the underlying biological processes is crucial. This study utilized a proteomic analysis to investigate dysregulated processes in the peripheral blood mononuclear cells of patients with COVID-19 compared to healthy volunteers. Samples were collected at different stages of the disease, including hospital admission, after 7 days of hospitalization, and 30 days after discharge. Metabolic pathway alterations and increased abundance of neutrophil-related proteins were observed in patients. Patients progressing to critical illness had significantly low-abundance proteins in the pentose phosphate and glycolysis pathways compared with those presenting clinical recovery. Important biological processes, such as fatty acid concentration and glucose metabolism disorder, remained altered even after 30 days of hospital discharge. Temporal proteomic changes revealed distinct pathways in critically ill and non-critically ill patients. Our study emphasizes the significance of longitudinal cellular proteomic studies in identifying disease progression-related pathways and persistent protein changes post-hospitalization.
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Affiliation(s)
| | - Milena Karina Colo Brunialti
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Paula M. Peçanha-Pietrobom
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Paulo R. Abrão Ferreira
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jaquelina Sonoe Ota-Arakaki
- Division of Respiratory Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Bianca Lima Ferreira
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Graziella E. Ronsein
- Department of Biochemistry, Chemistry Institute, University of São Paulo, SP, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Reinaldo Salomão
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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12
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Werner AD, Schauflinger M, Norris MJ, Klüver M, Trodler A, Herwig A, Brandstädter C, Dillenberger M, Klebe G, Heine A, Saphire EO, Becker K, Becker S. The C-terminus of Sudan ebolavirus VP40 contains a functionally important CX nC motif, a target for redox modifications. Structure 2023; 31:1038-1051.e7. [PMID: 37392738 DOI: 10.1016/j.str.2023.06.004] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 06/06/2023] [Indexed: 07/03/2023]
Abstract
The Ebola virus matrix protein VP40 mediates viral budding and negatively regulates viral RNA synthesis. The mechanisms by which these two functions are exerted and regulated are unknown. Using a high-resolution crystal structure of Sudan ebolavirus (SUDV) VP40, we show here that two cysteines in the flexible C-terminal arm of VP40 form a stabilizing disulfide bridge. Notably, the two cysteines are targets of posttranslational redox modifications and interact directly with the host`s thioredoxin system. Mutation of the cysteines impaired the budding function of VP40 and relaxed its inhibitory role for viral RNA synthesis. In line with these results, the growth of recombinant Ebola viruses carrying cysteine mutations was impaired and the released viral particles were elongated. Our results revealed the exact positions of the cysteines in the C-terminal arm of SUDV VP40. The cysteines and/or their redox status are critically involved in the differential regulation of viral budding and viral RNA synthesis.
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Affiliation(s)
| | | | - Michael J Norris
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Michael Klüver
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Anna Trodler
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Astrid Herwig
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany
| | - Christina Brandstädter
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | | | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Stephan Becker
- Institute for Virology, Philipps-University of Marburg, Marburg, Germany.
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13
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Zinzula L. Ebolavirus VP40 redux. Or rather, redox. Structure 2023; 31:1008-1010. [PMID: 37683615 DOI: 10.1016/j.str.2023.08.010] [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: 08/05/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
The virion protein 40 (VP40) forms the viral matrix, mediates budding, and downregulates viral RNA synthesis in ebolaviruses. In this issue of Structure, Werner et al. present a structure of VP40 from Sudan ebolavirus with a previously unresolved disulfide bridge that enables regulation of VP40 functions via human thioredoxin.
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Affiliation(s)
- Luca Zinzula
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
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14
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Liang X, Li P, Jiang J, Xin J, Luo J, Li J, Chen P, Ren K, Zhou Q, Guo B, Zhou X, Chen J, He L, Yang H, Hu W, Ma S, Li B, Chen X, Shi D, Li J. Transcriptomics unveils immune metabolic disruption and a novel biomarker of mortality in patients with HBV-related acute-on-chronic liver failure. JHEP Rep 2023; 5:100848. [PMID: 37583946 PMCID: PMC10424217 DOI: 10.1016/j.jhepr.2023.100848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/16/2023] [Accepted: 07/01/2023] [Indexed: 08/17/2023] Open
Abstract
Background & Aims HBV-related acute-on-chronic liver failure (HBV-ACLF) is a complex syndrome associated with high short-term mortality. This study aims to reveal the molecular basis and identify novel HBV-ACLF biomarkers. Methods Seventy patients with HBV-ACLF and different short-term (28 days) outcomes underwent transcriptome sequencing using peripheral blood mononuclear cells. Candidate biomarkers were confirmed in two external cohorts using ELISA. Results Cellular composition analysis with peripheral blood mononuclear cell transcriptomics showed that the proportions of monocytes, T cells and natural killer cells were significantly correlated with 28-day mortality. Significant metabolic dysregulation of carbohydrate, energy and amino acid metabolism was observed in ACLF non-survivors. V-set and immunoglobulin domain-containing 4 (VSIG4) was the most robust predictor of patient survival (adjusted p = 1.74 × 10-16; variable importance in the projection = 1.21; AUROC = 0.89) and was significantly correlated with pathways involved in the progression of ACLF, including inflammation, oxidative phosphorylation, tricarboxylic acid cycle and T-cell activation/differentiation. Plasma VSIG4 analysis externally validated its diagnostic value in ACLF (compared with chronic liver disease and healthy groups, AUROC = 0.983). The prognostic performance for 28-/90-day mortality (AUROCs = 0.769/0.767) was comparable to that of three commonly used scores (COSSH-ACLFs, 0.867/0.884; CLIF-C ACLFs, 0.840/0.835; MELD-Na, 0.710/0.737). Plasma VSIG4 level, as an independent predictor, could be used to improve the prognostic performance of clinical scores. Risk stratification based on VSIG4 expression levels (>122 μg/ml) identified patients with ACLF at a high risk of death. The generality of VSIG4 in other etiologies was validated. Conclusions This study reveals that immune-metabolism disorder underlies poor ACLF outcomes. VSIG4 may be helpful as a diagnostic and prognostic biomarker in clinical practice. Impact and implications Acute-on-chronic liver failure (ACLF) is a lethal clinical syndrome associated with high mortality. We found significant immune cell alterations and metabolic dysregulation that were linked to high mortality in patients with HBV-ACLF based on transcriptomics using peripheral blood mononuclear cells. We identified VSIG4 (V-set and immunoglobulin domain-containing 4) as a diagnostic and prognostic biomarker in ACLF, which could specifically identify patients with ACLF at a high risk of death.
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Affiliation(s)
- Xi Liang
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Peng Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jing Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jiaojiao Xin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jinjin Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jiaqi Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Pengcheng Chen
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou, China
| | - Keke Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qian Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Beibei Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xingping Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jiaxian Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Lulu He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Hui Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Wen Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shiwen Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Bingqi Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xin Chen
- Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital, Department of Radiation Oncology, Zhejiang University School of Medicine, Hangzhou, China
- Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
| | - Dongyan Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jun Li
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chinese Group on the Study of Severe Hepatitis B (COSSH)
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou, China
- Institute of Pharmaceutical Biotechnology and the First Affiliated Hospital, Department of Radiation Oncology, Zhejiang University School of Medicine, Hangzhou, China
- Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
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15
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Hussein HA. Brief review on ebola virus disease and one health approach. Heliyon 2023; 9:e19036. [PMID: 37600424 PMCID: PMC10432691 DOI: 10.1016/j.heliyon.2023.e19036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
Ebola virus disease (EVD) is a severe and highly fatal zoonotic disease caused by viruses in the family Filoviridae and genus Ebolavirus. The disease first appeared in Zaire near the Ebola River in 1976, now in the Democratic Republic of the Congo. Since then, several outbreaks have been reported in different parts of the world, mainly in Africa, leading to the identification of six distinct viral strains that cause disease in humans and other primates. Bats are assumed to be the main reservoir hosts of the virus, and the initial incidence of human epidemics invariably follows exposure to infected forest animals through contact or consumption of bush meat and body fluids of forest animals harboring the disease. Human-to-human transmission occurs when contaminated body fluids, utensils, and equipment come in contact with broken or abraded skin and mucous membranes. EVD is characterized by sudden onset of 'flu-like' symptoms (fever, myalgia, chills), vomiting and diarrhea, then disease rapidly evolves into a severe state with a rapid clinical decline which may lead potential hemorrhagic complications and multiple organ failure. Effective EVD prevention, detection, and response necessitate strong coordination across the animal, human, and environmental health sectors, as well as well-defined roles and responsibilities evidencing the significance of one health approach; the natural history, epidemiology, pathogenesis, and diagnostic procedures of the Ebola virus, as well as prevention and control efforts in light of one health approach, are discussed in this article.
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Affiliation(s)
- Hassan Abdi Hussein
- College of Veterinary Medicine, Department of One Health Tropical Infectious Disease, Jigjiga University, P.O. Box: 1020, Jigjiga, Ethiopia
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16
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Gunn BM, McNamara RP, Wood L, Taylor S, Devadhasan A, Guo W, Das J, Nilsson A, Shurtleff A, Dubey S, Eichberg M, Suscovich TJ, Saphire EO, Lauffenburger D, Coller BA, Simon JK, Alter G. Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates. Cell Rep 2023; 42:112402. [PMID: 37061918 PMCID: PMC10576837 DOI: 10.1016/j.celrep.2023.112402] [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: 09/29/2022] [Revised: 01/30/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023] Open
Abstract
The 2013 Ebola epidemic in Central and West Africa heralded the emergence of wide-spread, highly pathogenic viruses. The successful recombinant vector vaccine against Ebola (rVSVΔG-ZEBOV-GP) will limit future outbreaks, but identifying mechanisms of protection is essential to protect the most vulnerable. Vaccine-induced antibodies are key determinants of vaccine efficacy, yet the mechanism by which vaccine-induced antibodies prevent Ebola infection remains elusive. Here, we exploit a break in long-term vaccine efficacy in non-human primates to identify predictors of protection. Using unbiased humoral profiling that captures neutralization and Fc-mediated functions, we find that antibodies specific for soluble glycoprotein (sGP) drive neutrophil-mediated phagocytosis and predict vaccine-mediated protection. Similarly, we show that protective sGP-specific monoclonal antibodies have elevated neutrophil-mediated phagocytic activity compared with non-protective antibodies, highlighting the importance of sGP in vaccine protection and monoclonal antibody therapeutics against Ebola virus.
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Affiliation(s)
- Bronwyn M Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
| | - Lianna Wood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Sabian Taylor
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Wenyu Guo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Avlant Nilsson
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Amy Shurtleff
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | | | | | - Douglas Lauffenburger
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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17
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Tang H, Abouleila Y, Saris A, Shimizu Y, Ottenhoff THM, Mashaghi A. Ebola virus-like particles reprogram cellular metabolism. J Mol Med (Berl) 2023; 101:557-568. [PMID: 36959259 PMCID: PMC10036248 DOI: 10.1007/s00109-023-02309-4] [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: 05/04/2022] [Revised: 02/02/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023]
Abstract
Ebola virus can trigger a release of pro-inflammatory cytokines with subsequent vascular leakage and impairment of clotting finally leading to multiorgan failure and shock after entering and infecting patients. Ebola virus is known to directly target endothelial cells and macrophages, even without infecting them, through direct interactions with viral proteins. These interactions affect cellular mechanics and immune processes, which are tightly linked to other key cellular functions such as metabolism. However, research regarding metabolic activity of these cells upon viral exposure remains limited, hampering our understanding of its pathophysiology and progression. Therefore, in the present study, an untargeted cellular metabolomic approach was performed to investigate the metabolic alterations of primary human endothelial cells and M1 and M2 macrophages upon exposure to Ebola virus-like particles (VLP). The results show that Ebola VLP led to metabolic changes among endothelial, M1, and M2 cells. Differential metabolite abundance and perturbed signaling pathway analysis further identified specific metabolic features, mainly in fatty acid-, steroid-, and amino acid-related metabolism pathways for all the three cell types, in a host cell specific manner. Taken together, this work characterized for the first time the metabolic alternations of endothelial cells and two primary human macrophage subtypes after Ebola VLP exposure, and identified the potential metabolites and pathways differentially affected, highlighting the important role of those host cells in disease development and progression. KEY MESSAGES: • Ebola VLP can lead to metabolic alternations in endothelial cells and M1 and M2 macrophages. • Differential abundance of metabolites, mainly including fatty acids and sterol lipids, was observed after Ebola VLP exposure. • Multiple fatty acid-, steroid-, and amino acid-related metabolism pathways were observed perturbed.
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Affiliation(s)
- Huaqi Tang
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Yasmine Abouleila
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Anno Saris
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
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18
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Bramer LM, Hontz RD, Eisfeld AJ, Sims AC, Kim YM, Stratton KG, Nicora CD, Gritsenko MA, Schepmoes AA, Akasaka O, Koga M, Tsutsumi T, Nakamura M, Nakachi I, Baba R, Tateno H, Suzuki S, Nakajima H, Kato H, Ishida K, Ishii M, Uwamino Y, Mitamura K, Paurus VL, Nakayasu ES, Attah IK, Letizia AG, Waters KM, Metz TO, Corson K, Kawaoka Y, Gerbasi VR, Yotsuyanagi H, Iwatsuki-Horimoto K. Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections. Heliyon 2023; 9:e13795. [PMID: 36915486 PMCID: PMC9988701 DOI: 10.1016/j.heliyon.2023.e13795] [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: 05/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.
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Affiliation(s)
- Lisa M Bramer
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert D Hontz
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy C Sims
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | | | | | - Osamu Akasaka
- Emergency Medical Center, Fujisawa City Hospital 2-6-1 Fujisawa, Fujisawa, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Morio Nakamura
- Department of Pulmonary Medicine, Tokyo Saiseikai Central, Tokyo, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Hiroki Tateno
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Shoji Suzuki
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | | | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, Tokyo, Japan
| | | | | | - Isaac K Attah
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrew G Letizia
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | | | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karen Corson
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.,Department of Microbiology and Immunology, Japan.,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
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19
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Liu B, Cheng L, Gao H, Zhang J, Dong Y, Gao W, Yuan S, Gong T, Huang W. The biology of VSIG4: Implications for the treatment of immune-mediated inflammatory diseases and cancer. Cancer Lett 2023; 553:215996. [PMID: 36343787 DOI: 10.1016/j.canlet.2022.215996] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
V-set and immunoglobulin domain containing 4 (VSIG4), a type I transmembrane receptor exclusively expressed in a subset of tissue-resident macrophages, plays a pivotal role in clearing C3-opsonized pathogens and their byproducts from the circulation. VSIG4 maintains immune homeostasis by suppressing the activation of complement pathways or T cells and inducing regulatory T-cell differentiation, thereby inhibiting the development of immune-mediated inflammatory diseases but enhancing cancer progression. Consequently, VSIG4 exhibits a potential therapeutic effect for immune-mediated inflammatory diseases, but also is regarded as a novel target of immune checkpoint inhibition in cancer therapy. Recently, soluble VSIG4, the extracellular domain of VSIG4, shed from the surface of macrophages, has been found to be a biomarker to define macrophage activation-related diseases. This review mainly summarizes recent new findings of VSIG4 in macrophage phagocytosis and immune homeostasis, and discusses its potential diagnostic and therapeutic usage in infection, inflammation, and cancer.
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Affiliation(s)
- Bei Liu
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China; PLA 307 Clinical College of Anhui Medical University, Beijing, 100071, China
| | - Li Cheng
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Honghao Gao
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Jiale Zhang
- Department of Thoracic Surgery, The Sixth Medical Center of PLA General Hospital, Fuchenglu 6#, Haidian District, Beijing, 100048, China
| | - Yanxin Dong
- Department of Thoracic Surgery, The Sixth Medical Center of PLA General Hospital, Fuchenglu 6#, Haidian District, Beijing, 100048, China
| | - Wenda Gao
- Antagen Institute for Biomedical Research, Boston, MA, 02021, USA
| | - Shunzong Yuan
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China; PLA 307 Clinical College of Anhui Medical University, Beijing, 100071, China.
| | - Taiqian Gong
- Department of Thoracic Surgery, The Sixth Medical Center of PLA General Hospital, Fuchenglu 6#, Haidian District, Beijing, 100048, China.
| | - Wenrong Huang
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China.
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20
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Aydillo T, Gonzalez-Reiche AS, Stadlbauer D, Amper MA, Nair VD, Mariottini C, Sealfon SC, van Bakel H, Palese P, Krammer F, García-Sastre A. Transcriptome signatures preceding the induction of anti-stalk antibodies elicited after universal influenza vaccination. NPJ Vaccines 2022; 7:160. [PMID: 36496417 PMCID: PMC9741632 DOI: 10.1038/s41541-022-00583-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
A phase 1 clinical trial to test the immunogenicity of a chimeric group 1 HA (cHA) universal influenza virus vaccine targeting the conserved stalk domain of the hemagglutinin of influenza viruses was carried out. Vaccination with adjuvanted-inactivated vaccines induced high anti-stalk antibody titers. We sought to identify gene expression signatures that correlate with such induction. Messenger-RNA sequencing in whole blood was performed on the peripheral blood of 53 vaccinees. We generated longitudinal data on the peripheral blood of 53 volunteers, at early (days 3 and 7) and late (28 days) time points after priming and boosting with cHAs. Differentially expressed gene analysis showed no differences between placebo and live-attenuated vaccine groups. However, an upregulation of genes involved in innate immune responses and type I interferon signaling was found at day 3 after vaccination with inactivated adjuvanted formulations. Cell type deconvolution analysis revealed a significant enrichment for monocyte markers and different subsets of dendritic cells as mediators for optimal B cell responses and significant increase of anti-stalk antibodies in sera. A significant upregulation of immunoglobulin-related genes was only observed after administration of adjuvanted vaccines (either as primer or booster) with specific induction of anti-stalk IGVH1-69. This approach informed of specific immune signatures that correlate with robust anti-stalk antibody responses, while also helping to understand the regulation of gene expression induced by cHA proteins under different vaccine regimens.
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Affiliation(s)
- Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna, Cambridge, MA, USA
| | - Mary Anne Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Mariottini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Argemi J, Kedia K, Gritsenko MA, Clemente-Sanchez A, Asghar A, Herranz JM, Liu ZX, Atkinson SR, Smith RD, Norden-Krichmar TM, Day LZ, Stolz A, Tayek JA, Bataller R, Morgan TR, Jacobs JM. Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1658-1669. [PMID: 36243044 PMCID: PMC9765311 DOI: 10.1016/j.ajpath.2022.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/08/2022] [Accepted: 08/31/2022] [Indexed: 11/07/2022]
Abstract
Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent studies have shown that defective function of hepatocyte nuclear factor 4 alpha (HNF4a) and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein, an integrative analysis of hepatic RNA sequencing and liquid chromatography-tandem mass spectrometry was performed to identify plasma protein signatures for patients with mild and severe AH. Alcohol-related liver disease cirrhosis, nonalcoholic fatty liver disease, and healthy subjects were used as comparator groups. Levels of identified proteins primarily involved in hepatocellular function were decreased in patients with AH, which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified, including thrombin, hepatocyte growth factor α, clusterin, human serum factor H-related protein, and kallistatin, which exhibited large abundance shifts between severe and nonsevere AH. The combination of thrombin and hepatocyte growth factor α discriminated between severe and nonsevere AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.
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Affiliation(s)
- Josepmaria Argemi
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Komal Kedia
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co, Inc., West Point, Pennsylvania
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Ana Clemente-Sanchez
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Biomedical Research Networking Center in Hepatic and Digestive Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Aliya Asghar
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California
| | - Jose M Herranz
- Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Zhang-Xu Liu
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Stephen R Atkinson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Trina M Norden-Krichmar
- Department of Epidemiology, School of Medicine, University of California, Irvine, Irvine, California
| | - Le Z Day
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Andrew Stolz
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - John A Tayek
- Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R Morgan
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California.
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington.
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22
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Žarković N, Orehovec B, Baršić B, Tarle M, Kmet M, Lukšić I, Tatzber F, Wonisch W, Skrzydlewska E, Łuczaj W. Lipidomics Revealed Plasma Phospholipid Profile Differences between Deceased and Recovered COVID-19 Patients. Biomolecules 2022; 12:biom12101488. [PMID: 36291697 PMCID: PMC9599609 DOI: 10.3390/biom12101488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 01/08/2023] Open
Abstract
Thorough understanding of metabolic changes, including lipidome alteration, associated with the development of COVID-19 appears to be crucial, as new types of coronaviruses are still reported. In this study, we analyzed the differences in the plasma phospholipid profiles of the deceased COVID-19 patients, those who recovered and healthy people. Due to identified abnormalities in plasma phospholipid profiles, deceased patients were further divided into two subgroups (D1 and D2). Increased levels of phosphatidylethanolamines (PE), phosphatidylcholines (PC) and phosphatidylserines (PS) were found in the plasma of recovered patients and the majority of deceased patients (first subgroup D1) compared to the control group. However, abundances of all relevant PE, PC and PS species decreased dramatically in the plasma of the second subgroup (D2) of five deceased patients. These patients also had significantly decreased plasma COX-2 activity when compared to the control, in contrast to unchanged and increased COX-2 activity in the plasma of the other deceased patients and recovered patients, respectively. Moreover, these five deceased patients were characterized by abnormally low CRP levels and tremendous increase in LDH levels, which may be the result of other pathophysiological disorders, including disorders of the immune system, liver damage and haemolytic anemia. In addition, an observed trend to decrease the autoantibodies against oxidative modifications of low-density lipoprotein (oLAb) titer in all, especially in deceased patients, indicate systemic oxidative stress and altered immune system that may have prognostic value in COVID-19.
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Affiliation(s)
- Neven Žarković
- Ruđer Bošković Institute, Laboratory for Oxidative Stress, 10000 Zagreb, Croatia
- Correspondence:
| | | | - Bruno Baršić
- Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marko Tarle
- Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marta Kmet
- Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Ivica Lukšić
- Clinical Hospital Dubrava, 10000 Zagreb, Croatia
- Department of Pathology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Franz Tatzber
- Omnignostica Ltd., 3421 Höflein an der Donau, Austria
| | | | - Elżbieta Skrzydlewska
- Department of Analytical Chemistry, Medical University of Bialystok, A. Mickiewicza 2D, 15-222 Bialystok, Poland
| | - Wojciech Łuczaj
- Department of Analytical Chemistry, Medical University of Bialystok, A. Mickiewicza 2D, 15-222 Bialystok, Poland
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23
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Occelli C, Guigonis JM, Lindenthal S, Cagnard A, Graslin F, Brglez V, Seitz-Polski B, Dellamonica J, Levraut J, Pourcher T. Untargeted plasma metabolomic fingerprinting highlights several biomarkers for the diagnosis and prognosis of coronavirus disease 19. Front Med (Lausanne) 2022; 9:995069. [PMID: 36250098 PMCID: PMC9556858 DOI: 10.3389/fmed.2022.995069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesThe COVID-19 pandemic has been a serious worldwide public health crisis since 2020 and is still challenging healthcare systems. New tools for the prognosis and diagnosis of COVID-19 patients remain important issues.DesignHere, we studied the metabolome of plasma samples of COVID-19 patients for the identification of prognosis biomarkers.PatientsPlasma samples of eighty-six SARS-CoV-2-infected subjects and 24 healthy controls were collected during the first peak of the COVID-19 pandemic in France in 2020.Main resultsPlasma metabolome fingerprinting allowed the successful discrimination of healthy controls, mild SARS-CoV-2 subjects, and moderate and severe COVID-19 patients at hospital admission. We found a strong effect of SARS-CoV-2 infection on the plasma metabolome in mild cases. Our results revealed that plasma lipids and alterations in their saturation level are important biomarkers for the detection of the infection. We also identified deoxy-fructosyl-amino acids as new putative plasma biomarkers for SARS-CoV-2 infection and COVID-19 severity. Finally, our results highlight a key role for plasma levels of tryptophan and kynurenine in the symptoms of COVID-19 patients.ConclusionOur results showed that plasma metabolome profiling is an efficient tool for the diagnosis and prognosis of SARS-CoV-2 infection.
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Affiliation(s)
- Céline Occelli
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
- Department of Emergency, University Hospital, Nice, France
- School of Medicine, Université Côte d’Azur, Nice, France
| | - Jean-Marie Guigonis
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
| | - Sabine Lindenthal
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
| | - Alexandre Cagnard
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
| | - Fanny Graslin
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
| | - Vesna Brglez
- Unité de Recherche Clinique Côte d’Azur (UR2CA), Université Côte d’Azur, Nice, France
- Department of Immunology, University Hospital, Nice, France
| | - Barbara Seitz-Polski
- School of Medicine, Université Côte d’Azur, Nice, France
- Unité de Recherche Clinique Côte d’Azur (UR2CA), Université Côte d’Azur, Nice, France
- Department of Immunology, University Hospital, Nice, France
| | - Jean Dellamonica
- School of Medicine, Université Côte d’Azur, Nice, France
- Unité de Recherche Clinique Côte d’Azur (UR2CA), Université Côte d’Azur, Nice, France
- Medical Intensive Care Unit, University Hospital, Nice, France
| | - Jacques Levraut
- Department of Emergency, University Hospital, Nice, France
- School of Medicine, Université Côte d’Azur, Nice, France
| | - Thierry Pourcher
- Transporter in Imaging and Radiotherapy in Oncology Laboratory (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Côte d’Azur, School of Medicine, Nice, France
- *Correspondence: Thierry Pourcher,
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24
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Ciccarelli M, Merciai F, Carrizzo A, Sommella E, Di Pietro P, Caponigro V, Salviati E, Musella S, Sarno VD, Rusciano M, Toni AL, Iesu P, Izzo C, Schettino G, Conti V, Venturini E, Vitale C, Scarpati G, Bonadies D, Rispoli A, Polverino B, Poto S, Pagliano P, Piazza O, Licastro D, Vecchione C, Campiglia P. Untargeted lipidomics reveals specific lipid profiles in COVID-19 patients with different severity from Campania region (Italy). J Pharm Biomed Anal 2022; 217:114827. [PMID: 35569273 PMCID: PMC9085356 DOI: 10.1016/j.jpba.2022.114827] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023]
Abstract
COVID-19 infection evokes various systemic alterations that push patients not only towards severe acute respiratory syndrome but causes an important metabolic dysregulation with following multi-organ alteration and potentially poor outcome. To discover novel potential biomarkers able to predict disease's severity and patient's outcome, in this study we applied untargeted lipidomics, by a reversed phase ultra-high performance liquid chromatography-trapped ion mobility mass spectrometry platform (RP-UHPLC-TIMS-MS), on blood samples collected at hospital admission in an Italian cohort of COVID-19 patients (45 mild, 54 severe, 21 controls). In a subset of patients, we also collected a second blood sample in correspondence of clinical phenotype modification (longitudinal population). Plasma lipid profiles revealed several lipids significantly modified in COVID-19 patients with respect to controls and able to discern between mild and severe clinical phenotype. Severe patients were characterized by a progressive decrease in the levels of LPCs, LPC-Os, PC-Os, and, on the contrary, an increase in overall TGs, PEs, and Ceramides. A machine learning model was built by using both the entire dataset and with a restricted lipid panel dataset, delivering comparable results in predicting severity (AUC= 0.777, CI: 0.639-0.904) and outcome (AUC= 0.789, CI: 0.658-0.910). Finally, re-building the model with 25 longitudinal (t1) samples, this resulted in 21 patients correctly classified. In conclusion, this study highlights specific lipid profiles that could be used monitor the possible trajectory of COVID-19 patients at hospital admission, which could be used in targeted approaches.
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Affiliation(s)
- Michele Ciccarelli
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Fabrizio Merciai
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy,PhD Program in Drug Discovery and Development, University of Salerno, Fisciano, SA, Italy
| | - Albino Carrizzo
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy,IRCCS Neuromed, Loc. Camerelle, Pozzilli, IS, Italy
| | - Eduardo Sommella
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Paola Di Pietro
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Vicky Caponigro
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | | | - Simona Musella
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | | | | | - Anna Laura Toni
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Paola Iesu
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Carmine Izzo
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | | | - Valeria Conti
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | | | - Carolina Vitale
- San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Giuliana Scarpati
- San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Domenico Bonadies
- San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Antonella Rispoli
- San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | | | - Sergio Poto
- San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Pasquale Pagliano
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Ornella Piazza
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | | | - Carmine Vecchione
- Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy,IRCCS Neuromed, Loc. Camerelle, Pozzilli, IS, Italy,Corresponding author at: Department of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy,Corresponding author
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Dhanya CR, Shailaja A, Mary AS, Kandiyil SP, Savithri A, Lathakumari VS, Veettil JT, Vandanamthadathil JJ, Madhavan M. RNA Viruses, Pregnancy and Vaccination: Emerging Lessons from COVID-19 and Ebola Virus Disease. Pathogens 2022; 11:800. [PMID: 35890044 PMCID: PMC9322689 DOI: 10.3390/pathogens11070800] [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: 05/26/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Pathogenic viruses with an RNA genome represent a challenge for global human health since they have the tremendous potential to develop into devastating pandemics/epidemics. The management of the recent COVID-19 pandemic was possible to a certain extent only because of the strong foundations laid by the research on previous viral outbreaks, especially Ebola Virus Disease (EVD). A clear understanding of the mechanisms of the host immune response generated upon viral infections is a prime requisite for the development of new therapeutic strategies. Hence, we present here a comparative study of alterations in immune response upon SARS-CoV-2 and Ebola virus infections that illustrate many common features. Vaccination and pregnancy are two important aspects that need to be studied from an immunological perspective. So, we summarize the outcomes and immune responses in vaccinated and pregnant individuals in the context of COVID-19 and EVD. Considering the significance of immunomodulatory approaches in combating both these diseases, we have also presented the state of the art of such therapeutics and prophylactics. Currently, several vaccines against these viruses have been approved or are under clinical trials in various parts of the world. Therefore, we also recapitulate the latest developments in these which would inspire researchers to look for possibilities of developing vaccines against many other RNA viruses. We hope that the similar aspects in COVID-19 and EVD open up new avenues for the development of pan-viral therapies.
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Affiliation(s)
| | - Aswathy Shailaja
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Aarcha Shanmugha Mary
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur 610105, India;
| | | | - Ambili Savithri
- Department of Biochemistry, Sree Narayana College, Kollam 691001, India;
| | | | | | | | - Maya Madhavan
- Department of Biochemistry, Government College for Women, Thiruvananthapuram 695014, India
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26
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Zhao T, Wang C, Duan B, Yang P, Wu J, Zhang Q. Altered Lipid Profile in COVID-19 Patients and Metabolic Reprogramming. Front Microbiol 2022; 13:863802. [PMID: 35633693 PMCID: PMC9133671 DOI: 10.3389/fmicb.2022.863802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/28/2022] [Indexed: 01/09/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is a global pandemic. Previous studies have reported dyslipidemia in patients with COVID-19. Herein, we conducted a retrospective study and a bioinformatics analysis to evaluate the essential data of the lipid profile as well as the possible mechanism in patients with COVID-19. Methods First of all, the retrospective study included three cohorts: patients with COVID-19, a healthy population, and patients with chronic obstructive pulmonary disease (COPD). For each subject, serum lipid profiles in the biochemical data were compared, including triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C). Furthermore, bioinformatics analyses were performed for exploring the biological or immunological mechanisms. Results In line with the biochemical data of the three cohorts, the statistical result displayed that patients with COVID-19 were more likely to have lower levels of TC and HDL-C as compared with healthy individuals. The differential proteins associated with COVID-19 are involved in the lipid pathway and can target and regulate cytokines and immune cells. Additionally, a heatmap revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were possibly involved in lipid metabolic reprogramming. The viral proteins, such as spike (S) and non-structural protein 2 (Nsp2) of SARS-CoV-2, may be involved in metabolic reprogramming. Conclusion The metabolic reprogramming after SARS-CoV-2 infections is probably associated with the immune and clinical phenotype of patients. Hence, metabolic reprogramming may be targeted for developing antivirals against COVID-19.
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Affiliation(s)
- Tie Zhao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, Hengyang Medical College, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Chunhui Wang
- Department of Clinical Laboratory, Huizhou Central People’s Hospital, Huizhou, China
| | - Biyan Duan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Peipei Yang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, China
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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27
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Galão RP, Wilson H, Schierhorn KL, Debeljak F, Bodmer BS, Goldhill D, Hoenen T, Wilson SJ, Swanson CM, Neil SJD. TRIM25 and ZAP target the Ebola virus ribonucleoprotein complex to mediate interferon-induced restriction. PLoS Pathog 2022; 18:e1010530. [PMID: 35533151 PMCID: PMC9119685 DOI: 10.1371/journal.ppat.1010530] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 05/19/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Ebola virus (EBOV) causes highly pathogenic disease in primates. Through screening a library of human interferon-stimulated genes (ISGs), we identified TRIM25 as a potent inhibitor of EBOV transcription-and-replication-competent virus-like particle (trVLP) propagation. TRIM25 overexpression inhibited the accumulation of viral genomic and messenger RNAs independently of the RNA sensor RIG-I or secondary proinflammatory gene expression. Deletion of TRIM25 strongly attenuated the sensitivity of trVLPs to inhibition by type-I interferon. The antiviral activity of TRIM25 required ZAP and the effect of type-I interferon was modulated by the CpG dinucleotide content of the viral genome. We find that TRIM25 interacts with the EBOV vRNP, resulting in its autoubiquitination and ubiquitination of the viral nucleoprotein (NP). TRIM25 is recruited to incoming vRNPs shortly after cell entry and leads to dissociation of NP from the vRNA. We propose that TRIM25 targets the EBOV vRNP, exposing CpG-rich viral RNA species to restriction by ZAP.
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Affiliation(s)
- Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Kristina L. Schierhorn
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Franka Debeljak
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Bianca S. Bodmer
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Daniel Goldhill
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sam J. Wilson
- MRC Centre for Virus Research, University of Glasgow, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, United Kingdom
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28
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Gourronc FA, Rebagliati M, Kramer-Riesberg B, Fleck AM, Patten JJ, Geohegan-Barek K, Messingham KN, Davey RA, Maury W, Klingelhutz AJ. Adipocytes are susceptible to Ebola Virus infection. Virology 2022; 573:12-22. [DOI: 10.1016/j.virol.2022.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
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Abstract
Ebola virus (EBV) disease (EVD) is a highly virulent systemic disease characterized by an aggressive systemic inflammatory response and impaired vascular and coagulation systems, often leading to uncontrolled hemorrhaging and death. In this study, the proteomes of 38 sequential plasma samples from 12 confirmed EVD patients were analyzed. Of these 12 cases, 9 patients received treatment with interferon beta 1a (IFN-β-1a), 8 survived EVD, and 4 died; 2 of these 4 fatalities had received IFN-β-1a. Our analytical strategy combined three platforms targeting different plasma subproteomes: a liquid chromatography-mass spectrometry (LC-MS)-based analysis of the classical plasma proteome, a protocol that combines the depletion of abundant plasma proteins and LC-MS to detect less abundant plasma proteins, and an antibody-based cytokine/chemokine multiplex assay. These complementary platforms provided comprehensive data on 1,000 host and viral proteins. Examination of the early plasma proteomes revealed protein signatures that differentiated between fatalities and survivors. Moreover, IFN-β-1a treatment was associated with a distinct protein signature. Next, we examined those proteins whose abundances reflected viral load measurements and the disease course: resolution or progression. Our data identified a prognostic 4-protein biomarker panel (histone H1-5, moesin, kininogen 1, and ribosomal protein L35 [RPL35]) that predicted EVD outcomes more accurately than the onset viral load. IMPORTANCE As evidenced by the 2013-2016 outbreak in West Africa, Ebola virus (EBV) disease (EVD) poses a major global health threat. In this study, we characterized the plasma proteomes of 12 individuals infected with EBV, using two different LC-MS-based proteomics platforms and an antibody-based multiplexed cytokine/chemokine assay. Clear differences were observed in the host proteome between individuals who survived and those who died, at both early and late stages of the disease. From our analysis, we derived a 4-protein prognostic biomarker panel that may help direct care. Given the ease of implementation, a panel of these 4 proteins or subsets thereof has the potential to be widely applied in an emergency setting in resource-limited regions.
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30
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Masoodi M, Peschka M, Schmiedel S, Haddad M, Frye M, Maas C, Lohse A, Huber S, Kirchhof P, Nofer JR, Renné T. Disturbed lipid and amino acid metabolisms in COVID-19 patients. J Mol Med (Berl) 2022; 100:555-568. [PMID: 35064792 PMCID: PMC8783191 DOI: 10.1007/s00109-022-02177-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is overwhelming the healthcare systems. Identification of systemic reactions underlying COVID-19 will lead to new biomarkers and therapeutic targets for monitoring and early intervention in this viral infection. We performed targeted metabolomics covering up to 630 metabolites within several key metabolic pathways in plasma samples of 20 hospitalized COVID-19 patients and 37 matched controls. Plasma metabolic signatures specifically differentiated severe COVID-19 from control patients. The identified metabolic signatures indicated distinct alterations in both lipid and amino acid metabolisms in COVID-19 compared to control patient plasma. Systems biology-based analyses identified sphingolipid, tryptophan, tyrosine, glutamine, arginine, and arachidonic acid metabolism as mostly impacted pathways in COVID-19 patients. Notably, gamma-aminobutyric acid (GABA) was significantly reduced in COVID-19 patients and GABA plasma levels allowed for stratification of COVID-19 patients with high sensitivity and specificity. The data reveal large metabolic disturbances in COVID-19 patients and suggest use of GABA as potential biomarker and therapeutic target for the infection.
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Affiliation(s)
- Mojgan Masoodi
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Manuela Peschka
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Stefan Schmiedel
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Munif Haddad
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, University, Utrecht, the Netherlands
| | - Ansgar Lohse
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paulus Kirchhof
- Department of Cardiology, University Heart and Vascular Center UKE Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Kiel/Lubeck, Hamburg, Germany
| | - Jerzy-Roch Nofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
- Central Laboratory Facility, University Hospital Münster, Münster, Germany
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany.
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland.
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany.
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Yamaoka S, Ebihara H. Pathogenicity and Virulence of Ebolaviruses with Species- and Variant-specificity. Virulence 2021; 12:885-901. [PMID: 33734027 PMCID: PMC7993122 DOI: 10.1080/21505594.2021.1898169] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 01/05/2023] Open
Abstract
Ebola virus (EBOV), belonging to the species Zaire ebolavirus in the genus Ebolavirus, causes a severe febrile illness in humans with case fatality rates (CFRs) up to 90%. While there have been six virus species classified, which each have a single type virus in the genus Ebolavirus, CFRs of ebolavirus infections vary among viruses belonging to each distinct species. In this review, we aim to define the ebolavirus species-specific virulence on the basis of currently available laboratory and experimental findings. In addition, this review will also cover the variant-specific virulence of EBOV by referring to the unique biological and pathogenic characteristics of EBOV variant Makona, a new EBOV variant isolated from the 2013-2016 EBOV disease outbreak in West Africa. A better definition of species-specific and variant-specific virulence of ebolaviruses will facilitate our comprehensive knowledge on genus Ebolavirus biology, leading to the development of therapeutics against well-focused pathogenic mechanisms of each Ebola disease.
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Affiliation(s)
- Satoko Yamaoka
- Department of Molecular Medicine, Mayo Clinic, Rochester, USA
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, USA
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32
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Leiser OP, Hobbs EC, Sims AC, Korch GW, Taylor KL. Beyond the List: Bioagent-Agnostic Signatures Could Enable a More Flexible and Resilient Biodefense Posture Than an Approach Based on Priority Agent Lists Alone. Pathogens 2021; 10:1497. [PMID: 34832652 PMCID: PMC8623450 DOI: 10.3390/pathogens10111497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 12/23/2022] Open
Abstract
As of 2021, the biothreat policy and research communities organize their efforts around lists of priority agents, which elides consideration of novel pathogens and biotoxins. For example, the Select Agents and Toxins list is composed of agents that historic biological warfare programs had weaponized or that have previously caused great harm during natural outbreaks. Similarly, lists of priority agents promulgated by the World Health Organization and the National Institute of Allergy and Infectious Diseases are composed of previously known pathogens and biotoxins. To fill this gap, we argue that the research/scientific and biodefense/biosecurity communities should categorize agents based on how they impact their hosts to augment current list-based paradigms. Specifically, we propose integrating the results of multi-omics studies to identify bioagent-agnostic signatures (BASs) of disease-namely, patterns of biomarkers that accurately and reproducibly predict the impacts of infection or intoxication without prior knowledge of the causative agent. Here, we highlight three pathways that investigators might exploit as sources of signals to construct BASs and their applicability to this framework. The research community will need to forge robust interdisciplinary teams to surmount substantial experimental, technical, and data analytic challenges that stand in the way of our long-term vision. However, if successful, our functionality-based BAS model could present a means to more effectively surveil for and treat known and novel agents alike.
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Affiliation(s)
- Owen P. Leiser
- Pacific Northwest National Laboratory, Seattle, WA 98109, USA; (O.P.L.); (E.C.H.)
| | - Errett C. Hobbs
- Pacific Northwest National Laboratory, Seattle, WA 98109, USA; (O.P.L.); (E.C.H.)
| | - Amy C. Sims
- Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - George W. Korch
- Battelle National Biodefense Institute, LLC, Fort Detrick, MD 21072, USA;
| | - Karen L. Taylor
- Pacific Northwest National Laboratory, Seattle, WA 98109, USA; (O.P.L.); (E.C.H.)
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33
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Downs I, Johnson JC, Rossi F, Dyer D, Saunders DL, Twenhafel NA, Esham HL, Pratt WD, Trefry J, Zumbrun E, Facemire PR, Johnston SC, Tompkins EL, Jansen NK, Honko A, Cardile AP. Natural History of Aerosol-Induced Ebola Virus Disease in Rhesus Macaques. Viruses 2021; 13:v13112297. [PMID: 34835103 PMCID: PMC8619410 DOI: 10.3390/v13112297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023] Open
Abstract
Ebola virus disease (EVD) is a serious global health concern because case fatality rates are approximately 50% due to recent widespread outbreaks in Africa. Well-defined nonhuman primate (NHP) models for different routes of Ebola virus exposure are needed to test the efficacy of candidate countermeasures. In this natural history study, four rhesus macaques were challenged via aerosol with a target titer of 1000 plaque-forming units per milliliter of Ebola virus. The course of disease was split into the following stages for descriptive purposes: subclinical, clinical, and decompensated. During the subclinical stage, high levels of venous partial pressure of carbon dioxide led to respiratory acidemia in three of four of the NHPs, and all developed lymphopenia. During the clinical stage, all animals had fever, viremia, and respiratory alkalosis. The decompensatory stage involved coagulopathy, cytokine storm, and liver and renal injury. These events were followed by hypotension, elevated lactate, metabolic acidemia, shock and mortality similar to historic intramuscular challenge studies. Viral loads in the lungs of aerosol-exposed animals were not distinctly different compared to previous intramuscularly challenged studies. Differences in the aerosol model, compared to intramuscular model, include an extended subclinical stage, shortened clinical stage, and general decompensated stage. Therefore, the shortened timeframe for clinical detection of the aerosol-induced disease can impair timely therapeutic administration. In summary, this nonhuman primate model of aerosol-induced EVD characterizes early disease markers and additional details to enable countermeasure development.
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Affiliation(s)
- Isaac Downs
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
- Correspondence: ; Tel.: +1-301-619-0369
| | - Joshua C. Johnson
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
- Moderna, Inc., Cambridge, MA 02139, USA
| | - Franco Rossi
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - David Dyer
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - David L. Saunders
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Nancy A. Twenhafel
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Heather L. Esham
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - William D. Pratt
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - John Trefry
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Elizabeth Zumbrun
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Paul R. Facemire
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Sara C. Johnston
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Erin L. Tompkins
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Nathan K. Jansen
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
| | - Anna Honko
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
- Investigator at National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anthony P. Cardile
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; (J.C.J.); (F.R.); (D.D.); (D.L.S.); (N.A.T.); (H.L.E.); (W.D.P.); (J.T.); (E.Z.); (P.R.F.); (S.C.J.); (E.L.T.); (N.K.J.); (A.H.); (A.P.C.)
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Tang Z, Fan W, Li Q, Wang D, Wen M, Wang J, Li X, Zhou Y. MVIP: multi-omics portal of viral infection. Nucleic Acids Res 2021; 50:D817-D827. [PMID: 34718748 PMCID: PMC8689837 DOI: 10.1093/nar/gkab958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
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Affiliation(s)
- Zhidong Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weiliang Fan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qiming Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Miaomiao Wen
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Junhao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xingqiao Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.,RNA Institute, Wuhan University, Wuhan 430072, China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China
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35
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Paparisto E, Hunt NR, Labach DS, Coleman MD, Di Gravio EJ, Dodge MJ, Friesen NJ, Côté M, Müller A, Hoenen T, Barr SD. Interferon-Induced HERC5 Inhibits Ebola Virus Particle Production and Is Antagonized by Ebola Glycoprotein. Cells 2021; 10:cells10092399. [PMID: 34572049 PMCID: PMC8472148 DOI: 10.3390/cells10092399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
Survival following Ebola virus (EBOV) infection correlates with the ability to mount an early and robust interferon (IFN) response. The host IFN-induced proteins that contribute to controlling EBOV replication are not fully known. Among the top genes with the strongest early increases in expression after infection in vivo is IFN-induced HERC5. Using a transcription- and replication-competent VLP system, we showed that HERC5 inhibits EBOV virus-like particle (VLP) replication by depleting EBOV mRNAs. The HERC5 RCC1-like domain was necessary and sufficient for this inhibition and did not require zinc finger antiviral protein (ZAP). Moreover, we showed that EBOV (Zaire) glycoprotein (GP) but not Marburg virus GP antagonized HERC5 early during infection. Our data identify a novel ‘protagonist–antagonistic’ relationship between HERC5 and GP in the early stages of EBOV infection that could be exploited for the development of novel antiviral therapeutics.
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Affiliation(s)
- Ermela Paparisto
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nina R. Hunt
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Daniel S. Labach
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Macon D. Coleman
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Eric J. Di Gravio
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Nicole J. Friesen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
| | - Marceline Côté
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Roger-Guindon Hall Room 4214, Ottawa, ON K1H 8M5 , Canada;
| | - Andreas Müller
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Thomas Hoenen
- Friedrich-Loeffler-Institut, Institute of Molecular Virology and Cell Biology, Südufer 10, 17493 Greifswald—Insel Riems, Germany; (A.M.); (T.H.)
| | - Stephen D. Barr
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, Dental Sciences Building Room 3007, London, ON N6A 5C1, Canada; (E.P.); (N.R.H.); (D.S.L.); (M.D.C.); (E.J.D.G.); (M.J.D.); (N.J.F.)
- Correspondence:
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Leite GGF, Ferreira BL, Tashima AK, Nishiduka ES, Cunha-Neto E, Brunialti MKC, Assuncao M, Azevedo LCP, Freitas F, van der Poll T, Scicluna BP, Salomão R. Combined Transcriptome and Proteome Leukocyte's Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis. Front Immunol 2021; 12:744799. [PMID: 34594344 PMCID: PMC8477441 DOI: 10.3389/fimmu.2021.744799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/24/2021] [Indexed: 01/20/2023] Open
Abstract
Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in "omics" technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co-differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down-regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up-regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host-defense system.
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Affiliation(s)
- Giuseppe Gianini Figueirêdo Leite
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Bianca Lima Ferreira
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Erika Sayuri Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratorio de Imunologia, Instituto do Coracao, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Milena Karina Colo Brunialti
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Murillo Assuncao
- Intensive Care Unit, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Flávio Freitas
- Intensive Care Unit, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P. Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Applied Biomedical Sciences, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Msida, Malta
| | - Reinaldo Salomão
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
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Maroney KJ, Pinski AN, Marzi A, Messaoudi I. Transcriptional Analysis of Infection With Early or Late Isolates From the 2013-2016 West Africa Ebola Virus Epidemic Does Not Suggest Attenuated Pathogenicity as a Result of Genetic Variation. Front Microbiol 2021; 12:714817. [PMID: 34484156 PMCID: PMC8415004 DOI: 10.3389/fmicb.2021.714817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
The 2013-2016 West Africa Ebola virus (EBOV) epidemic caused by the EBOV-Makona isolate is the largest and longest recorded to date. It incurred over 28,000 infections and ∼11,000 deaths. Early in this epidemic, several mutations in viral glycoprotein (A82V), nucleoprotein (R111C), and polymerase L (D759G) emerged and stabilized. In vitro studies of these new EBOV-Makona isolates showed enhanced fitness and viral replication capacity. However, in vivo studies in mice and rhesus macaques did not provide any evidence of enhanced viral fitness or shedding. Infection with late isolates carrying or early isolates lacking (early) these mutations resulted in uniformly lethal disease in nonhuman primates (NHPs), albeit with slightly delayed kinetics with late isolates. The recent report of a possible reemergence of EBOV from a persistent infection in a survivor of the epidemic highlights the urgency for understanding the impact of genetic variation on EBOV pathogenesis. However, potential molecular differences in host responses remain unknown. To address this gap in knowledge, we conducted the first comparative analysis of the host responses to lethal infection with EBOV-Mayinga and EBOV-Makona isolates using bivariate, longitudinal, regression, and discrimination transcriptomic analyses. Our analysis shows a conserved core of differentially expressed genes (DEGs) involved in antiviral defense, immune cell activation, and inflammatory processes in response to EBOV-Makona and EBOV-Mayinga infections. Additionally, EBOV-Makona and EBOV-Mayinga infections could be discriminated based on the expression pattern of a small subset of genes. Transcriptional responses to EBOV-Makona isolates that emerged later during the epidemic, specifically those from Mali and Liberia, lacked signatures of profound lymphopenia and excessive inflammation seen following infection with EBOV-Mayinga and early EBOV-Makona isolate C07. Overall, these findings provide novel insight into the mechanisms underlying the lower case fatality rate (CFR) observed with EBOV-Makona compared to EBOV-Mayinga.
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Affiliation(s)
- Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Rocky Mountain Laboratories, Hamilton, MT, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.,Center for Virus Research, University of California, Irvine, Irvine, CA, United States.,Institute for Immunology, University of California, Irvine, Irvine, CA, United States
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Zhang S, Luo P, Xu J, Yang L, Ma P, Tan X, Chen Q, Zhou M, Song S, Xia H, Wang S, Ma Y, Yang F, Liu Y, Li Y, Ma G, Wang Z, Duan Y, Jin Y. Plasma Metabolomic Profiles in Recovered COVID-19 Patients without Previous Underlying Diseases 3 Months After Discharge. J Inflamm Res 2021; 14:4485-4501. [PMID: 34522117 PMCID: PMC8434912 DOI: 10.2147/jir.s325853] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND It remains unclear whether discharged COVID-19 patients have fully recovered from severe complications, including the differences in the post-infection metabolomic profiles of patients with different disease severities. METHODS COVID-19-recovered patients, who had no previous underlying diseases and were discharged from Wuhan Union Hospital for 3 months, and matched healthy controls (HCs) were recruited in this prospective cohort study. We examined the blood biochemical indicators, cytokines, lung computed tomography scans, including 39 HCs, 18 recovered asymptomatic (RAs), 34 recovered moderate (RMs), and 44 recovered severe/ critical patients (RCs). A liquid chromatography-mass spectrometry-based metabolomics approach was employed to profile the global metabolites of fasting plasma of these participants. RESULTS Clinical data and metabolomic profiles suggested that RAs recovered well, but some clinical indicators and plasma metabolites in RMs and RCs were still abnormal as compared with HCs, such as decreased taurine, succinic acid, hippuric acid, some indoles, and lipid species. The disturbed metabolic pathway mainly involved the tricarboxylic cycle, purine, and glycerophospholipid metabolism. Moreover, metabolite alterations differ between RMs and RCs when compared with HCs. Correlation analysis revealed that many differential metabolites were closely associated with inflammation and the renal, pulmonary, heart, hepatic, and coagulation system functions. CONCLUSION We uncovered metabolite clusters pathologically relevant to the recovery state in discharged COVID-19 patients which may provide new insights into the pathogenesis of potential organ damage in recovered patients.
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Affiliation(s)
- Shujing Zhang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Ping Luo
- Department of Translational Medicine Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Pei Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Xueyun Tan
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Qing Chen
- Health Checkup Department, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Mei Zhou
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Siwei Song
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Hui Xia
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Yanling Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Fan Yang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Yu Liu
- Health Checkup Department, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Yumei Li
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Guanzhou Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Zhihui Wang
- Department of Scientific Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
| | - Yanran Duan
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People’s Republic of China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People’s Republic of China
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Bundibugyo ebolavirus Survival Is Associated with Early Activation of Adaptive Immunity and Reduced Myeloid-Derived Suppressor Cell Signaling. mBio 2021; 12:e0151721. [PMID: 34372693 PMCID: PMC8406165 DOI: 10.1128/mbio.01517-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebolaviruses Bundibugyo virus (BDBV) and Ebola virus (EBOV) cause fatal hemorrhagic disease in humans and nonhuman primates. While the host response to EBOV is well characterized, less is known about BDBV infection. Moreover, immune signatures that mediate natural protection against all ebolaviruses remain poorly defined. To explore these knowledge gaps, we transcriptionally profiled BDBV-infected rhesus macaques, a disease model that results in incomplete lethality. This approach enabled us to identify prognostic indicators. As expected, survival (∼60%) correlated with reduced clinical pathology and circulating infectious virus, although peak viral RNA loads were not significantly different between surviving and nonsurviving macaques. Survivors had higher anti-BDBV antibody titers and transcriptionally derived cytotoxic T cell-, memory B cell-, and plasma cell-type quantities, demonstrating activation of adaptive immunity. Conversely, a poor prognosis was associated with lack of an appropriate adaptive response, sustained innate immune signaling, and higher expression of myeloid-derived suppressor cell (MDSC)-related transcripts (S100A8, S100A9, CEBPB, PTGS2, CXCR1, and LILRA3). MDSCs are potent immunosuppressors of cellular and humoral immunity, and therefore, they represent a potential therapeutic target. Circulating plasminogen activator inhibitor 1 (PAI-1) and tissue plasminogen activator (tPA) levels were also elevated in nonsurvivors and in survivors exhibiting severe illness, emphasizing the importance of maintaining coagulation homeostasis to control disease progression.
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Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. mBio 2021; 12:e0157221. [PMID: 34372702 PMCID: PMC8406233 DOI: 10.1128/mbio.01572-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Tissue- and cell-specific expression patterns are highly variable within and across individuals, leading to altered host responses after acute virus infection. Unraveling key tissue-specific response patterns provides novel opportunities for defining fundamental mechanisms of virus-host interaction in disease and the identification of critical tissue-specific networks for disease intervention in the lung. Currently, there are no approved therapeutics for Middle East respiratory syndrome coronavirus (MERS-CoV) patients, and little is understood about how lung cell types contribute to disease outcomes. MERS-CoV replicates equivalently in primary human lung microvascular endothelial cells (MVE) and fibroblasts (FB) and to equivalent peak titers but with slower replication kinetics in human airway epithelial cell cultures (HAE). However, only infected MVE demonstrate observable virus-induced cytopathic effect. To explore mechanisms leading to reduced MVE viability, donor-matched human lung MVE, HAE, and FB were infected, and their transcriptomes, proteomes, and lipidomes were monitored over time. Validated functional enrichment analysis demonstrated that MERS-CoV-infected MVE were dying via an unfolded protein response (UPR)-mediated apoptosis. Pharmacologic manipulation of the UPR in MERS-CoV-infected primary lung cells reduced viral titers and in male mice improved respiratory function with accompanying reductions in weight loss, pathological signatures of acute lung injury, and times to recovery. Systems biology analysis and validation studies of global kinetic transcript, protein, and lipid data sets confirmed that inhibition of host stress pathways that are differentially regulated following MERS-CoV infection of different tissue types can alleviate symptom progression to end-stage lung disease commonly seen following emerging coronavirus outbreaks.
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Pang H, Jiang Y, Li J, Wang Y, Nie M, Xiao N, Wang S, Song Z, Ji F, Chang Y, Zheng Y, Yao K, Yao L, Li S, Li P, Song L, Lan X, Xu Z, Hu Z. Aberrant NAD + metabolism underlies Zika virus-induced microcephaly. Nat Metab 2021; 3:1109-1124. [PMID: 34385701 DOI: 10.1038/s42255-021-00437-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy can cause microcephaly in newborns, yet the underlying mechanisms remain largely unexplored. Here, we reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multi-omics study comprising transcriptomics, proteomics, phosphoproteomics and metabolomics approaches. Our proteomics and metabolomics analyses uncover dramatic alteration of nicotinamide adenine dinucleotide (NAD+)-related metabolic pathways, including oxidative phosphorylation, TCA cycle and tryptophan metabolism. Phosphoproteomics analysis indicates that MAPK and cyclic GMP-protein kinase G signaling may be associated with ZIKV-induced microcephaly. Notably, we demonstrate the utility of our rich multi-omics datasets with follow-up in vivo experiments, which confirm that boosting NAD+ by NAD+ or nicotinamide riboside supplementation alleviates cell death and increases cortex thickness in ZIKV-infected mouse brains. Nicotinamide riboside supplementation increases the brain and body weight as well as improves the survival in ZIKV-infected mice. Our study provides a comprehensive resource of biological data to support future investigations of ZIKV-induced microcephaly and demonstrates that metabolic alterations can be potentially exploited for developing therapeutic strategies.
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Affiliation(s)
- Huanhuan Pang
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yisheng Jiang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yushen Wang
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China
| | - Meng Nie
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Nan Xiao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihong Song
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Fansen Ji
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yafei Chang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zheng
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - LiAng Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Peng Li
- School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China.
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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Gray N, Lawler NG, Zeng AX, Ryan M, Bong SH, Boughton BA, Bizkarguenaga M, Bruzzone C, Embade N, Wist J, Holmes E, Millet O, Nicholson JK, Whiley L. Diagnostic Potential of the Plasma Lipidome in Infectious Disease: Application to Acute SARS-CoV-2 Infection. Metabolites 2021; 11:467. [PMID: 34357361 PMCID: PMC8306636 DOI: 10.3390/metabo11070467] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 infection, healthy controls, and non-SARS-CoV-2 respiratory infections. Targeted liquid chromatography-mass spectrometry lipid profiling was performed on discovery (20 SARS-CoV-2-positive; 37 healthy controls; 22 COVID-19 symptoms but SARS-CoV-2negative) and validation (312 SARS-CoV-2-positive; 100 healthy controls) cohorts. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and Kruskal-Wallis tests were applied to establish discriminant lipids, significance, and effect size, followed by logistic regression to evaluate classification performance. OPLS-DA reported separation of SARS-CoV-2 infection from healthy controls in the discovery cohort, with an area under the curve (AUC) of 1.000. A refined panel of discriminant features consisted of six lipids from different subclasses (PE, PC, LPC, HCER, CER, and DCER). Logistic regression in the discovery cohort returned a training ROC AUC of 1.000 (sensitivity = 1.000, specificity = 1.000) and a test ROC AUC of 1.000. The validation cohort produced a training ROC AUC of 0.977 (sensitivity = 0.855, specificity = 0.948) and a test ROC AUC of 0.978 (sensitivity = 0.948, specificity = 0.922). The lipid panel was also able to differentiate SARS-CoV-2-positive individuals from SARS-CoV-2-negative individuals with COVID-19-like symptoms (specificity = 0.818). Lipid profiling and multivariate modelling revealed a signature offering mechanistic insights into SARS-CoV-2, with strong predictive power, and the potential to facilitate effective diagnosis and clinical management.
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Affiliation(s)
- Nicola Gray
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Nathan G. Lawler
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Annie Xu Zeng
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Monique Ryan
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Sze How Bong
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Berin A. Boughton
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Maider Bizkarguenaga
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Chiara Bruzzone
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Nieves Embade
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Julien Wist
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Chemistry Department, Universidad del Valle, Cali 76001, Colombia
| | - Elaine Holmes
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Oscar Millet
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Jeremy K. Nicholson
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Institute of Global Health Innovation, Faculty Building South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Luke Whiley
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
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Meyer M, Gunn BM, Malherbe DC, Gangavarapu K, Yoshida A, Pietzsch C, Kuzmina NA, Saphire EO, Collins PL, Crowe JE, Zhu JJ, Suchard MA, Brining DL, Mire CE, Cross RW, Geisbert JB, Samal SK, Andersen KG, Alter G, Geisbert TW, Bukreyev A. Ebola vaccine-induced protection in nonhuman primates correlates with antibody specificity and Fc-mediated effects. Sci Transl Med 2021; 13:eabg6128. [PMID: 34261800 PMCID: PMC8675601 DOI: 10.1126/scitranslmed.abg6128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
Although substantial progress has been made with Ebola virus (EBOV) vaccine measures, the immune correlates of vaccine-mediated protection remain uncertain. Here, five mucosal vaccine vectors based on human and avian paramyxoviruses provided nonhuman primates with varying degrees of protection, despite expressing the same EBOV glycoprotein (GP) immunogen. Each vaccine produced antibody responses that differed in Fc-mediated functions and isotype composition, as well as in magnitude and coverage toward GP and its conformational and linear epitopes. Differences in the degree of protection and comprehensive characterization of the response afforded the opportunity to identify which features and functions were elevated in survivors and could therefore serve as vaccine correlates of protection. Pairwise network correlation analysis of 139 immune- and vaccine-related parameters was performed to demonstrate relationships with survival. Total GP-specific antibodies, as measured by biolayer interferometry, but not neutralizing IgG or IgA titers, correlated with survival. Fc-mediated functions and the amount of receptor binding domain antibodies were associated with improved survival outcomes, alluding to the protective mechanisms of these vaccines. Therefore, functional qualities of the antibody response, particularly Fc-mediated effects and GP specificity, rather than simply magnitude of the response, appear central to vaccine-induced protection against EBOV. The heterogeneity of the response profile between the vaccines indicates that each vaccine likely exhibits its own protective signature and the requirements for an efficacious EBOV vaccine are complex.
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Affiliation(s)
- Michelle Meyer
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, Galveston, TX 77555, USA
| | - Bronwyn M Gunn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Delphine C Malherbe
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, Galveston, TX 77555, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Asuka Yoshida
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, MD 20742, USA
| | - Colette Pietzsch
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, Galveston, TX 77555, USA
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Galveston National Laboratory, Galveston, TX 77555, USA
| | | | - Peter L Collins
- RNA Virology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James J Zhu
- USDA-ARS, FADRU, Plum Island Animal Disease Center, Orient, NY 11957, USA
| | - Marc A Suchard
- Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Douglas L Brining
- Animal Resource Center, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chad E Mire
- Galveston National Laboratory, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert W Cross
- Galveston National Laboratory, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joan B Geisbert
- Galveston National Laboratory, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Siba K Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, MD 20742, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Thomas W Geisbert
- Galveston National Laboratory, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Galveston National Laboratory, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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Pinski AN, Maroney KJ, Marzi A, Messaoudi I. Distinct transcriptional responses to fatal Ebola virus infection in cynomolgus and rhesus macaques suggest species-specific immune responses. Emerg Microbes Infect 2021; 10:1320-1330. [PMID: 34112056 PMCID: PMC8253202 DOI: 10.1080/22221751.2021.1942229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ebola virus (EBOV) is a negative single-stranded RNA virus within the Filoviridae family and the causative agent of Ebola virus disease (EVD). Nonhuman primates (NHPs), including cynomolgus and rhesus macaques, are considered the gold standard animal model to interrogate mechanisms of EBOV pathogenesis. However, despite significant genetic similarity (>90%), NHP species display different clinical presentation following EBOV infection, notably a ∼1-2 days delay in disease progression. Consequently, evaluation of therapeutics is generally conducted in rhesus macaques, whereas cynomolgus macaques are utilized to determine efficacy of preventative treatments, notably vaccines. This observation is in line with reported differences in disease severity and host responses between these two NHP following infection with simian varicella virus, influenza A and SARS-CoV-2. However, the molecular underpinnings of these differential outcomes following viral infections remain poorly defined. In this study, we compared published transcriptional profiles obtained from cynomolgus and rhesus macaques infected with the EBOV-Makona Guinea C07 using bivariate and regression analyses to elucidate differences in host responses. We report the presence of a shared core of differentially expressed genes (DEGs) reflecting EVD pathology, including aberrant inflammation, lymphopenia, and coagulopathy. However, the magnitudes of change differed between the two macaque species. These findings suggest that the differential clinical presentation of EVD in these two species is mediated by altered transcriptional responses.
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Affiliation(s)
- Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA
| | - Kevin J Maroney
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine CA, USA.,Center for Virus Research, University of California Irvine, Irvine, CA, USA.,Institute for Immunology, University of California Irvine, Irvine, CA, USA
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45
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Kyle JE. How lipidomics can transform our understanding of virus infections. Expert Rev Proteomics 2021; 18:329-332. [PMID: 34030561 DOI: 10.1080/14789450.2021.1929177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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46
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Zandstra J, Jongerius I, Kuijpers TW. Future Biomarkers for Infection and Inflammation in Febrile Children. Front Immunol 2021; 12:631308. [PMID: 34079538 PMCID: PMC8165271 DOI: 10.3389/fimmu.2021.631308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 01/08/2023] Open
Abstract
Febrile patients, suffering from an infection, inflammatory disease or autoimmunity may present with similar or overlapping clinical symptoms, which makes early diagnosis difficult. Therefore, biomarkers are needed to help physicians form a correct diagnosis and initiate the right treatment to improve patient outcomes following first presentation or admittance to hospital. Here, we review the landscape of novel biomarkers and approaches of biomarker discovery. We first discuss the use of current plasma parameters and whole blood biomarkers, including results obtained by RNA profiling and mass spectrometry, to discriminate between bacterial and viral infections. Next we expand upon the use of biomarkers to distinguish between infectious and non-infectious disease. Finally, we discuss the strengths as well as the potential pitfalls of current developments. We conclude that the use of combination tests, using either protein markers or transcriptomic analysis, have advanced considerably and should be further explored to improve current diagnostics regarding febrile infections and inflammation. If proven effective when combined, these biomarker signatures will greatly accelerate early and tailored treatment decisions.
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Affiliation(s)
- Judith Zandstra
- Division Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
| | - Ilse Jongerius
- Division Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
| | - Taco W. Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
- Division Research and Landsteiner Laboratory, Department of Blood Cell Research, Sanquin Blood Supply, Amsterdam UMC, Amsterdam, Netherlands
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021; 12:652335. [PMID: 34054532 PMCID: PMC8149611 DOI: 10.3389/fphar.2021.652335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/21/2021] [Indexed: 02/05/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A. Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A. Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M. Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md. Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery. Signal Transduct Target Ther 2021; 6:155. [PMID: 33859163 PMCID: PMC8047575 DOI: 10.1038/s41392-021-00508-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Disease progression prediction and therapeutic drug target discovery for Coronavirus disease 2019 (COVID-19) are particularly important, as there is still no effective strategy for severe COVID-19 patient treatment. Herein, we performed multi-platform omics analysis of serial plasma and urine samples collected from patients during the course of COVID-19. Integrative analyses of these omics data revealed several potential therapeutic targets, such as ANXA1 and CLEC3B. Molecular changes in plasma indicated dysregulation of macrophage and suppression of T cell functions in severe patients compared to those in non-severe patients. Further, we chose 25 important molecular signatures as potential biomarkers for the prediction of disease severity. The prediction power was validated using corresponding urine samples and plasma samples from new COVID-19 patient cohort, with AUC reached to 0.904 and 0.988, respectively. In conclusion, our omics data proposed not only potential therapeutic targets, but also biomarkers for understanding the pathogenesis of severe COVID-19.
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Yan Q, Li P, Ye X, Huang X, Feng B, Ji T, Chen Z, Li F, Zhang Y, Luo K, Chen F, Mo X, Wang J, Feng L, Hu F, Lei C, Qu L, Chen L. Longitudinal Peripheral Blood Transcriptional Analysis Reveals Molecular Signatures of Disease Progression in COVID-19 Patients. THE JOURNAL OF IMMUNOLOGY 2021; 206:2146-2159. [PMID: 33846224 DOI: 10.4049/jimmunol.2001325] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/21/2021] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with some patients developing severe illness or even death. Disease severity has been associated with increased levels of proinflammatory cytokines and lymphopenia. To elucidate the atlas of peripheral immune response and pathways that might lead to immunopathology during COVID-19 disease course, we performed a peripheral blood RNA sequencing analysis of the same patient's samples collected from symptom onset to full recovery. We found that PBMCs at different disease stages exhibited unique transcriptome characteristics. We observed that SARS-CoV-2 infection caused excessive release of inflammatory cytokines and lipid mediators as well as an aberrant increase of low-density neutrophils. Further analysis revealed an increased expression of RNA sensors and robust IFN-stimulated genes expression but a repressed type I IFN production. SARS-CoV-2 infection activated T and B cell responses during the early onset but resulted in transient adaptive immunosuppression during severe disease state. Activation of apoptotic pathways and functional exhaustion may contribute to the reduction of lymphocytes and dysfunction of adaptive immunity, whereas increase in IL2, IL7, and IL15 may facilitate the recovery of the number and function of lymphocytes. Our study provides comprehensive transcriptional signatures of peripheral blood response in patients with moderate COVID-19.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pingchao Li
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Xianmiao Ye
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Tianxing Ji
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Zhilong Chen
- Xiamen Institutes of Respiratory Health, Xiamen, China
| | - Feng Li
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kun Luo
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fengjuan Chen
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Xiaoneng Mo
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Jianhua Wang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Liqiang Feng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fengyu Hu
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Chunliang Lei
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China;
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; .,Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China; and
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50
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Bai Y, Huang W, Li Y, Lai C, Huang S, Wang G, He Y, Hu L, Chen C. Lipidomic alteration of plasma in cured COVID-19 patients using ultra high-performance liquid chromatography with high-resolution mass spectrometry. Biosci Rep 2021; 41:BSR20204305. [PMID: 33635316 PMCID: PMC7937909 DOI: 10.1042/bsr20204305] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The pandemic of novel coronavirus disease 2019 (COVID-19) has become a serious public health crisis worldwide. The symptoms of COVID-19 vary from mild to severe among different age groups, but the physiological changes related to COVID-19 are barely understood. METHODS In the present study, a high-resolution mass spectrometry (HRMS)-based lipidomic strategy was used to characterize the endogenous plasma lipids for cured COVID-19 patients with different ages and symptoms. These patients were further divided into two groups: those with severe symptoms or who were elderly and relatively young patients with mild symptoms. In addition, automated lipidomic identification and alignment was conducted by LipidSearch software. Multivariate and univariate analyses were used for differential comparison. RESULTS Nearly 500 lipid compounds were identified in each cured COVID-19 group through LipidSearch software. At the level of lipid subclasses, patients with severe symptoms or elderly patients displayed dramatic changes in plasma lipidomic alterations, such as increased triglycerides and decreased cholesteryl esters (ChE). Some of these differential lipids might also have essential biological functions. Furthermore, the differential analysis of plasma lipids among groups was performed to provide potential prognostic indicators, and the change in signaling pathways. CONCLUSIONS Dyslipidemia was observed in cured COVID-19 patients due to the viral infection and medical treatment, and the discharged patients should continue to undergo consolidation therapy. This work provides valuable knowledge about plasma lipid markers and potential therapeutic targets of COVID-19 and essential resources for further research on the pathogenesis of COVID-19.
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Affiliation(s)
- Yunpeng Bai
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming 525000, China
| | - Wendong Huang
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
- Department of Cardiology, Maoming People’s Hospital, Maoming 525000, China
| | - Yaocai Li
- Department of Infectious Diseases, Maoming People’s Hospital, Maoming 525000, China
| | - Changchun Lai
- Department of Clinical Laboratory, Maoming People’s Hospital, Maoming 525000, China
| | - Sumei Huang
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
- Biological Resource Center of Maoming People’s Hospital, Maoming 525000, China
| | - Guangwen Wang
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
| | - Yuemei He
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
| | - Linhui Hu
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming 525000, China
| | - Chunbo Chen
- Center of Scientific Research, Maoming People’s Hospital, Maoming 525000, China
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming 525000, China
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