1
|
Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem 2024:10.1038/s41557-024-01601-1. [PMID: 39138346 DOI: 10.1038/s41557-024-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds-termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.
Collapse
Affiliation(s)
- Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | | | | | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | | | | | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | | |
Collapse
|
2
|
Shafqat A, Masters MC, Tripathi U, Tchkonia T, Kirkland JL, Hashmi SK. Long COVID as a disease of accelerated biological aging: An opportunity to translate geroscience interventions. Ageing Res Rev 2024; 99:102400. [PMID: 38945306 DOI: 10.1016/j.arr.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
It has been four years since long COVID-the protracted consequences that survivors of COVID-19 face-was first described. Yet, this entity continues to devastate the quality of life of an increasing number of COVID-19 survivors without any approved therapy and a paucity of clinical trials addressing its biological root causes. Notably, many of the symptoms of long COVID are typically seen with advancing age. Leveraging this similarity, we posit that Geroscience-which aims to target the biological drivers of aging to prevent age-associated conditions as a group-could offer promising therapeutic avenues for long COVID. Bearing this in mind, this review presents a translational framework for studying long COVID as a state of effectively accelerated biological aging, identifying research gaps and offering recommendations for future preclinical and clinical studies.
Collapse
Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Utkarsh Tripathi
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA; Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shahrukh K Hashmi
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Research and Innovation Center, Department of Health, Abu Dhabi, UAE; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
3
|
Essex M, Millet Pascual-Leone B, Löber U, Kuhring M, Zhang B, Brüning U, Fritsche-Guenther R, Krzanowski M, Fiocca Vernengo F, Brumhard S, Röwekamp I, Anna Bielecka A, Lesker TR, Wyler E, Landthaler M, Mantei A, Meisel C, Caesar S, Thibeault C, Corman VM, Marko L, Suttorp N, Strowig T, Kurth F, Sander LE, Li Y, Kirwan JA, Forslund SK, Opitz B. Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19. NPJ Biofilms Microbiomes 2024; 10:66. [PMID: 39085233 PMCID: PMC11291933 DOI: 10.1038/s41522-024-00538-0] [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: 11/10/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.
Collapse
Affiliation(s)
- Morgan Essex
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Belén Millet Pascual-Leone
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mathias Kuhring
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Core Unit Bioinformatics, Berlin, Germany
| | - Bowen Zhang
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ulrike Brüning
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
| | | | - Marta Krzanowski
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Facundo Fiocca Vernengo
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivo Röwekamp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Agata Anna Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Christian Meisel
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra Caesar
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor M Corman
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Lajos Marko
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Till Strowig
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Yang Li
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Jennifer A Kirwan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- University of Nottingham School of Veterinary Medicine and Science, Loughborough, UK
| | - Sofia K Forslund
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bastian Opitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany.
- German Center for Lung Research (DZL), Berlin, Germany.
| |
Collapse
|
4
|
Tsuge M, Ichihara E, Hasegawa K, Kudo K, Tanimoto Y, Nouso K, Oda N, Mitsumune S, Kimura G, Yamada H, Takata I, Mitsuhashi T, Taniguchi A, Tsukahara K, Aokage T, Hagiya H, Toyooka S, Tsukahara H, Maeda Y. Increased Oxidative Stress and Decreased Citrulline in Blood Associated with Severe Novel Coronavirus Pneumonia in Adult Patients. Int J Mol Sci 2024; 25:8370. [PMID: 39125944 PMCID: PMC11313210 DOI: 10.3390/ijms25158370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
This study investigated the correlation between oxidative stress and blood amino acids associated with nitric oxide metabolism in adult patients with coronavirus disease (COVID-19) pneumonia. Clinical data and serum samples were prospectively collected from 100 adult patients hospitalized for COVID-19 between July 2020 and August 2021. Patients with COVID-19 were categorized into three groups for analysis based on lung infiltrates, oxygen inhalation upon admission, and the initiation of oxygen therapy after admission. Blood data, oxidative stress-related biomarkers, and serum amino acid levels upon admission were compared in these groups. Patients with lung infiltrations requiring oxygen therapy upon admission or starting oxygen post-admission exhibited higher serum levels of hydroperoxides and lower levels of citrulline compared to the control group. No remarkable differences were observed in nitrite/nitrate, asymmetric dimethylarginine, and arginine levels. Serum citrulline levels correlated significantly with serum lactate dehydrogenase and C-reactive protein levels. A significant negative correlation was found between serum levels of citrulline and hydroperoxides. Levels of hydroperoxides decreased, and citrulline levels increased during the recovery period compared to admission. Patients with COVID-19 with extensive pneumonia or poor oxygenation showed increased oxidative stress and reduced citrulline levels in the blood compared to those with fewer pulmonary complications. These findings suggest that combined oxidative stress and abnormal citrulline metabolism may play a role in the pathogenesis of COVID-19 pneumonia.
Collapse
Affiliation(s)
- Mitsuru Tsuge
- Department of Pediatrics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Eiki Ichihara
- Department of Allergy and Respiratory Medicine, Okayama University Hospital, Okayama 700-8558, Japan; (E.I.); (A.T.)
| | - Kou Hasegawa
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (K.H.); (H.H.)
| | - Kenichiro Kudo
- Department of Respiratory Medicine, National Hospital Organization Minami-Okayama Medical Center, Okayama 701-1192, Japan; (K.K.); (S.M.)
| | - Yasushi Tanimoto
- Department of Allergy and Respiratory Medicine, National Hospital Organization Minami-Okayama Medical Center, Okayama 701-0304, Japan; (Y.T.); (G.K.)
| | - Kazuhiro Nouso
- Department of Gastroenterology, Okayama City Hospital, Okayama 700-0962, Japan;
| | - Naohiro Oda
- Department of Internal Medicine, Fukuyama City Hospital, Fukuyama 721-0971, Japan; (N.O.); (I.T.)
| | - Sho Mitsumune
- Department of Respiratory Medicine, National Hospital Organization Minami-Okayama Medical Center, Okayama 701-1192, Japan; (K.K.); (S.M.)
| | - Goro Kimura
- Department of Allergy and Respiratory Medicine, National Hospital Organization Minami-Okayama Medical Center, Okayama 701-0304, Japan; (Y.T.); (G.K.)
| | - Haruto Yamada
- Department of Infectious Disease, Okayama City Hospital, Okayama 700-0962, Japan;
| | - Ichiro Takata
- Department of Internal Medicine, Fukuyama City Hospital, Fukuyama 721-0971, Japan; (N.O.); (I.T.)
| | - Toshiharu Mitsuhashi
- Center for Innovative Clinical Medicine, Okayama University Hospital, Okayama 700-8558, Japan;
| | - Akihiko Taniguchi
- Department of Allergy and Respiratory Medicine, Okayama University Hospital, Okayama 700-8558, Japan; (E.I.); (A.T.)
| | - Kohei Tsukahara
- Department of Emergency, Critical Care and Disaster Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (K.T.); (T.A.)
| | - Toshiyuki Aokage
- Department of Emergency, Critical Care and Disaster Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (K.T.); (T.A.)
| | - Hideharu Hagiya
- Department of General Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (K.H.); (H.H.)
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrine Surgery, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Hirokazu Tsukahara
- Department of Pediatrics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Yoshinobu Maeda
- Department of Hematology, Oncology and Respiratory Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| |
Collapse
|
5
|
Sevim Bayrak C, Forst CV, Jones DR, Gresham DJ, Pushalkar S, Wu S, Vogel C, Mahal LK, Ghedin E, Ross T, García-Sastre A, Zhang B. Patient subtyping analysis of baseline multi-omic data reveals distinct pre-immune states associated with antibody response to seasonal influenza vaccination. Clin Immunol 2024; 266:110333. [PMID: 39089348 DOI: 10.1016/j.clim.2024.110333] [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: 06/18/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/03/2024]
Abstract
Understanding the molecular mechanisms underpinning diverse vaccination responses is critical for developing efficient vaccines. Molecular subtyping can offer insights into heterogeneous nature of responses and aid in vaccine design. We analyzed multi-omic data from 62 haemagglutinin seasonal influenza vaccine recipients (2019-2020), including transcriptomics, proteomics, glycomics, and metabolomics data collected pre-vaccination. We performed a subtyping analysis on the integrated data revealing five subtypes with distinct molecular signatures. These subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining the effectiveness of seasonal vaccines. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.
Collapse
Affiliation(s)
- Cigdem Sevim Bayrak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Microbiology, Icahn School of Medicine at Mt Sinai, New York, NY, USA
| | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, NY, New York, USA
| | - David J Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Smruti Pushalkar
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Shaohuan Wu
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Ted Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA; Department of Infectious Diseases, University of Georgia, Athens, GA, 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 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
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt Sinai, New York, NY, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
6
|
Hawryłkowicz V, Stasiewicz B, Maciejewska D, Sołek-Pastuszka J, Komorniak N, Skonieczna-Żydecka K, Martynova-Van Kley A, Stachowska E. The Link between Inflammation, Lipid Derivatives, and Microbiota Metabolites in COVID-19 Patients: Implications on Eating Behaviors and Nutritional Status. Int J Mol Sci 2024; 25:7899. [PMID: 39063142 PMCID: PMC11276903 DOI: 10.3390/ijms25147899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Extreme inflammation that continues even after infections can lead to a cytokine storm. In recent times, one of the most common causes of cytokine storm activation has been SARS-CoV-2 infection. A cytokine storm leads to dysregulation and excessive stimulation of the immune system, producing symptoms typical of post-COVID syndrome, including chronic fatigue, shortness of breath, joint pain, trouble concentrating (known as "brain fog"), and even direct organ damage in the heart, lungs, kidneys, and brain. This work summarizes the current knowledge regarding inflammation and the cytokine storm related to SARS-CoV-2 infection. Additionally, changes in lipid metabolism and microbiota composition under the influence of inflammation in COVID-19, along with the possible underlying mechanisms, are described. Finally, this text explores potential health implications related to changes in eating behaviors and nutritional status in COVID-19 patients. Although research on the cytokine storm is still ongoing, there is convincing evidence suggesting that severe immune and inflammatory responses during the acute phase of COVID-19 may lead to long-term health consequences. Understanding these links is key to developing treatment strategies and supporting patients after infection.
Collapse
Affiliation(s)
- Viktoria Hawryłkowicz
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland; (V.H.); (D.M.); (N.K.)
| | - Beata Stasiewicz
- Department of Human Nutrition, The Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Sloneczna 45f, 10-718 Olsztyn, Poland
| | - Dominika Maciejewska
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland; (V.H.); (D.M.); (N.K.)
| | - Joanna Sołek-Pastuszka
- Department of Anesthesiology and Intensive Care, Pomeranian Medical University, 71-242 Szczecin, Poland;
| | - Natalia Komorniak
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland; (V.H.); (D.M.); (N.K.)
| | | | | | - Ewa Stachowska
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland; (V.H.); (D.M.); (N.K.)
| |
Collapse
|
7
|
Agamah FE, Ederveen THA, Skelton M, Martin DP, Chimusa ER, ’t Hoen PAC. Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases. Front Mol Biosci 2024; 11:1393240. [PMID: 39040605 PMCID: PMC11260748 DOI: 10.3389/fmolb.2024.1393240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/24/2024] Open
Abstract
Background COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. Aim To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. Method We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Results Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state. Conclusion This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.
Collapse
Affiliation(s)
- Francis E. Agamah
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Science, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
| |
Collapse
|
8
|
Bouzari B, Chugaeva UY, Karampoor S, Mirzaei R. Immunometabolites in viral infections: Action mechanism and function. J Med Virol 2024; 96:e29807. [PMID: 39037069 DOI: 10.1002/jmv.29807] [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: 01/18/2024] [Revised: 05/10/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
The interplay between viral pathogens and host metabolism plays a pivotal role in determining the outcome of viral infections. Upon viral detection, the metabolic landscape of the host cell undergoes significant changes, shifting from oxidative respiration via the tricarboxylic acid (TCA) cycle to increased aerobic glycolysis. This metabolic shift is accompanied by elevated nutrient accessibility, which is vital for cell function, development, and proliferation. Furthermore, depositing metabolites derived from fatty acids, TCA intermediates, and amino acid catabolism accelerates the immunometabolic transition, facilitating pro-inflammatory and antimicrobial responses. Immunometabolites refer to small molecules involved in cellular metabolism regulating the immune response. These molecules include nutrients, such as glucose and amino acids, along with metabolic intermediates and signaling molecules adenosine, lactate, itaconate, succinate, kynurenine, and prostaglandins. Emerging evidence suggests that immunometabolites released by immune cells establish a complex interaction network within local niches, orchestrating and fine-tuning immune responses during viral diseases. However, our current understanding of the immense capacity of metabolites to convey essential cell signals from one cell to another or within cellular compartments remains incomplete. Unraveling these complexities would be crucial for harnessing the potential of immunometabolites in therapeutic interventions. In this review, we discuss specific immunometabolites and their mechanisms of action in viral infections, emphasizing recent findings and future directions in this rapidly evolving field.
Collapse
Affiliation(s)
- Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Uliana Y Chugaeva
- Department of Pediatric, Preventive Dentistry and Orthodontics, Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
9
|
Buchynskyi M, Oksenych V, Kamyshna I, Vorobets I, Halabitska I, Kamyshnyi O. Modulatory Roles of AHR, FFAR2, FXR, and TGR5 Gene Expression in Metabolic-Associated Fatty Liver Disease and COVID-19 Outcomes. Viruses 2024; 16:985. [PMID: 38932276 PMCID: PMC11209102 DOI: 10.3390/v16060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is a risk factor for severe COVID-19. This study explores the potential influence of gut hormone receptor and immune response gene expression on COVID-19 outcomes in MAFLD patients. METHODS We investigated gene expression levels of AHR, FFAR2, FXR, and TGR5 in patients with MAFLD and COVID-19 compared to controls. We examined associations between gene expression and clinical outcomes. RESULTS COVID-19 patients displayed altered AHR expression, potentially impacting immune response and recovery. Downregulated AHR in patients with MAFLD correlated with increased coagulation parameters. Elevated FFAR2 expression in patients with MAFLD was linked to specific immune cell populations and hospital stay duration. A significantly lower FXR expression was observed in both MAFLD and severe COVID-19. CONCLUSION Our findings suggest potential modulatory roles for AHR, FFAR2, and FXR in COVID-19 and MAFLD.
Collapse
Affiliation(s)
- Mykhailo Buchynskyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Iryna Kamyshna
- Department of Medical Rehabilitation, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Ihor Vorobets
- Ophthalmology Clinic “Vizex”, Naukova St. 96B, 79060 Lviv, Ukraine
| | - Iryna Halabitska
- Department of Therapy and Family Medicine, I. Horbachevsky Ternopil National Medical University, Voli Square, 1, 46001 Ternopil, Ukraine;
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| |
Collapse
|
10
|
Wang X, Mei J, Zhang F, Wei M, Xie Y, Bayoude A, Liu X, Zhang B, Yu B. A ternary correlation multi-symptom network strategy based on in vivo chemical profile identification and metabolomics to explore the molecular basis of Ephedra herb against viral pneumonia. J Sep Sci 2024; 47:e2400090. [PMID: 38819782 DOI: 10.1002/jssc.202400090] [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: 02/01/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024]
Abstract
Ephedra herb (EH), an important medicine prescribed in herbal formulas by Traditional Chinese Medicine practitioners, has been widely used in the treatment of viral pneumonia in China. However, the molecular basis of EH in viral pneumonia remains unclear. In this study, a ternary correlation multi-symptom network strategy was established based on in vivo chemical profile identification and metabolomics to explore the molecular basis of EH against viral pneumonia. Results showed that 143 compounds of EH and 70 prototype components were identified in vivo. EH could reduce alveolar-capillary barrier disruption in rats with viral pneumonia and significantly downregulate the expression of inflammatory factors and bronchoalveolar lavage fluid. Plasma metabolomics revealed that EH may be involved in the regulation of arachidonic acid, tryptophan, tyrosine, nicotinate, and nicotinamide metabolism. The multi-symptom network showed that 12 compounds have an integral function in the treatment of viral pneumonia by intervening in many pathways related to viruses, immunity and inflammation, and lung injury. Further verification demonstrated that sinapic acid and frambinone can regulate the expression of related genes. It has been shown to be a promising representative of the pharmacological constituents of ephedra.
Collapse
Affiliation(s)
- Xiaoyan Wang
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Jie Mei
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Fan Zhang
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Miaomiao Wei
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Yujun Xie
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Alamusi Bayoude
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Xiufeng Liu
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Research Center for Traceability and Standardization of TCMs, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| | - Boli Zhang
- State Key Laboratory of Component-Based Chinese Medicine, School of Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Boyang Yu
- State Key Laboratory of Natural Medicines, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
- Research Center for Traceability and Standardization of TCMs, School of Chinese Materia Medica, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
11
|
Zhang J, Liu Y, Zhi X, Xu L, Tao J, Cui D, Liu TF. Tryptophan catabolism via the kynurenine pathway regulates infection and inflammation: from mechanisms to biomarkers and therapies. Inflamm Res 2024; 73:979-996. [PMID: 38592457 DOI: 10.1007/s00011-024-01878-5] [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: 12/06/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND L-Tryptophan (L-Trp), an essential amino acid, is the only amino acid whose level is regulated specifically by immune signals. Most proportions of Trp are catabolized via the kynurenine (Kyn) pathway (KP) which has evolved to align the food availability and environmental stimulation with the host pathophysiology and behavior. Especially, the KP plays an indispensable role in balancing the immune activation and tolerance in response to pathogens. SCOPE OF REVIEW In this review, we elucidate the underlying immunological regulatory network of Trp and its KP-dependent catabolites in the pathophysiological conditions by participating in multiple signaling pathways. Furthermore, the KP-based regulatory roles, biomarkers, and therapeutic strategies in pathologically immune disorders are summarized covering from acute to chronic infection and inflammation. MAJOR CONCLUSIONS The immunosuppressive effects dominate the functions of KP induced-Trp depletion and KP-produced metabolites during infection and inflammation. However, the extending minor branches from the KP are not confined to the immune tolerance, instead they go forward to various functions according to the specific condition. Nevertheless, persistent efforts should be made before the clinical use of KP-based strategies to monitor and cure infectious and inflammatory diseases.
Collapse
Affiliation(s)
- Jingpu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China.
| | - Yanlei Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xiao Zhi
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, People's Republic of China
| | - Li Xu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China
| | - Jie Tao
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Tie Fu Liu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Highway, Shanghai, 201508, People's Republic of China.
| |
Collapse
|
12
|
Chao AS, Lin CY, Chiang MH, Lu KY, Tsai CK, Chen KJ, Chien CW, Wu TS, Chang YL, Chao A, Lin G, Chiu CY. Metabolomic profiling of maternal plasma identifies inverse associations of acetate and urea with anti-SARS-CoV-2 antibody titers following COVID-19 vaccination during pregnancy. J Mol Med (Berl) 2024; 102:819-830. [PMID: 38568327 DOI: 10.1007/s00109-024-02438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 05/21/2024]
Abstract
We conducted a comprehensive metabolomic analysis of plasma samples obtained from pregnant women who displayed varying post-vaccination antibody titers after receiving mRNA-1273-SARS-CoV-2 vaccines. The study involved 62 pregnant women, all of whom had been vaccinated after reaching 24 weeks of gestation. To quantify post-vaccination plasma antibody titers, we employed binding antibody units (BAU) in accordance with the World Health Organization International Standard. Subsequently, we classified the study participants into three distinct BAU/mL categories: those with high titers (above 2000), medium titers (ranging from 1000 to 2000), and low titers (below 1000). Plasma metabolomic profiling was conducted using 1H nuclear magnetic resonance spectroscopy, and the obtained data were correlated with the categorized antibody titers. Notably, in pregnant women exhibiting elevated anti-SARS-CoV-2 antibody titers, reduced plasma concentrations of acetate and urea were observed. A significant negative correlation between these compounds and antibody titers was also evident. An analysis of metabolomics pathways revealed significant inverse associations between antibody titers and four distinct amino acid metabolic pathways: (1) biosynthesis of phenylalanine, tyrosine, and tryptophan; (2) biosynthesis of valine, leucine, and isoleucine; (3) phenylalanine metabolism; and (4) degradation of valine, leucine, and isoleucine. Additionally, an association between the synthesis and degradation pathways of ketone bodies was evident. In conclusion, we identified different metabolic pathways that underlie the diverse humoral responses triggered by COVID-19 mRNA vaccines during pregnancy. Our data hold significant implications for refining COVID-19 vaccination approaches in expectant mothers. KEY MESSAGES : Anti-SARS-CoV-2 antibody titers decline as the number of days since COVID-19 vaccination increases. Anti-SARS-CoV-2 antibody titers are inversely associated with acetate, a microbial-derived metabolite, and urea. Amino acid metabolism is significantly associated with SARS-CoV-2 antibody titers.
Collapse
Affiliation(s)
- An-Shine Chao
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan.
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Meng-Han Chiang
- Clinical Metabolomics Core Lab, Chang , Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kuan-Ying Lu
- Clinical Metabolomics Core Lab, Chang , Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Cheng-Kun Tsai
- Clinical Metabolomics Core Lab, Chang , Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kuan-Ju Chen
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chih-Wei Chien
- Department of Obstetrics and Gynecology, New Taipei Municipal Tu Cheng Hospital, New Taipei City, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ting-Shu Wu
- Department of Infectious Control, Chang , Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yao-Lung Chang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Angel Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Gigin Lin
- Clinical Metabolomics Core Lab, Chang , Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Department of Medical Imaging and Intervention and Institute for Radiological Research, Chang Gung Memorial Hospital at Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yung Chiu
- Clinical Metabolomics Core Lab, Chang , Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
- Division of Pediatric Pulmonology, Department of Pediatrics, Chang , Gung Memorial Hospital at Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan.
| |
Collapse
|
13
|
Dehhaghi M, Heydari M, Panahi HKS, Lewin SR, Heng B, Brew BJ, Guillemin GJ. The roles of the kynurenine pathway in COVID-19 neuropathogenesis. Infection 2024:10.1007/s15010-024-02293-y. [PMID: 38802702 DOI: 10.1007/s15010-024-02293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly contagious respiratory disease Corona Virus Disease 2019 (COVID-19) that may lead to various neurological and psychological disorders that can be acute, lasting days to weeks or months and possibly longer. The latter is known as long-COVID or more recently post-acute sequelae of COVID (PASC). During acute COVID-19 infection, a strong inflammatory response, known as the cytokine storm, occurs in some patients. The levels of interferon-γ (IFN-γ), interferon-β (IFN-β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are particularly increased. These cytokines are known to activate the enzyme indoleamine 2,3-dioxygenase 1 (IDO-1), catalysing the first step of tryptophan (Trp) catabolism through the kynurenine pathway (KP) leading to the production of several neurotoxic and immunosuppressive metabolites. There is already data showing elevation in KP metabolites both acutely and in PASC, especially regarding cognitive impairment. Thus, it is likely that KP involvement is significant in SARS-CoV-2 pathogenesis especially neurologically.
Collapse
Affiliation(s)
- Mona Dehhaghi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mostafa Heydari
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Hamed Kazemi Shariat Panahi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, VIC, Australia
| | - Benjamin Heng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Bruce J Brew
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW Sydney, NSW, Australia.
- Departments of Neurology and Immunology, St. Vincent's Hospital, Sydney, NSW, Australia.
- University of Notre Dame, Darlinghurst, Sydney, NSW, Australia.
| | - Gilles J Guillemin
- Peter Duncan Neurosciences Unit, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor University, Bogor, Indonesia
| |
Collapse
|
14
|
Abdallah AM, Doudin A, Sulaiman TO, Jamil O, Arif R, Sada FA, Yassine HM, Elrayess MA, Elzouki AN, Emara MM, Thillaiappan NB, Cyprian FS. Metabolic predictors of COVID-19 mortality and severity: a survival analysis. Front Immunol 2024; 15:1353903. [PMID: 38799469 PMCID: PMC11127595 DOI: 10.3389/fimmu.2024.1353903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The global healthcare burden of COVID-19 pandemic has been unprecedented with a high mortality. Metabolomics, a powerful technique, has been increasingly utilized to study the host response to infections and to understand the progression of multi-system disorders such as COVID-19. Analysis of the host metabolites in response to SARS-CoV-2 infection can provide a snapshot of the endogenous metabolic landscape of the host and its role in shaping the interaction with SARS-CoV-2. Disease severity and consequently the clinical outcomes may be associated with a metabolic imbalance related to amino acids, lipids, and energy-generating pathways. Hence, the host metabolome can help predict potential clinical risks and outcomes. Methods In this prospective study, using a targeted metabolomics approach, we studied the metabolic signature in 154 COVID-19 patients (males=138, age range 48-69 yrs) and related it to disease severity and mortality. Blood plasma concentrations of metabolites were quantified through LC-MS using MxP Quant 500 kit, which has a coverage of 630 metabolites from 26 biochemical classes including distinct classes of lipids and small organic molecules. We then employed Kaplan-Meier survival analysis to investigate the correlation between various metabolic markers, disease severity and patient outcomes. Results A comparison of survival outcomes between individuals with high levels of various metabolites (amino acids, tryptophan, kynurenine, serotonin, creatine, SDMA, ADMA, 1-MH and carnitine palmitoyltransferase 1 and 2 enzymes) and those with low levels revealed statistically significant differences in survival outcomes. We further used four key metabolic markers (tryptophan, kynurenine, asymmetric dimethylarginine, and 1-Methylhistidine) to develop a COVID-19 mortality risk model through the application of multiple machine-learning methods. Conclusions Metabolomics analysis revealed distinct metabolic signatures among different severity groups, reflecting discernible alterations in amino acid levels and perturbations in tryptophan metabolism. Notably, critical patients exhibited higher levels of short chain acylcarnitines, concomitant with higher concentrations of SDMA, ADMA, and 1-MH in severe cases and non-survivors. Conversely, levels of 3-methylhistidine were lower in this context.
Collapse
Affiliation(s)
| | - Asmma Doudin
- Biomedical Research Center (BRC), Qatar University, Doha, Qatar
| | - Theeb Osama Sulaiman
- Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Omar Jamil
- Department of Radiology, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Rida Arif
- Emergency Medicine Department, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Fatima Al Sada
- Neurosurgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Hadi M. Yassine
- Biomedical Research Center (BRC), Qatar University, Doha, Qatar
| | - Mohamed A. Elrayess
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
- Biomedical Research Center (BRC), Qatar University, Doha, Qatar
| | - Abdel-Naser Elzouki
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
- Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Mohamed M. Emara
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
| | | | - Farhan S. Cyprian
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
| |
Collapse
|
15
|
Fongsaran C, Dineley KT, Paessler S, Cisneros IE. VEEV TC-83 Triggers Dysregulation of the Tryptophan-Kynurenine Pathway in the Central Nervous System That Correlates with Cognitive Impairment in Tg2576 Mice. Pathogens 2024; 13:397. [PMID: 38787249 PMCID: PMC11124172 DOI: 10.3390/pathogens13050397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Neurodegenerative diseases are chronic conditions affecting the central nervous system (CNS). Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of amyloid beta in the limbic and cortical brain regions. AD is presumed to result from genetic abnormalities or environmental factors, including viral infections, which may have deleterious, long-term effects. In this study, we demonstrate that the Venezuelan equine encephalitis virus (VEEV) commonly induces neurodegeneration and long-term neurological or cognitive sequelae. Notably, the effects of VEEV infection can persistently influence gene expression in the mouse brain, suggesting a potential link between the observed neurodegenerative outcomes and long-term alterations in gene expression. Additionally, we show that alphavirus encephalitis exacerbates the neuropathological profile of AD through crosstalk between inflammatory and kynurenine pathways, generating a range of metabolites with potent effects. Using a mouse model for β-amyloidosis, Tg2576 mice, we found that cognitive deficits and brain pathology were more severe in Tg2576 mice infected with VEEV TC-83 compared to mock-infected controls. Thus, during immune activation, the kynurenine pathway plays a more active role in the VEEV TC-83-infected cells, leading to increases in the abundance of transcripts related to the kynurenine pathway of tryptophan metabolism. This pathway generates several metabolites with potent effects on neurotransmitter systems as well as on inflammation, as observed in VEEV TC-83-infected animals.
Collapse
Affiliation(s)
- Chanida Fongsaran
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (C.F.); (S.P.)
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Neuroinfectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Kelly T. Dineley
- Neuroinfectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (C.F.); (S.P.)
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Neuroinfectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Irma E. Cisneros
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (C.F.); (S.P.)
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Neuroinfectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
16
|
Ji X, Ji HL. Metabolic signatures of acute respiratory distress syndrome: COVID versus non-COVID. Am J Physiol Lung Cell Mol Physiol 2024; 326:L596-L603. [PMID: 38469648 DOI: 10.1152/ajplung.00266.2023] [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: 09/27/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a fatal pulmonary disorder characterized by severe hypoxia and inflammation. ARDS is commonly triggered by systemic and pulmonary infections, with bacteria and viruses. Notable pathogens include Pseudomonas aeruginosa, Streptococcus aureus, Enterobacter species, coronaviruses, influenza viruses, and herpesviruses. COVID-19 ARDS represents the latest etiological phenotype of the disease. The pathogenesis of ARDS caused by bacteria and viruses exhibits variations in host immune responses and lung mesenchymal injury. We postulate that the systemic and pulmonary metabolomics profiles of ARDS induced by COVID-19 pathogens may exhibit distinctions compared with those induced by other infectious agents. This review aims to compare metabolic signatures in blood and lung specimens specifically within the context of ARDS. Both prevalent and phenotype-specific metabolomic signatures, including but not limited to glycolysis, ketone body production, lipid oxidation, and dysregulation of the kynurenine pathways, were thoroughly examined in this review. The distinctions in metabolic signatures between COVID-19 and non-COVID ARDS have the potential to reveal new biomarkers, elucidate pathogenic mechanisms, identify druggable targets, and facilitate differential diagnosis in the future.
Collapse
Affiliation(s)
- Xiangming Ji
- Department of Nutrition, Georgia State University, Atlanta, Georgia, United States
| | - Hong-Long Ji
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
| |
Collapse
|
17
|
Lopuhaä BV, Guzel C, van der Lee A, van den Bosch TPP, van Kemenade FJ, Huisman MV, Kruip MJHA, Luider TM, von der Thüsen JH. Increase in venous thromboembolism in SARS-CoV-2 infected lung tissue: proteome analysis of lung parenchyma, isolated endothelium, and thrombi. Histopathology 2024; 84:967-982. [PMID: 38253958 DOI: 10.1111/his.15143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
AIMS COVID-19 pneumonia is characterized by an increased rate of deep venous thrombosis and pulmonary embolism. To better understand the pathophysiology behind thrombosis in COVID-19, we performed proteomics analysis on SARS-CoV-2 infected lung tissue. METHODS Liquid chromatography mass spectrometry was performed on SARS-CoV-2 infected postmortem lung tissue samples. Five protein profiling analyses were performed: whole slide lung parenchyma analysis, followed by analysis of isolated thrombi and endothelium, both stratified by disease (COVID-19 versus influenza) and thrombus morphology (embolism versus in situ). Influenza autopsy cases with pulmonary thrombi were used as controls. RESULTS Compared to influenza controls, both analyses of COVID-19 whole-tissue and isolated endothelium showed upregulation of proteins and pathways related to liver metabolism including urea cycle activation, with arginase being among the top upregulated proteins in COVID-19 lung tissue. Analysis of isolated COVID-19 thrombi showed significant downregulation of pathways related to platelet activation compared to influenza thrombi. Analysis of isolated thrombi based on histomorphology shows that in situ thrombi have significant upregulation of coronavirus pathogenesis proteins. CONCLUSIONS The decrease in platelet activation pathways in severe COVID-19 thrombi suggests a relative increase in venous thromboembolism, as thrombi from venous origin tend to contain fewer platelets than arterial thrombi. Based on histomorphology, in situ thrombi show upregulation of various proteins related to SARS-CoV-2 pathogenesis compared to thromboemboli, which may indicate increased in situ pulmonary thrombosis in COVID-19. Therefore, this study supports the increase of venous thromboembolism without undercutting the involvement of in situ thrombosis in severe COVID-19.
Collapse
Affiliation(s)
- Boaz V Lopuhaä
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Coşkun Guzel
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | | | | | - Menno V Huisman
- Department of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke J H A Kruip
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Theo M Luider
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| |
Collapse
|
18
|
Büyüktuna SA, Yerlitaş Sİ, Zararsız GE, Doğan K, Kablan D, Bağcı G, Özer S, Baysal C, Çakır Y, Cephe A, Koçhan N, Zararız G, Doğan HO. Exploring free amino acid profiles in Crimean-Congo hemorrhagic fever patients: Implications for disease progression. J Med Virol 2024; 96:e29637. [PMID: 38773825 DOI: 10.1002/jmv.29637] [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: 12/29/2023] [Revised: 03/29/2024] [Accepted: 04/18/2024] [Indexed: 05/24/2024]
Abstract
This study investigated the intricate interplay between Crimean-Congo hemorrhagic fever virus infection and alterations in amino acid metabolism. The primary aim is to elucidate the impact of Crimean-Congo hemorrhagic fever (CCHF) on specific amino acid concentrations and identify potential metabolic markers associated with viral infection. One hundred ninety individuals participated in this study, comprising 115 CCHF patients, 30 CCHF negative patients, and 45 healthy controls. Liquid chromatography-tandem mass spectrometry techniques were employed to quantify amino acid concentrations. The amino acid metabolic profiles in CCHF patients exhibit substantial distinctions from those in the control group. Patients highlight distinct metabolic reprogramming, notably characterized by arginine, histidine, taurine, glutamic acid, and glutamine metabolism shifts. These changes have been associated with the underlying molecular mechanisms of the disease. Exploring novel therapeutic and diagnostic strategies addressing specific amino acids may offer potential means to mitigate the severity of the disease.
Collapse
Affiliation(s)
- Seyit Ali Büyüktuna
- Department of Infectious Disease and Clinical Microbiology, Cumhuriyet University School of Medicine, Sivas, Türkiye
| | - Serra İlayda Yerlitaş
- Department of Biostatistics, Erciyes University School of Medicine, Kayseri, Türkiye
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Türkiye
| | - Gözde Ertük Zararsız
- Department of Biostatistics, Erciyes University School of Medicine, Kayseri, Türkiye
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Türkiye
| | - Kübra Doğan
- Department of Biochemistry, Minister of Health Sivas Numan Hospital, Sivas, Türkiye
| | - Demet Kablan
- Department of Biochemistry, Cumhuriyet University School of Medicine, Sivas, Türkiye
| | - Gökhan Bağcı
- Faculty of Medicine, Medical Biochemistry, Altinbas University, Istanbul, Türkiye
| | - Selda Özer
- Department of Biochemistry, Cumhuriyet University School of Medicine, Sivas, Türkiye
| | - Cihad Baysal
- Department of Infectious Disease and Clinical Microbiology, Cumhuriyet University School of Medicine, Sivas, Türkiye
| | - Yasemin Çakır
- Department of Infectious Disease and Clinical Microbiology, Cumhuriyet University School of Medicine, Sivas, Türkiye
| | - Ahu Cephe
- Institutional Data Management and Analytics Unit, Erciyes University Rectorate, Kayseri, Türkiye
| | - Necla Koçhan
- İzmir Biomedicine and Genome Center (IBG), İzmir, Türkiye
| | - Gökmen Zararız
- Department of Biostatistics, Erciyes University School of Medicine, Kayseri, Türkiye
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Türkiye
| | - Halef Okan Doğan
- Department of Biochemistry, Cumhuriyet University School of Medicine, Sivas, Türkiye
| |
Collapse
|
19
|
Naidu AS, Wang CK, Rao P, Mancini F, Clemens RA, Wirakartakusumah A, Chiu HF, Yen CH, Porretta S, Mathai I, Naidu SAG. Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID. NPJ Sci Food 2024; 8:19. [PMID: 38555403 PMCID: PMC10981760 DOI: 10.1038/s41538-024-00261-2] [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: 10/12/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.
Collapse
Affiliation(s)
- A Satyanarayan Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA.
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA.
| | - Chin-Kun Wang
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- School of Nutrition, Chung Shan Medical University, 110, Section 1, Jianguo North Road, Taichung, 40201, Taiwan
| | - Pingfan Rao
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- College of Food and Bioengineering, Fujian Polytechnic Normal University, No.1, Campus New Village, Longjiang Street, Fuqing City, Fujian, China
| | - Fabrizio Mancini
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President-Emeritus, Parker University, 2540 Walnut Hill Lane, Dallas, TX, 75229, USA
| | - Roger A Clemens
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- University of Southern California, Alfred E. Mann School of Pharmacy/D. K. Kim International Center for Regulatory & Quality Sciences, 1540 Alcazar St., CHP 140, Los Angeles, CA, 90089, USA
| | - Aman Wirakartakusumah
- International Union of Food Science and Technology (IUFoST), Guelph, ON, Canada
- IPMI International Business School Jakarta; South East Asian Food and Agriculture Science and Technology, IPB University, Bogor, Indonesia
| | - Hui-Fang Chiu
- Department of Chinese Medicine, Taichung Hospital, Ministry of Health & Well-being, Taichung, Taiwan
| | - Chi-Hua Yen
- Department of Family and Community Medicine, Chung Shan Medical University Hospital; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sebastiano Porretta
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President, Italian Association of Food Technology (AITA), Milan, Italy
- Experimental Station for the Food Preserving Industry, Department of Consumer Science, Viale Tanara 31/a, I-43121, Parma, Italy
| | - Issac Mathai
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- Soukya International Holistic Health Center, Whitefield, Bengaluru, India
| | - Sreus A G Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA
| |
Collapse
|
20
|
Lonati C, Berezhnoy G, Lawler N, Masuda R, Kulkarni A, Sala S, Nitschke P, Zizmare L, Bucci D, Cannet C, Schäfer H, Singh Y, Gray N, Lodge S, Nicholson J, Merle U, Wist J, Trautwein C. Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD + pathway and SIRT1 activation. Clin Chem Lab Med 2024; 62:770-788. [PMID: 37955280 DOI: 10.1515/cclm-2023-1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/22/2023] [Indexed: 11/14/2023]
Abstract
OBJECTIVES The stratification of individuals suffering from acute and post-acute SARS-CoV-2 infection remains a critical challenge. Notably, biomarkers able to specifically monitor viral progression, providing details about patient clinical status, are still not available. Herein, quantitative metabolomics is progressively recognized as a useful tool to describe the consequences of virus-host interactions considering also clinical metadata. METHODS The present study characterized the urinary metabolic profile of 243 infected individuals by quantitative nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography mass spectrometry (LC-MS). Results were compared with a historical cohort of noninfected subjects. Moreover, we assessed the concentration of recently identified antiviral nucleosides and their association with other metabolites and clinical data. RESULTS Urinary metabolomics can stratify patients into classes of disease severity, with a discrimination ability comparable to that of clinical biomarkers. Kynurenines showed the highest fold change in clinically-deteriorated patients and higher-risk subjects. Unique metabolite clusters were also generated based on age, sex, and body mass index (BMI). Changes in the concentration of antiviral nucleosides were associated with either other metabolites or clinical variables. Increased kynurenines and reduced trigonelline excretion indicated a disrupted nicotinamide adenine nucleotide (NAD+) and sirtuin 1 (SIRT1) pathway. CONCLUSIONS Our results confirm the potential of urinary metabolomics for noninvasive diagnostic/prognostic screening and show that the antiviral nucleosides could represent novel biomarkers linking viral load, immune response, and metabolism. Moreover, we established for the first time a casual link between kynurenine accumulation and deranged NAD+/SIRT1, offering a novel mechanism through which SARS-CoV-2 manipulates host physiology.
Collapse
Affiliation(s)
- Caterina Lonati
- Center for Preclinical Research, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| | - Georgy Berezhnoy
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| | - Nathan Lawler
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Reika Masuda
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Aditi Kulkarni
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| | - Samuele Sala
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Philipp Nitschke
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Laimdota Zizmare
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| | - Daniele Bucci
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| | - Claire Cannet
- Bruker BioSpin GmbH, AIC Division, Ettlingen, Germany
| | | | - Yogesh Singh
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Nicola Gray
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Samantha Lodge
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Jeremy Nicholson
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Uta Merle
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Julien Wist
- Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University Perth, Australia
| | - Christoph Trautwein
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
21
|
Conte C, Cipponeri E, Roden M. Diabetes Mellitus, Energy Metabolism, and COVID-19. Endocr Rev 2024; 45:281-308. [PMID: 37934800 PMCID: PMC10911957 DOI: 10.1210/endrev/bnad032] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Obesity, diabetes mellitus (mostly type 2), and COVID-19 show mutual interactions because they are not only risk factors for both acute and chronic COVID-19 manifestations, but also because COVID-19 alters energy metabolism. Such metabolic alterations can lead to dysglycemia and long-lasting effects. Thus, the COVID-19 pandemic has the potential for a further rise of the diabetes pandemic. This review outlines how preexisting metabolic alterations spanning from excess visceral adipose tissue to hyperglycemia and overt diabetes may exacerbate COVID-19 severity. We also summarize the different effects of SARS-CoV-2 infection on the key organs and tissues orchestrating energy metabolism, including adipose tissue, liver, skeletal muscle, and pancreas. Last, we provide an integrative view of the metabolic derangements that occur during COVID-19. Altogether, this review allows for better understanding of the metabolic derangements occurring when a fire starts from a small flame, and thereby help reducing the impact of the COVID-19 pandemic.
Collapse
Affiliation(s)
- Caterina Conte
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome 00166, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan 20099, Italy
| | - Elisa Cipponeri
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan 20099, Italy
| | - Michael Roden
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- German Center for Diabetes Research, Partner Düsseldorf, Neuherberg 85764, Germany
| |
Collapse
|
22
|
Ding D, Zhao H, Liu Y, Li S, Wei J, Yang Y, Wang S, Xing G, Hou S, Wang X, Zhang Y. Whole-transcriptome sequencing revealed the role of noncoding RNAs in susceptibility and resistance of Pekin ducks to DHAV-3. Poult Sci 2024; 103:103416. [PMID: 38301494 PMCID: PMC10846394 DOI: 10.1016/j.psj.2023.103416] [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: 10/21/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
As the most prevalent pathogen of duck viral hepatitis (DVH), duck hepatitis A virus genotype 3 (DHAV-3) has caused huge economic losses to the duck industry in China. Herein, we obtained whole-transcriptome sequencing data of susceptible (S) and resistant (R) Pekin duckling samples at 0 h, 12 h, and 24 h after DHAV-3 infection. We found that DHAV-3 infection induces 5,396 differentially expressed genes (DEGs), 85 differentially expressed miRNAs (DEMs), and 727 differentially expressed lncRNAs (DELs) at 24 hpi in S vs. R ducks, those upregulated genes were enriched in inflammation and cell communications pathways and downregulated genes were related to metabolic processes. Upregulated genes showed high connectivity with the miR-33, miR-193, and miR-11591, and downregulated genes were mainly regulated by miR-2954, miR-125, and miR-146b. With the construction of lncRNA-miRNA-mRNA axis, we further identified a few aberrantly expressed lncRNAs (e.g., MSTRG.36194.1, MSTRG.50601.1, MSTRG.34328.7, and MSTRG.29445.1) that regulate expression of hub genes (e.g., THBD, CLIC2, IL8, ACOX2, GPHN, SMLR1, and HAO1) by sponging those highly connected miRNAs. Altogether, our findings defined a dual role of ncRNAs in immune and metabolic regulation during DHAV-3 infection, suggesting potential new targets for treating DHAV-3 infected ducks.
Collapse
Affiliation(s)
- Dingbang Ding
- 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
| | - Ying Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shaofei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuze Yang
- Beijing General Station of Animal Husbandry, Beijing 100101, China
| | - Shuaiqin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangnan Xing
- 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
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yunsheng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
23
|
Walitt B, Singh K, LaMunion SR, Hallett M, Jacobson S, Chen K, Enose-Akahata Y, Apps R, Barb JJ, Bedard P, Brychta RJ, Buckley AW, Burbelo PD, Calco B, Cathay B, Chen L, Chigurupati S, Chen J, Cheung F, Chin LMK, Coleman BW, Courville AB, Deming MS, Drinkard B, Feng LR, Ferrucci L, Gabel SA, Gavin A, Goldstein DS, Hassanzadeh S, Horan SC, Horovitz SG, Johnson KR, Govan AJ, Knutson KM, Kreskow JD, Levin M, Lyons JJ, Madian N, Malik N, Mammen AL, McCulloch JA, McGurrin PM, Milner JD, Moaddel R, Mueller GA, Mukherjee A, Muñoz-Braceras S, Norato G, Pak K, Pinal-Fernandez I, Popa T, Reoma LB, Sack MN, Safavi F, Saligan LN, Sellers BA, Sinclair S, Smith B, Snow J, Solin S, Stussman BJ, Trinchieri G, Turner SA, Vetter CS, Vial F, Vizioli C, Williams A, Yang SB, Nath A. Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome. Nat Commun 2024; 15:907. [PMID: 38383456 PMCID: PMC10881493 DOI: 10.1038/s41467-024-45107-3] [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: 06/24/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Post-infectious myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) is a disabling disorder, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit PI-ME/CFS participants with matched controls to conduct deep phenotyping. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical conditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.
Collapse
Affiliation(s)
- Brian Walitt
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Komudi Singh
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Samuel R LaMunion
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | - Mark Hallett
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Steve Jacobson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kong Chen
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | - Richard Apps
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | - Patrick Bedard
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Robert J Brychta
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research (NIDCR), Bethesda, MD, USA
| | - Brice Calco
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Brianna Cathay
- Texas A&M School of Engineering Medicine, College Station, TX, USA
| | - Li Chen
- Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Snigdha Chigurupati
- George Washington University Hospital, District of Columbia, Washington, DC, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | | | - Amber B Courville
- National Institute of Diabetes, Digestion, and Kidney Disease (NIDDK), Bethesda, MD, USA
| | | | | | | | | | - Scott A Gabel
- National Institute of Environmental Health Sciences (NIEHS), Chapel Hill, NC, USA
| | - Angelique Gavin
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - David S Goldstein
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | | | - Sean C Horan
- Sidney Kimmel Medical College, Philadelphia, PA, USA
| | - Silvina G Horovitz
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kory R Johnson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Anita Jones Govan
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Kristine M Knutson
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Joy D Kreskow
- National Institute of Nursing Research (NINR), Bethesda, MD, USA
| | - Mark Levin
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Jonathan J Lyons
- National Institute of Allergy and Infectious Disease (NIAID), Bethesda, MD, USA
| | - Nicholas Madian
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD, USA
| | - Nasir Malik
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Andrew L Mammen
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | | | - Patrick M McGurrin
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | | | - Ruin Moaddel
- National Institute of Aging (NIA), Baltimore, MD, USA
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences (NIEHS), Chapel Hill, NC, USA
| | - Amrita Mukherjee
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | - Sandra Muñoz-Braceras
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Gina Norato
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Katherine Pak
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Iago Pinal-Fernandez
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), Bethesda, MD, USA
| | - Traian Popa
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Lauren B Reoma
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Michael N Sack
- National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Farinaz Safavi
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
- National Institute of Allergy and Infectious Disease (NIAID), Bethesda, MD, USA
| | - Leorey N Saligan
- National Institute of Nursing Research (NINR), Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, MD, USA
| | | | - Bryan Smith
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Joseph Snow
- National Institute of Mental Health (NIMH), Bethesda, MD, USA
| | | | - Barbara J Stussman
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD, USA
| | | | | | | | - Felipe Vial
- Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Carlotta Vizioli
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA
| | - Ashley Williams
- Oakland University William Beaumont School of Medicine, Rochester, NY, USA
| | | | - Avindra Nath
- National Institute of Neurological Diseases and Stroke (NINDS), Bethesda, MD, USA.
| |
Collapse
|
24
|
Nemkov T, Stephenson D, Erickson C, Dzieciatkowska M, Key A, Moore A, Earley EJ, Page GP, Lacroix IS, Stone M, Deng X, Raife T, Kleinman S, Zimring JC, Roubinian N, Hansen KC, Busch MP, Norris PJ, D’Alessandro A. Regulation of kynurenine metabolism by blood donor genetics and biology impacts red cell hemolysis in vitro and in vivo. Blood 2024; 143:456-472. [PMID: 37976448 PMCID: PMC10862365 DOI: 10.1182/blood.2023022052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT In the field of transfusion medicine, the clinical relevance of the metabolic markers of the red blood cell (RBC) storage lesion is incompletely understood. Here, we performed metabolomics of RBC units from 643 donors enrolled in the Recipient Epidemiology and Donor Evaluation Study, REDS RBC Omics. These units were tested on storage days 10, 23, and 42 for a total of 1929 samples and also characterized for end-of-storage hemolytic propensity after oxidative and osmotic insults. Our results indicate that the metabolic markers of the storage lesion poorly correlated with hemolytic propensity. In contrast, kynurenine was not affected by storage duration and was identified as the top predictor of osmotic fragility. RBC kynurenine levels were affected by donor age and body mass index and were reproducible within the same donor across multiple donations from 2 to 12 months apart. To delve into the genetic underpinnings of kynurenine levels in stored RBCs, we thus tested kynurenine levels in stored RBCs on day 42 from 13 091 donors from the REDS RBC Omics study, a population that was also genotyped for 879 000 single nucleotide polymorphisms. Through a metabolite quantitative trait loci analysis, we identified polymorphisms in SLC7A5, ATXN2, and a series of rate-limiting enzymes (eg, kynurenine monooxygenase, indoleamine 2,3-dioxygenase, and tryptophan dioxygenase) in the kynurenine pathway as critical factors affecting RBC kynurenine levels. By interrogating a donor-recipient linkage vein-to-vein database, we then report that SLC7A5 polymorphisms are also associated with changes in hemoglobin and bilirubin levels, suggestive of in vivo hemolysis in 4470 individuals who were critically ill and receiving single-unit transfusions.
Collapse
Affiliation(s)
- Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
- Omix Technologies Inc, Aurora, CO
| | - Daniel Stephenson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Christopher Erickson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Alicia Key
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Amy Moore
- Research Triangle Institute International, Atlanta, GA
| | | | - Grier P. Page
- Research Triangle Institute International, Atlanta, GA
| | - Ian S. Lacroix
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Thomas Raife
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Steven Kleinman
- Department of Pathology, University of British Columbia, Victoria, BC, Canada
| | - James C. Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA
| | - Nareg Roubinian
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
- Kaiser Permanente Northern California Division of Research, Oakland, CA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
| | - Michael P. Busch
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Philip J. Norris
- Vitalant Research Institute, San Francisco, CA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO
- Omix Technologies Inc, Aurora, CO
| |
Collapse
|
25
|
Yang D, Chan JFW, Yoon C, Luk TY, Shuai H, Hou Y, Huang X, Hu B, Chai Y, Yuen TTT, Liu Y, Zhu T, Liu H, Shi J, Wang Y, He Y, Sit KY, Au WK, Zhang AJ, Yuan S, Zhang BZ, Huang YW, Chu H. Type-II IFN inhibits SARS-CoV-2 replication in human lung epithelial cells and ex vivo human lung tissues through indoleamine 2,3-dioxygenase-mediated pathways. J Med Virol 2024; 96:e29472. [PMID: 38373201 DOI: 10.1002/jmv.29472] [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: 08/08/2023] [Revised: 01/22/2024] [Accepted: 01/28/2024] [Indexed: 02/21/2024]
Abstract
Interferons (IFNs) are critical for immune defense against pathogens. While type-I and -III IFNs have been reported to inhibit SARS-CoV-2 replication, the antiviral effect and mechanism of type-II IFN against SARS-CoV-2 remain largely unknown. Here, we evaluate the antiviral activity of type-II IFN (IFNγ) using human lung epithelial cells (Calu3) and ex vivo human lung tissues. In this study, we found that IFNγ suppresses SARS-CoV-2 replication in both Calu3 cells and ex vivo human lung tissues. Moreover, IFNγ treatment does not significantly modulate the expression of SARS-CoV-2 entry-related factors and induces a similar level of pro-inflammatory response in human lung tissues when compared with IFNβ treatment. Mechanistically, we show that overexpression of indoleamine 2,3-dioxygenase 1 (IDO1), which is most profoundly induced by IFNγ, substantially restricts the replication of ancestral SARS-CoV-2 and the Alpha and Delta variants. Meanwhile, loss-of-function study reveals that IDO1 knockdown restores SARS-CoV-2 replication restricted by IFNγ in Calu3 cells. We further found that the treatment of l-tryptophan, a substrate of IDO1, partially rescues the IFNγ-mediated inhibitory effect on SARS-CoV-2 replication in both Calu3 cells and ex vivo human lung tissues. Collectively, these results suggest that type-II IFN potently inhibits SARS-CoV-2 replication through IDO1-mediated antiviral response.
Collapse
Affiliation(s)
- Dong Yang
- Xianghu Laboratory, Hangzhou, Zhejiang, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China
- The University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China
- Guangzhou Laboratory, Guangdong Province, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tsz-Yat Luk
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yixin He
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ko-Yung Sit
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wing-Kuk Au
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | | | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| |
Collapse
|
26
|
Gonjilashvili A, Tatishvili S. The interplay between Sars-Cov-2 infection related cardiovascular diseases and depression. Common mechanisms, shared symptoms. AMERICAN HEART JOURNAL PLUS : CARDIOLOGY RESEARCH AND PRACTICE 2024; 38:100364. [PMID: 38510743 PMCID: PMC10945907 DOI: 10.1016/j.ahjo.2024.100364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 03/22/2024]
Abstract
In 2020 the World Health organization announced a pandemic due to the outbreak of the Coronavirus disease 19. Pneumonia was the most common manifestation of the Sars-Cov-2 infection, however, clinical papers describe Sars-Cov-2 associated cardiovascular pathologies, such as ACS, myopericarditis, cardiomyopathies, dysrhythmias, as leading causes of increased morbidity and mortality. The short and long term prognosis of Sars-Cov-2-related cardiovascular diseases was defined not only by the disease severity itself but also by associated conditions and complications, among which mental health issues (stress, depression and anxiety) have a negative impact. The interplay between Sars-Cov-2 infection, cardiovascular disease and depression may be explained by hyperinflammation, unhealthy lifestyle and inter-organ communication, mediated by extracellular vesicles (EV) and non-coding MicroRNA (miRNA). The long Covid syndrome is characterized with orthostatic hypotension, impaired cardiac and cerebral perfusion, postural orthostatic tachycardia syndrome (POTS), syncope, chest pain, dyspnea, palpitation, chronic fatigue syndrome, 'brain fog', memory, cognitive and sleep difficulties, depression and anxiety. From a clinical point of view these symptoms may be considered as common symptoms representing not only a cardiac but also a neurological/psychiatric problem. Consequently assessment of these symptoms are of paramount importance. Due to their complexity, management of these patients requires multidisciplinary care.
Collapse
|
27
|
Bayrak CS, Forst C, Jones DR, Gresham D, Pushalkar S, Wu S, Vogel C, Mahal L, Ghedin E, Ross T, García-Sastre A, Zhang B. Patient Subtyping Analysis of Baseline Multi-omic Data Reveals Distinct Pre-immune States Predictive of Vaccination Responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576213. [PMID: 38328256 PMCID: PMC10849502 DOI: 10.1101/2024.01.18.576213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Understanding the molecular mechanisms that underpin diverse vaccination responses is a critical step toward developing efficient vaccines. Molecular subtyping approaches can offer valuable insights into the heterogeneous nature of responses and aid in the design of more effective vaccines. In order to explore the molecular signatures associated with the vaccine response, we analyzed baseline transcriptomics data from paired samples of whole blood, proteomics and glycomics data from serum, and metabolomics data from urine, obtained from influenza vaccine recipients (2019-2020 season) prior to vaccination. After integrating the data using a network-based model, we performed a subtyping analysis. The integration of multiple data modalities from 62 samples resulted in five baseline molecular subtypes with distinct molecular signatures. These baseline subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation across subtypes in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these significant differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining vaccine response and efficacy. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.
Collapse
|
28
|
Saito S, Shahbaz S, Luo X, Osman M, Redmond D, Cohen Tervaert JW, Li L, Elahi S. Metabolomic and immune alterations in long COVID patients with chronic fatigue syndrome. Front Immunol 2024; 15:1341843. [PMID: 38304426 PMCID: PMC10830702 DOI: 10.3389/fimmu.2024.1341843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Introduction A group of SARS-CoV-2 infected individuals present lingering symptoms, defined as long COVID (LC), that may last months or years post the onset of acute disease. A portion of LC patients have symptoms similar to myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS), which results in a substantial reduction in their quality of life. A better understanding of the pathophysiology of LC, in particular, ME/CFS is urgently needed. Methods We identified and studied metabolites and soluble biomarkers in plasma from LC individuals mainly exhibiting ME/CFS compared to age-sex-matched recovered individuals (R) without LC, acute COVID-19 patients (A), and to SARS-CoV-2 unexposed healthy individuals (HC). Results Through these analyses, we identified alterations in several metabolomic pathways in LC vs other groups. Plasma metabolomics analysis showed that LC differed from the R and HC groups. Of note, the R group also exhibited a different metabolomic profile than HC. Moreover, we observed a significant elevation in the plasma pro-inflammatory biomarkers (e.g. IL-1α, IL-6, TNF-α, Flt-1, and sCD14) but the reduction in ATP in LC patients. Our results demonstrate that LC patients exhibit persistent metabolomic abnormalities 12 months after the acute COVID-19 disease. Of note, such metabolomic alterations can be observed in the R group 12 months after the acute disease. Hence, the metabolomic recovery period for infected individuals with SARS-CoV-2 might be long-lasting. In particular, we found a significant reduction in sarcosine and serine concentrations in LC patients, which was inversely correlated with depression, anxiety, and cognitive dysfunction scores. Conclusion Our study findings provide a comprehensive metabolomic knowledge base and other soluble biomarkers for a better understanding of the pathophysiology of LC and suggests sarcosine and serine supplementations might have potential therapeutic implications in LC patients. Finally, our study reveals that LC disproportionally affects females more than males, as evidenced by nearly 70% of our LC patients being female.
Collapse
Affiliation(s)
- Suguru Saito
- School of Dentistry, Division of Foundational Sciences, Edmonton, AB, Canada
| | - Shima Shahbaz
- School of Dentistry, Division of Foundational Sciences, Edmonton, AB, Canada
| | - Xian Luo
- The Metabolomics Innovation Centre, University of Alberta, Edmonton, AB, Canada
| | - Mohammed Osman
- Department of Medicine, Division of Rheumatology, Edmonton, AB, Canada
| | - Desiree Redmond
- Department of Medicine, Division of Rheumatology, Edmonton, AB, Canada
| | | | - Liang Li
- The Metabolomics Innovation Centre, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- School of Dentistry, Division of Foundational Sciences, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
29
|
Sun Y, Saito K, Ushiki A, Abe M, Saito Y, Kashiwada T, Horimasu Y, Gemma A, Tatsumi K, Hattori N, Tsushima K, Takemoto K, Ishikawa R, Momiyama T, Matsuyama SI, Arakawa N, Akane H, Toyoda T, Ogawa K, Sato M, Takamatsu K, Mori K, Nishiya T, Izumi T, Ohno Y, Saito Y, Hanaoka M. Identification of kynurenine and quinolinic acid as promising serum biomarkers for drug-induced interstitial lung diseases. Respir Res 2024; 25:31. [PMID: 38221627 PMCID: PMC10788992 DOI: 10.1186/s12931-023-02653-6] [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: 08/10/2023] [Accepted: 12/24/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Drug-induced interstitial lung disease (DILD) is a lung injury caused by various types of drugs and is a serious problem in both clinical practice and drug development. Clinical management of the condition would be improved if there were DILD-specific biomarkers available; this study aimed to meet that need. METHODS Biomarker candidates were identified by non-targeted metabolomics focusing on hydrophilic molecules, and further validated by targeted approaches using the serum of acute DILD patients, DILD recovery patients, DILD-tolerant patients, patients with other related lung diseases, and healthy controls. RESULTS Serum levels of kynurenine and quinolinic acid (and kynurenine/tryptophan ratio) were elevated significantly and specifically in acute DILD patients. The diagnostic potentials of these biomarkers were superior to those of conventional lung injury biomarkers, Krebs von den Lungen-6 and surfactant protein-D, in discriminating between acute DILD patients and patients with other lung diseases, including idiopathic interstitial pneumonia and lung diseases associated with connective tissue diseases. In addition to identifying and evaluating the biomarkers, our data showed that kynurenine/tryptophan ratios (an indicator of kynurenine pathway activation) were positively correlated with serum C-reactive protein concentrations in patients with DILD, suggesting the potential association between the generation of these biomarkers and inflammation. Our in vitro experiments demonstrated that macrophage differentiation and inflammatory stimulations typified by interferon gamma could activate the kynurenine pathway, resulting in enhanced kynurenine levels in the extracellular space in macrophage-like cell lines or lung endothelial cells. Extracellular quinolinic acid levels were elevated only in macrophage-like cells but not endothelial cells owing to the lower expression levels of metabolic enzymes converting kynurenine to quinolinic acid. These findings provide clues about the molecular mechanisms behind their specific elevation in the serum of acute DILD patients. CONCLUSIONS The serum concentrations of kynurenine and quinolinic acid as well as kynurenine/tryptophan ratios are promising and specific biomarkers for detecting and monitoring DILD and its recovery, which could facilitate accurate decisions for appropriate clinical management of patients with DILD.
Collapse
Affiliation(s)
- Yuchen Sun
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kosuke Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Atsuhito Ushiki
- First Department of Internal Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Mitsuhiro Abe
- Department of Respirology (B2), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba, 260-8677, Japan
| | - Yoshinobu Saito
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Takeru Kashiwada
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Yasushi Horimasu
- Department of Respiratory Medicine, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, Hiroshima, 734-8551, Japan
| | - Akihiko Gemma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Koichiro Tatsumi
- Department of Respirology (B2), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba, 260-8677, Japan
| | - Noboru Hattori
- Department of Respiratory Medicine, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, Hiroshima, 734-8551, Japan
| | - Kenji Tsushima
- Division of General Internal Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa, 216-8511, Japan
| | - Kazuhisa Takemoto
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Rika Ishikawa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Toshiko Momiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Shin-Ichiro Matsuyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Noriaki Arakawa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Hirotoshi Akane
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takeshi Toyoda
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Motonobu Sato
- Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kazuhiko Takamatsu
- Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kazuhiko Mori
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Takayoshi Nishiya
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Takashi Izumi
- Kihara Memorial Yokohama Foundation, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasuo Ohno
- Kihara Memorial Yokohama Foundation, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
| | - Masayuki Hanaoka
- First Department of Internal Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| |
Collapse
|
30
|
Yoon H, Dean LS, Jiyarom B, Khadka VS, Deng Y, Nerurkar VR, Chow DC, Shikuma CM, Devendra G, Koh Y, Park J. Single-cell RNA sequencing reveals characteristics of myeloid cells in post-acute sequelae of SARS-CoV-2 patients with persistent respiratory symptoms. Front Immunol 2024; 14:1268510. [PMID: 38259488 PMCID: PMC10800799 DOI: 10.3389/fimmu.2023.1268510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Although our understanding of the immunopathology and subsequent risk and severity of COVID-19 disease is evolving, a detailed account of immune responses that contribute to the long-term consequences of pulmonary complications in COVID-19 infection remains unclear. Few studies have detailed the immune and cytokine profiles associated with post-acute sequelae of SARS-CoV-2 infection (PASC) with persistent pulmonary symptoms. The dysregulation of the immune system that drives pulmonary sequelae in COVID-19 survivors and PASC sufferers remains largely unknown. Results To characterize the immunological features of pulmonary PASC (PPASC), we performed droplet-based single-cell RNA sequencing (scRNA-seq) to study the transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) from a participant naïve to SARS-CoV-2 (Control) (n=1) and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC) (n=2). After integrating scRNA-seq data with a naïve participant from a published dataset, 11 distinct cell populations were identified based on the expression of canonical markers. The proportion of myeloid-lineage cells ([MLCs]; CD14+/CD16+monocytes, and dendritic cells) was increased in PPASC (n=2) compared to controls (n=2). MLCs from PPASC displayed up-regulation of genes associated with pulmonary symptoms/fibrosis, while glycolysis metabolism-related genes were downregulated. Similarly, pathway analysis showed that fibrosis-related (VEGF, WNT, and SMAD) and cell death pathways were up-regulated, but immune pathways were down-regulated in PPASC. Further comparison of PPASC with scRNA-seq data with Severe COVID-19 (n=4) data demonstrated enrichment of fibrotic transcriptional signatures. In PPASC, we observed interactive VEGF ligand-receptor pairs among MLCs, and network modules in CD14+ (cluster 4) and CD16+ (Cluster 5) monocytes displayed a significant enrichment for biological pathways linked to adverse COVID-19 outcomes, fibrosis, and angiogenesis. Further analysis revealed a distinct metabolic alteration in MLCs with a down-regulation of glycolysis/gluconeogenesis in PPASC compared to SARS-CoV-2 naïve samples. Conclusion Analysis of a small scRNA-seq dataset demonstrated alterations in the immune response and cellular landscape in PPASC. The presence of elevated MLC levels and their corresponding gene signatures associated with fibrosis, immune response suppression, and altered metabolic states suggests a potential role in PPASC development.
Collapse
Affiliation(s)
- Hyundong Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Logan S. Dean
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Boonyanudh Jiyarom
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI, United States
| | - Vivek R. Nerurkar
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Dominic C. Chow
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Gehan Devendra
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Pulmonary and Critical Care, Queen’s Medical Center, Honolulu, HI, United States
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Juwon Park
- Hawaii Center for AIDS, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| |
Collapse
|
31
|
Narayanan SA, Jamison DA, Guarnieri JW, Zaksas V, Topper M, Koutnik AP, Park J, Clark KB, Enguita FJ, Leitão AL, Das S, Moraes-Vieira PM, Galeano D, Mason CE, Trovão NS, Schwartz RE, Schisler JC, Coelho-Dos-Reis JGA, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection. Eur J Hum Genet 2024; 32:10-20. [PMID: 37938797 PMCID: PMC10772081 DOI: 10.1038/s41431-023-01462-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 11/09/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.
Collapse
Affiliation(s)
- S Anand Narayanan
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32301, USA.
| | - David A Jamison
- COVID-19 International Research Team, Medford, MA, 02155, USA
| | - Joseph W Guarnieri
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Michael Topper
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Departments of Oncology and Medicine and the Sidney Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andrew P Koutnik
- Human Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, FL, 32502, USA
- Sansum Diabetes Research Institute, Santa Barbara, CA, 93015, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, 10065, USA
| | - Kevin B Clark
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Cures Within Reach, Chicago, IL, 60602, USA
- Campus and Domain Champions Program, Multi-Tier Assistance, Training, and Computational Help (MATCH) Track, National Science Foundation's Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS), Philadelphia, PA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, 10016, USA
- Peace Innovation Institute, The Hague 2511, Netherlands and Stanford University, Palo Alto, 94305, CA, USA
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Saswati Das
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Atal Bihari Vajpayee Institute of Medical Sciences and Dr Ram Mannohar Lohia Hospital, New Delhi, 110001, India
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC) and Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
| | - Diego Galeano
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nídia S Trovão
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA, 02155, USA
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jordana G A Coelho-Dos-Reis
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Basic and Applied Virology Lab, Department of Microbiology, Institute for Biological Sciences (ICB), Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA, 02155, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Bioinformatics and Computational Biology Program, Center for Metabolomics, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA, 02155, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Santa Clara, CA, 94035, USA.
| |
Collapse
|
32
|
Chatelaine HAS, Chen Y, Braisted J, Chu SH, Chen Q, Stav M, Begum S, Diray-Arce J, Sanjak J, Huang M, Lasky-Su J, Mathé EA. Nucleotide, Phospholipid, and Kynurenine Metabolites Are Robustly Associated with COVID-19 Severity and Time of Plasma Sample Collection in a Prospective Cohort Study. Int J Mol Sci 2023; 25:346. [PMID: 38203516 PMCID: PMC10779247 DOI: 10.3390/ijms25010346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Understanding the molecular underpinnings of disease severity and progression in human studies is necessary to develop metabolism-related preventative strategies for severe COVID-19. Metabolites and metabolic pathways that predispose individuals to severe disease are not well understood. In this study, we generated comprehensive plasma metabolomic profiles in >550 patients from the Longitudinal EMR and Omics COVID-19 Cohort. Samples were collected before (n = 441), during (n = 86), and after (n = 82) COVID-19 diagnosis, representing 555 distinct patients, most of which had single timepoints. Regression models adjusted for demographics, risk factors, and comorbidities, were used to determine metabolites associated with predisposition to and/or persistent effects of COVID-19 severity, and metabolite changes that were transient/lingering over the disease course. Sphingolipids/phospholipids were negatively associated with severity and exhibited lingering elevations after disease, while modified nucleotides were positively associated with severity and had lingering decreases after disease. Cytidine and uridine metabolites, which were positively and negatively associated with COVID-19 severity, respectively, were acutely elevated, reflecting the particular importance of pyrimidine metabolism in active COVID-19. This is the first large metabolomics study using COVID-19 plasma samples before, during, and/or after disease. Our results lay the groundwork for identifying putative biomarkers and preventive strategies for severe COVID-19.
Collapse
Affiliation(s)
- Haley A. S. Chatelaine
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; (H.A.S.C.)
| | - Yulu Chen
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John Braisted
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; (H.A.S.C.)
| | - Su H. Chu
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Meryl Stav
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sofina Begum
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jaleal Sanjak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; (H.A.S.C.)
| | - Mengna Huang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; (H.A.S.C.)
| |
Collapse
|
33
|
Mwangi VI, Netto RLA, Borba MGS, Santos GF, Lima GS, Machado LS, Yakubu MN, Val FFA, Sampaio VS, Sartim MA, Koolen HHF, Costa AG, Toméi MCM, Guimarães TP, Chaves AR, Vaz BG, Lacerda MVG, Monteiro WM, Gardinassi LG, Melo GC. Methylprednisolone therapy induces differential metabolic trajectories in severe COVID-19 patients. mSystems 2023; 8:e0072623. [PMID: 37874139 PMCID: PMC10734516 DOI: 10.1128/msystems.00726-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/17/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The SARS-CoV-2 virus infection in humans induces significant inflammatory and systemic reactions and complications of which corticosteroids like methylprednisolone have been recommended as treatment. Our understanding of the metabolic and metabolomic pathway dysregulations while using intravenous corticosteroids in COVID-19 is limited. This study will help enlighten the metabolic and metabolomic pathway dysregulations underlying high daily doses of intravenous methylprednisolone in COVID-19 patients compared to those receiving placebo. The information on key metabolites and pathways identified in this study together with the crosstalk with the inflammation and biochemistry components may be used, in the future, to leverage the use of methylprednisolone in any future pandemics from the coronavirus family.
Collapse
Affiliation(s)
- Victor I. Mwangi
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Rebeca L. A. Netto
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Mayla G. S. Borba
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Gabriel F. Santos
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Gesiane S. Lima
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lucas S. Machado
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Michael N. Yakubu
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Fernando F. A. Val
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciência da Saúde, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciências do Movimento Humano, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Vanderson S. Sampaio
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Marco A. Sartim
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Pró-reitoria de Pesquisa e Pós-graduação, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - Hector H. F. Koolen
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Allyson G. Costa
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Amazonas, Brazil
- Escola de Enfermagem de Manaus, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
| | - Maria C. M. Toméi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Tiago P. Guimarães
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Andrea R. Chaves
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Boniek G. Vaz
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcus V. G. Lacerda
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Leônidas & Maria Deane/Fundação Oswaldo Cruz (ILMD/Fiocruz Amazônia), Manaus, Amazonas, Brazil
| | - Wuelton M. Monteiro
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Luiz G. Gardinassi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Gisely C. Melo
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
| |
Collapse
|
34
|
D'Alessandro A, Nouraie SM, Zhang Y, Cendali F, Gamboni F, Reisz JA, Zhang X, Bartsch KW, Galbraith MD, Espinosa JM, Gordeuk VR, Gladwin MT. Metabolic signatures of cardiorenal dysfunction in plasma from sickle cell patients as a function of therapeutic transfusion and hydroxyurea treatment. Haematologica 2023; 108:3418-3432. [PMID: 37439373 PMCID: PMC10690926 DOI: 10.3324/haematol.2023.283288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
Metabolomics studies in sickle cell disease (SCD) have been so far limited to tens of samples, owing to technical and experimental limitations. To overcome these limitations, we performed plasma metabolomics analyses on 596 samples from patients with SCD enrolled in the WALK-PHaSST study (clinicaltrials gov. Identifier: NCT00492531). Clinical covariates informed the biological interpretation of metabolomics data, including genotypes (hemoglobin [Hb] SS, hemoglobin SC), history of recent transfusion (HbA%), response to hydroxyurea treatment (fetal Hb%). We investigated metabolic correlates to the degree of intravascular hemolysis, cardiorenal function, as determined by tricuspid regurgitation velocity (TRV), estimated glomerular filtration rate (eGFR), and overall hazard ratio (unadjusted or adjusted by age). Recent transfusion events or hydroxyurea treatment were associated with elevation in plasma-free fatty acids and decreases in acyl-carnitines, urate, kynurenine, indoles, carboxylic acids, and glycine- or taurine-conjugated bile acids. High levels of these metabolites, along with low levels of plasma S1P and L-arginine were identified as top markers of hemolysis, cardiorenal function (TRV, eGFR), and overall hazard ratio. We thus uploaded all omics and clinical data on a novel online portal that we used to identify a potential mechanism of dysregulated red cell S1P synthesis and export as a contributor to the more severe clinical manifestations in patients with the SS genotype compared to SC. In conclusion, plasma metabolic signatures - including low S1P, arginine and elevated kynurenine, acyl-carnitines and bile acids - are associated with clinical manifestation and therapeutic efficacy in SCD patients, suggesting new avenues for metabolic interventions in this patient population.
Collapse
Affiliation(s)
- Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; Department of Medicine - Division of Hematology, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO.
| | - S Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO
| | - Xu Zhang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Kyle W Bartsch
- Linda Crnic Institute for Down Syndrome, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus
| | - Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus; School of Medicine Information Services, University of Colorado Anschutz Medical Campus
| | - Victor R Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Mark T Gladwin
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD.
| |
Collapse
|
35
|
Miguel V, Rey-Serra C, Tituaña J, Sirera B, Alcalde-Estévez E, Herrero JI, Ranz I, Fernández L, Castillo C, Sevilla L, Nagai J, Reimer KC, Jansen J, Kramann R, Costa IG, Castro A, Sancho D, Rodríguez González-Moro JM, Lamas S. Enhanced fatty acid oxidation through metformin and baicalin as therapy for COVID-19 and associated inflammatory states in lung and kidney. Redox Biol 2023; 68:102957. [PMID: 37977043 PMCID: PMC10682832 DOI: 10.1016/j.redox.2023.102957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Progressive respiratory failure is the primary cause of death in the coronavirus disease 2019 (COVID-19) pandemic. It is the final outcome of the acute respiratory distress syndrome (ARDS), characterized by an initial exacerbated inflammatory response, metabolic derangement and ultimate tissue scarring. A positive balance of cellular energy may result crucial for the recovery of clinical COVID-19. Hence, we asked if two key pathways involved in cellular energy generation, AMP-activated protein kinase (AMPK)/acetyl-CoA carboxylase (ACC) signaling and fatty acid oxidation (FAO) could be beneficial. We tested the drugs metformin (AMPK activator) and baicalin (CPT1A activator) in different experimental models mimicking COVID-19 associated inflammation in lung and kidney. We also studied two different cohorts of COVID-19 patients that had been previously treated with metformin. These drugs ameliorated lung damage in an ARDS animal model, while activation of AMPK/ACC signaling increased mitochondrial function and decreased TGF-β-induced fibrosis, apoptosis and inflammation markers in lung epithelial cells. Similar results were observed with two indole derivatives, IND6 and IND8 with AMPK activating capacity. Consistently, a reduced time of hospitalization and need of intensive care was observed in COVID-19 patients previously exposed to metformin. Baicalin also mitigated the activation of pro-inflammatory bone marrow-derived macrophages (BMDMs) and reduced kidney fibrosis in two animal models of kidney injury, another key target of COVID-19. In human epithelial lung and kidney cells, both drugs improved mitochondrial function and prevented TGF-β-induced renal epithelial cell dedifferentiation. Our results support that favoring cellular energy production through enhanced FAO may prove useful in the prevention of COVID-19-induced lung and renal damage.
Collapse
Affiliation(s)
- Verónica Miguel
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029, Madrid, Spain.
| | - Carlos Rey-Serra
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Jessica Tituaña
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Belén Sirera
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Elena Alcalde-Estévez
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - J Ignacio Herrero
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Irene Ranz
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Laura Fernández
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Carolina Castillo
- Department of Pathology. University Hospital "Príncipe de Asturias", Alcalá de Henares, Madrid, Spain
| | - Lucía Sevilla
- Department of Pneumology, University Hospital "Principe de Asturias", Alcala de Henares, Madrid, Spain
| | - James Nagai
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany; Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Katharina C Reimer
- Department of Medicine 2, Nephrology, Rheumatology and Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany; Institute for Biomedical Technologies, Department of Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Jitske Jansen
- Department of Medicine 2, Nephrology, Rheumatology and Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rafael Kramann
- Department of Medicine 2, Nephrology, Rheumatology and Immunology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany; Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Ana Castro
- Instituto de Química Medica (IQM-CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - David Sancho
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029, Madrid, Spain
| | | | - Santiago Lamas
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain.
| |
Collapse
|
36
|
Hora S, Pahwa P, Siddiqui H, Saxena A, Kashyap M, Sevak JK, Singh R, Javed M, Yadav P, Kale P, Ramakrishna G, Bajpai M, Rathore A, Maras JS, Tyagi S, Sarin SK, Trehanpati N. Metabolic alterations unravel the maternofetal immune responses with disease severity in pregnant women infected with SARS-CoV-2. J Med Virol 2023; 95:e29257. [PMID: 38054548 DOI: 10.1002/jmv.29257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
Pregnancy being an immune compromised state, coronavirus disease of 2019 (COVID-19) disease poses high risk of premature delivery and threat to fetus. Plasma metabolome regulates immune cellular responses, therefore we aimed to analyze the change in plasma secretome, metabolome, and immune cells with disease severity in COVID-19 positive pregnant females and their cord blood. COVID-19 reverse transcriptase-polymerase chain reaction positive pregnant females (n = 112) with asymptomatic (Asy) (n = 82), mild (n = 21), or moderate (n = 9) disease, healthy pregnant (n = 18), COVID-19 positive nonpregnant females (n = 7) were included. Eighty-two cord blood from COVID-19 positive and seven healthy cord blood were also analyzed. Mother's peripheral blood and cord blood were analyzed for untargeted metabolome profiling and cytokines by using high-resolution mass spectrometry and cytokine bead array. Immune scan was performed only in mothers' blood by flow cytometry. In Asy severe acute respiratory syndrome coronavirus 2 infection, the amino acid metabolic pathways such as glycine, serine, l-lactate, and threonine metabolism were upregulated with downregulation of riboflavin and tyrosine metabolism. However, with mild-to-moderate disease, the pyruvate and nicotinamide adenine dinucleotide (NAD+ ) metabolism were mostly altered. Cord blood mimicked the mother's metabolomic profiles by showing altered valine, leucine, isoleucine, glycine, serine, threonine in Asy and NAD+ , riboflavin metabolism in mild and moderate. Additionally, with disease severity tumor necrosis factor-α, interferon (IFN)-α, IFN-γ, interleukin (IL)-6 cytokine storm, IL-9 was raised in both mothers and neonates. Pyruvate, NAD metabolism and increase in IL-9 and IFN-γ had an impact on nonclassical monocytes, exhausted T and B cells. Our results demonstrated that immune-metabolic interplay in mother and fetus is influenced with increase in IL-9 and IFN-γ regulated pyruvate, lactate tricarboxylic acid, and riboflavin metabolism with context to disease severity.
Collapse
Affiliation(s)
- Sandhya Hora
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Prabhjyoti Pahwa
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Hamda Siddiqui
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Anoushka Saxena
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Minal Kashyap
- Department of Gynecology and Obstetrics, Lok Nayak Jai Prakash Hospital, New Delhi, India
| | - Jayesh K Sevak
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ravinder Singh
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Maryam Javed
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Pushpa Yadav
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Pratibha Kale
- Department of Microbiology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gayatri Ramakrishna
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Meenu Bajpai
- Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Asmita Rathore
- Department of Gynecology and Obstetrics, Lok Nayak Jai Prakash Hospital, New Delhi, India
| | - Jaswinder S Maras
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shakun Tyagi
- Department of Gynecology and Obstetrics, Lok Nayak Jai Prakash Hospital, New Delhi, India
| | - Shiv K Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nirupama Trehanpati
- Department of Molecular and Cellular Medicine, Laboratory of Molecular Immunology, Institute of Liver and Biliary Sciences, New Delhi, India
| |
Collapse
|
37
|
Gupta T, Najumuddin, Rajendran D, Gujral A, Jangra A. Metabolism configures immune response across multi-systems: Lessons from COVID-19. Adv Biol Regul 2023; 90:100977. [PMID: 37690286 DOI: 10.1016/j.jbior.2023.100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/19/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023]
Abstract
Several studies over the last decade demonstrate the recruitment of immune cells, increased inflammatory cytokines, and chemokine in patients with metabolic diseases, including heart failure, parenchymal inflammation, obesity, tuberculosis, and diabetes mellitus. Metabolic rewiring of immune cells is associated with the severity and prevalence of these diseases. The risk of developing COVID-19/SARS-CoV-2 infection increases in patients with metabolic dysfunction (heart failure, diabetes mellitus, and obesity). Several etiologies, including fatigue, dyspnea, and dizziness, persist even months after COVID-19 infection, commonly known as Post-Acute Sequelae of CoV-2 (PASC) or long COVID. A chronic inflammatory state and metabolic dysfunction are the factors that contribute to long COVID. Here, this study explores the potential link between pathogenic metabolic and immune alterations across different organ systems that could underlie COVID-19 and PASC. These interactions could be utilized for targeted future therapeutic approaches.
Collapse
Affiliation(s)
- Tinku Gupta
- Department of Pharmacognosy & Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), M. B. Road, New Delhi 110062, India
| | - Najumuddin
- Program of Biotechnology, Department of Applied Sciences, Faculty of Engineering, Science and Technology, Hamdard University, Karachi, Pakistan
| | - Dhanya Rajendran
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Akash Gujral
- Department of Medicine, Nyu Grossman School of Medicine, NY, USA
| | - Ashok Jangra
- Department of Pharmaceutical Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
| |
Collapse
|
38
|
Zhang S, Cao Y, Xu C, Wang G, Huang Y, Bao W, Zhang S. Integrated metabolomics and transcriptomics analyses reveal metabolic responses to TGEV infection in porcine intestinal epithelial cells. J Gen Virol 2023; 104. [PMID: 38116760 DOI: 10.1099/jgv.0.001942] [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: 12/21/2023] Open
Abstract
Transmissible gastroenteritis virus (TGEV) is a coronavirus that infects piglets with severe diarrhoea, vomiting, dehydration, and even death, causing huge economic losses to the pig industry. The underlying pathogenesis of TGEV infection and the effects of TGEV infection on host metabolites remain poorly understood. To investigate the critical metabolites and regulatory factors during TGEV infection in intestinal porcine epithelial cells (IPEC-J2), we performed metabolomic and transcriptomic analyses of TGEV-infected IPEC-J2 cells by LC/MS and RNA-seq techniques. A total of 87 differential metabolites and 489 differentially expressed genes were detected. A series of metabolites and candidate genes from glutathione metabolism and AMPK signalling pathway were examined through combined analysis of metabolome and transcriptome. We found glutathione peroxidase 3 (GPX3) is markedly reduced after TGEV infection, and a significant negative correlation between AMPK signalling pathway and TGEV infection. Exogenous addition of the AMPK activator COH-SR4 significantly downregulates stearoyl coenzyme A (SCD1) mRNA and inhibits TGEV replication; while exogenous GSK-690693 significantly promotes TGEV infection by inhibiting AMPK signalling pathway. In summary, our study provides insights into the key metabolites and regulators for TGEV infection from the metabolome and transcriptome perspective, which will offer promising antiviral metabolic and molecular targets and enrich the understanding of the existence of a similar mechanism in the host.
Collapse
Affiliation(s)
- Shuoshuo Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Yanan Cao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Chao Xu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Guangzheng Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Yanjie Huang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-product Safety, Yangzhou University, Yangzhou 225009, PR China
| | - Shuai Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, PR China
| |
Collapse
|
39
|
Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A. A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. Commun Biol 2023; 6:1115. [PMID: 37923961 PMCID: PMC10624922 DOI: 10.1038/s42003-023-05478-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
The ketogenic diet (KD) has demonstrated benefits in numerous clinical studies and animal models of disease in modulating the immune response and promoting a systemic anti-inflammatory state. Here we investigate the effects of a KD on systemic toxicity in mice following SARS-CoV-2 infection. Our data indicate that under KD, SARS-CoV-2 reduces weight loss with overall improved animal survival. Muted multi-organ transcriptional reprogramming and metabolism rewiring suggest that a KD initiates and mitigates systemic changes induced by the virus. We observed reduced metalloproteases and increased inflammatory homeostatic protein transcription in the heart, with decreased serum pro-inflammatory cytokines (i.e., TNF-α, IL-15, IL-22, G-CSF, M-CSF, MCP-1), metabolic markers of inflammation (i.e., kynurenine/tryptophane ratio), and inflammatory prostaglandins, indicative of reduced systemic inflammation in animals infected under a KD. Taken together, these data suggest that a KD can alter the transcriptional and metabolic response in animals following SARS-CoV-2 infection with improved mice health, reduced inflammation, and restored amino acid, nucleotide, lipid, and energy currency metabolism.
Collapse
Affiliation(s)
- Amelia Palermo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA
| | - Shen Li
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Johanna Ten Hoeve
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA
| | - Akshay Chellappa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Alexandra Morris
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Barbara Dillon
- Department of Environment, Health and Safety, University of California, Los Angeles, CA, 90095, USA
| | - Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yijie Wang
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Edward Cao
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Genetics, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Rebeca Acín-Perez
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Anton Petcherski
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - A Jake Lusis
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Stanley Hazen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Orian S Shirihai
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA.
- UCLA Metabolomics Center, University of California, Los Angeles, CA, 90095, USA.
- Crump Institute for Molecular Imaging, University of California, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
| | - Arjun Deb
- California Nanosystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- UCLA Cardiovascular Research Theme, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Molecular, Cell and Developmental Biology, Division of Life Sciences, University of California, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
40
|
Arnsten AFT, Ishizawa Y, Xie Z. Scientific rationale for the use of α2A-adrenoceptor agonists in treating neuroinflammatory cognitive disorders. Mol Psychiatry 2023; 28:4540-4552. [PMID: 37029295 PMCID: PMC10080530 DOI: 10.1038/s41380-023-02057-4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/09/2023]
Abstract
Neuroinflammatory disorders preferentially impair the higher cognitive and executive functions of the prefrontal cortex (PFC). This includes such challenging disorders as delirium, perioperative neurocognitive disorder, and the sustained cognitive deficits from "long-COVID" or traumatic brain injury. There are no FDA-approved treatments for these symptoms; thus, understanding their etiology is important for generating therapeutic strategies. The current review describes the molecular rationale for why PFC circuits are especially vulnerable to inflammation, and how α2A-adrenoceptor (α2A-AR) actions throughout the nervous and immune systems can benefit the circuits in PFC needed for higher cognition. The layer III circuits in the dorsolateral PFC (dlPFC) that generate and sustain the mental representations needed for higher cognition have unusual neurotransmission and neuromodulation. They are wholly dependent on NMDAR neurotransmission, with little AMPAR contribution, and thus are especially vulnerable to kynurenic acid inflammatory signaling which blocks NMDAR. Layer III dlPFC spines also have unusual neuromodulation, with cAMP magnification of calcium signaling in spines, which opens nearby potassium channels to rapidly weaken connectivity and reduce neuronal firing. This process must be tightly regulated, e.g. by mGluR3 or α2A-AR on spines, to prevent loss of firing. However, the production of GCPII inflammatory signaling reduces mGluR3 actions and markedly diminishes dlPFC network firing. Both basic and clinical studies show that α2A-AR agonists such as guanfacine can restore dlPFC network firing and cognitive function, through direct actions in the dlPFC, but also by reducing the activity of stress-related circuits, e.g. in the locus coeruleus and amygdala, and by having anti-inflammatory actions in the immune system. This information is particularly timely, as guanfacine is currently the focus of large clinical trials for the treatment of delirium, and in open label studies for the treatment of cognitive deficits from long-COVID.
Collapse
Affiliation(s)
- Amy F T Arnsten
- Department Neuroscience, Yale University School of Medicine, New Haven, CT, 056510, USA.
| | - Yumiko Ishizawa
- Department Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Zhongcong Xie
- Department Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| |
Collapse
|
41
|
Shang W, Qian H, Shen X, Wen Z, Zhang S, Chen D. Human blood metabolites and risk of severe COVID-19: A Mendelian randomization study. Eur J Clin Invest 2023; 53:e14079. [PMID: 37589179 DOI: 10.1111/eci.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/25/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Evidence supports the observational associations of human blood metabolites with the risk of severe COVID-19. However, little is known about the potential pathological mechanisms and the analysis of blood metabolites may offer a better understanding of the underlying biological processes. METHODS We applied a two-sample Mendelian randomization (MR) analysis to evaluate relationships between 486 blood metabolites and the risk of severe COVID-19. The inverse-variance weighted (IVW) model was used as the primary two-sample MR analysis method to estimate the causal relationship of the exposure on the outcome. Sensitivity analyses were implemented with Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out analysis and the funnel plot. RESULTS Four hunderd and eighty six metabolites were included for MR analysis following rigorous genetic variants selection. After MR analyses and sensitivity analysis filtration, we found weak evidence of an association between 3-hydroxybutyrate (odds ratio [OR] = 1.21, 95% CI, 1.07-1.38, p = .0036) and the risk of severe COVID-19. A series of sensitivity analyses have been carried out to confirm the rigidity of the above results. CONCLUSION This study suggested a causal relationship between 3-hydroxybutyrate and the severity of COVID-19, thus providing novel insights into biomarkers and pathways for COVID-19 prevention and clinical interventions.
Collapse
Affiliation(s)
- Weifeng Shang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hang Qian
- Anhui Medical University, Hefei, China
| | - Xuan Shen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenliang Wen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Zhang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
42
|
Guo B, Xue M, Zhang T, Gan H, Lin R, Liu M, Liao Y, Lyu J, Zheng P, Sun B. Correlation between immune-related Tryptophan-Kynurenine pathway and severity of severe pneumonia and inflammation-related polyunsaturated fatty acids. Immun Inflamm Dis 2023; 11:e1088. [PMID: 38018595 PMCID: PMC10659755 DOI: 10.1002/iid3.1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Immune dysfunction and oxidative stress caused by severe pneumonia can lead to multiple organ dysfunction and even death, causing a significant impact on health and the economy. Currently, great progress has been made in the diagnosis and treatment of this disease, but the mortality rate remains high (approximately 50%). Therefore, there is still potential for further exploration of the immune response mechanisms against severe pneumonia. OBJECTIVE This study analyzed the difference in serum metabolic profiles between patients with severe pneumonia and health individuals through metabolomics, aiming to uncover the correlation between the Tryptophan-Kynurenine pathway and the severity of severe pneumonia, as well as N-3/N-6 polyunsaturated fatty acids (PUFAs). METHODS In this study, 44 patients with severe pneumonia and 37 health controls were selected. According to the changes in the disease symptoms within the 7 days of admission, the patients were divided into aggravation (n = 22) and remission (n = 22) groups. Targeted metabolomics techniques were performed to quantify serum metabolites and analyze changes between groups. RESULTS Metabolomics analysis showed that serum kynurenine and kynurenine/tryptophan (K/T) were significantly increased and tryptophan was significantly decreased in patients with severe pneumonia; HETE and HEPE in lipids increased significantly, while eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), α-linolenic acid (linolenic acid, α-LNA), arachidonic acid (ARA), Dihomo-γ-linolenic acid (DGLA), and 13(s)-hydroperoxylinoleic acid (HPODE) decreased significantly. Additionally, the longitudinal comparison revealed that Linolenic acid, DPA, and Tryptophan increased significantly in the remission group, while and kynurenine and K/T decreased significantly. In the aggravation group, Kynurenine and K/T increased significantly, while ARA, 8(S)-hydroxyeicosatetraenoic acid (HETE), 11(S)-HETE, and Tryptophan decreased significantly. The correlation analysis matrix demonstrated that Tryptophan was positively correlated with DGLA, 12(S)-hydroxyeicosapentaenoic acid (HEPE), ARA, EPA, α-LNA, DHA, and DPA. Kynurenine was positively correlated with 8(S)-HETE and negatively correlated with DHA. Additionally, K/T was negatively correlated with DGLA, ARA, EPA, α-LNA, DHA, and DPA. CONCLUSION This study revealed that during severe pneumonia, the Tryptophan-Kynurenine pathway was activated and was positively correlated with the disease progression. On the other hand, the activation of the Tryptophan-Kynurenine pathway was negatively correlated with N-3/N-6 PUFAs.
Collapse
Affiliation(s)
- Baojun Guo
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
- School of MedicineHenan UniversityKaifengHenanChina
| | - Mingshan Xue
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Teng Zhang
- China Institute for Radiation ProtectionTaiyuanChina
| | - Hui Gan
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Runpei Lin
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Mingtao Liu
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Yuhong Liao
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Jiali Lyu
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Peiyan Zheng
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| | - Baoqing Sun
- Department of Clinical LaboratoryNational Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University (The Key Laboratory of Advanced Interdisciplinary Studies Center, Advanced Interdisciplinary Studies Center)GuangzhouChina
| |
Collapse
|
43
|
Basak I, Harfoot R, Palmer JE, Kumar A, Quiñones-Mateu ME, Schweitzer L, Hughes SM. Neuroproteomic Analysis after SARS-CoV-2 Infection Reveals Overrepresented Neurodegeneration Pathways and Disrupted Metabolic Pathways. Biomolecules 2023; 13:1597. [PMID: 38002279 PMCID: PMC10669333 DOI: 10.3390/biom13111597] [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: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Besides respiratory illness, SARS-CoV-2, the causative agent of COVID-19, leads to neurological symptoms. The molecular mechanisms leading to neuropathology after SARS-CoV-2 infection are sparsely explored. SARS-CoV-2 enters human cells via different receptors, including ACE-2, TMPRSS2, and TMEM106B. In this study, we used a human-induced pluripotent stem cell-derived neuronal model, which expresses ACE-2, TMPRSS2, TMEM106B, and other possible SARS-CoV-2 receptors, to evaluate its susceptibility to SARS-CoV-2 infection. The neurons were exposed to SARS-CoV-2, followed by RT-qPCR, immunocytochemistry, and proteomic analyses of the infected neurons. Our findings showed that SARS-CoV-2 infects neurons at a lower rate than other human cells; however, the virus could not replicate or produce infectious virions in this neuronal model. Despite the aborted SARS-CoV-2 replication, the infected neuronal nuclei showed irregular morphology compared to other human cells. Since cytokine storm is a significant effect of SARS-CoV-2 infection in COVID-19 patients, in addition to the direct neuronal infection, the neurons were treated with pre-conditioned media from SARS-CoV-2-infected lung cells, and the neuroproteomic changes were investigated. The limited SARS-CoV-2 infection in the neurons and the neurons treated with the pre-conditioned media showed changes in the neuroproteomic profile, particularly affecting mitochondrial proteins and apoptotic and metabolic pathways, which may lead to the development of neurological complications. The findings from our study uncover a possible mechanism behind SARS-CoV-2-mediated neuropathology that might contribute to the lingering effects of the virus on the human brain.
Collapse
Affiliation(s)
- Indranil Basak
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand (M.E.Q.-M.)
| | - Jennifer E. Palmer
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Abhishek Kumar
- Centre for Protein Research, University of Otago, Dunedin 9016, New Zealand
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand (M.E.Q.-M.)
| | - Lucia Schweitzer
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie M. Hughes
- Brain Health Research Centre, Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| |
Collapse
|
44
|
Wong AC, Devason AS, Umana IC, Cox TO, Dohnalová L, Litichevskiy L, Perla J, Lundgren P, Etwebi Z, Izzo LT, Kim J, Tetlak M, Descamps HC, Park SL, Wisser S, McKnight AD, Pardy RD, Kim J, Blank N, Patel S, Thum K, Mason S, Beltra JC, Michieletto MF, Ngiow SF, Miller BM, Liou MJ, Madhu B, Dmitrieva-Posocco O, Huber AS, Hewins P, Petucci C, Chu CP, Baraniecki-Zwil G, Giron LB, Baxter AE, Greenplate AR, Kearns C, Montone K, Litzky LA, Feldman M, Henao-Mejia J, Striepen B, Ramage H, Jurado KA, Wellen KE, O'Doherty U, Abdel-Mohsen M, Landay AL, Keshavarzian A, Henrich TJ, Deeks SG, Peluso MJ, Meyer NJ, Wherry EJ, Abramoff BA, Cherry S, Thaiss CA, Levy M. Serotonin reduction in post-acute sequelae of viral infection. Cell 2023; 186:4851-4867.e20. [PMID: 37848036 PMCID: PMC11227373 DOI: 10.1016/j.cell.2023.09.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/27/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Post-acute sequelae of COVID-19 (PASC, "Long COVID") pose a significant global health challenge. The pathophysiology is unknown, and no effective treatments have been found to date. Several hypotheses have been formulated to explain the etiology of PASC, including viral persistence, chronic inflammation, hypercoagulability, and autonomic dysfunction. Here, we propose a mechanism that links all four hypotheses in a single pathway and provides actionable insights for therapeutic interventions. We find that PASC are associated with serotonin reduction. Viral infection and type I interferon-driven inflammation reduce serotonin through three mechanisms: diminished intestinal absorption of the serotonin precursor tryptophan; platelet hyperactivation and thrombocytopenia, which impacts serotonin storage; and enhanced MAO-mediated serotonin turnover. Peripheral serotonin reduction, in turn, impedes the activity of the vagus nerve and thereby impairs hippocampal responses and memory. These findings provide a possible explanation for neurocognitive symptoms associated with viral persistence in Long COVID, which may extend to other post-viral syndromes.
Collapse
Affiliation(s)
- Andrea C Wong
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Ashwarya S Devason
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iboro C Umana
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy O Cox
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lenka Dohnalová
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Molecular Bio Science, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lev Litichevskiy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Perla
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Patrick Lundgren
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zienab Etwebi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luke T Izzo
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jihee Kim
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Tetlak
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hélène C Descamps
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Stephen Wisser
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron D McKnight
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan D Pardy
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwon Kim
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Niklas Blank
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shaan Patel
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina Thum
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Mason
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Christophe Beltra
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michaël F Michieletto
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brittany M Miller
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Megan J Liou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bhoomi Madhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Oxana Dmitrieva-Posocco
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Alex S Huber
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter Hewins
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Petucci
- Metabolomics Core, Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Candice P Chu
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gwen Baraniecki-Zwil
- Department of Physical Medicine and Rehabilitation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charlotte Kearns
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen Montone
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie A Litzky
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorge Henao-Mejia
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Holly Ramage
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kellie A Jurado
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA; Rush Center for Integrated Microbiome and Chronobiology Research, Chicago, IL, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nuala J Meyer
- Division of Pulmonary and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Abramoff
- Department of Physical Medicine and Rehabilitation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Sara Cherry
- Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Obesity, Diabetes and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Maayan Levy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
45
|
Yang K, Kang Z, Guan W, Lotfi-Emran S, Mayer ZJ, Guerrero CR, Steffen BT, Puskarich MA, Tignanelli CJ, Lusczek E, Safo SE. Developing A Baseline Metabolomic Signature Associated with COVID-19 Severity: Insights from Prospective Trials Encompassing 13 U.S. Centers. Metabolites 2023; 13:1107. [PMID: 37999202 PMCID: PMC10672920 DOI: 10.3390/metabo13111107] [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: 09/26/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/25/2023] Open
Abstract
Metabolic disease is a significant risk factor for severe COVID-19 infection, but the contributing pathways are not yet fully elucidated. Using data from two randomized controlled trials across 13 U.S. academic centers, our goal was to characterize metabolic features that predict severe COVID-19 and define a novel baseline metabolomic signature. Individuals (n = 133) were dichotomized as having mild or moderate/severe COVID-19 disease based on the WHO ordinal scale. Blood samples were analyzed using the Biocrates platform, providing 630 targeted metabolites for analysis. Resampling techniques and machine learning models were used to determine metabolomic features associated with severe disease. Ingenuity Pathway Analysis (IPA) was used for functional enrichment analysis. To aid in clinical decision making, we created baseline metabolomics signatures of low-correlated molecules. Multivariable logistic regression models were fit to associate these signatures with severe disease on training data. A three-metabolite signature, lysophosphatidylcholine a C17:0, dihydroceramide (d18:0/24:1), and triacylglyceride (20:4_36:4), resulted in the best discrimination performance with an average test AUROC of 0.978 and F1 score of 0.942. Pathways related to amino acids were significantly enriched from the IPA analyses, and the mitogen-activated protein kinase kinase 5 (MAP2K5) was differentially activated between groups. In conclusion, metabolites related to lipid metabolism efficiently discriminated between mild vs. moderate/severe disease. SDMA and GABA demonstrated the potential to discriminate between these two groups as well. The mitogen-activated protein kinase kinase 5 (MAP2K5) regulator is differentially activated between groups, suggesting further investigation as a potential therapeutic pathway.
Collapse
Affiliation(s)
- Kaifeng Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA (S.E.S.)
| | - Zhiyu Kang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA (S.E.S.)
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA (S.E.S.)
| | - Sahar Lotfi-Emran
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J. Mayer
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Candace R. Guerrero
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian T. Steffen
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA (E.L.)
| | - Michael A. Puskarich
- Department of Emergency Medicine, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN 55455, USA
| | - Christopher J. Tignanelli
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA (E.L.)
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elizabeth Lusczek
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA (E.L.)
| | - Sandra E. Safo
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA (S.E.S.)
| |
Collapse
|
46
|
Roberts I, Wright Muelas M, Taylor JM, Davison AS, Winder CL, Goodacre R, Kell DB. Quantitative LC-MS study of compounds found predictive of COVID-19 severity and outcome. Metabolomics 2023; 19:87. [PMID: 37853293 PMCID: PMC10584727 DOI: 10.1007/s11306-023-02048-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/03/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Since the beginning of the SARS-CoV-2 pandemic in December 2019 multiple metabolomics studies have proposed predictive biomarkers of infection severity and outcome. Whilst some trends have emerged, the findings remain intangible and uninformative when it comes to new patients. OBJECTIVES In this study, we accurately quantitate a subset of compounds in patient serum that were found predictive of severity and outcome. METHODS A targeted LC-MS method was used in 46 control and 95 acute COVID-19 patient samples to quantitate the selected metabolites. These compounds included tryptophan and its degradation products kynurenine and kynurenic acid (reflective of immune response), butyrylcarnitine and its isomer (reflective of energy metabolism) and finally 3',4'-didehydro-3'-deoxycytidine, a deoxycytidine analogue, (reflective of host viral defence response). We subsequently examine changes in those markers by disease severity and outcome relative to those of control patients' levels. RESULTS & CONCLUSION Finally, we demonstrate the added value of the kynurenic acid/tryptophan ratio for severity and outcome prediction and highlight the viral detection potential of ddhC.
Collapse
Affiliation(s)
- Ivayla Roberts
- Department of Biochemistry and Systems Biology, Centre for Metabolomics Research (CMR), Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Centre for Metabolomics Research (CMR), Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joseph M Taylor
- Liverpool Clinical Laboratories, Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Andrew S Davison
- Liverpool Clinical Laboratories, Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Catherine L Winder
- Department of Biochemistry and Systems Biology, Centre for Metabolomics Research (CMR), Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Centre for Metabolomics Research (CMR), Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Douglas B Kell
- Department of Biochemistry and Systems Biology, Centre for Metabolomics Research (CMR), Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Chemitorvet, 2000, Kgs Lyngby, Denmark.
| |
Collapse
|
47
|
Nair S, Nova-Lamperti E, Labarca G, Kulasinghe A, Short KR, Carrión F, Salomon C. Genomic communication via circulating extracellular vesicles and long-term health consequences of COVID-19. J Transl Med 2023; 21:709. [PMID: 37817137 PMCID: PMC10563316 DOI: 10.1186/s12967-023-04552-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
COVID-19 continues to affect an unprecedented number of people with the emergence of new variants posing a serious challenge to global health. There is an expansion of knowledge in understanding the pathogenesis of Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the impact of the acute disease on multiple organs. In addition, growing evidence reports that the impact of COVID-19 on different organs persists long after the recovery phase of the disease, leading to long-term consequences of COVID-19. These long-term consequences involve pulmonary as well as extra-pulmonary sequelae of the disease. Noteably, recent research has shown a potential association between COVID-19 and change in the molecular cargo of extracellular vesicles (EVs). EVs are vesicles released by cells and play an important role in cell communication by transfer of bioactive molecules between cells. Emerging evidence shows a strong link between EVs and their molecular cargo, and regulation of metabolism in health and disease. This review focuses on current knowledge about EVs and their potential role in COVID-19 pathogenesis, their current and future implications as tools for biomarker and therapeutic development and their possible effects on long-term impact of COVID-19.
Collapse
Affiliation(s)
- Soumyalekshmi Nair
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Clinical Biochemistry and Immunology Department, Pharmacy Faculty, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Labarca
- Molecular and Translational Immunology Laboratory, Clinical Biochemistry and Immunology Department, Pharmacy Faculty, Universidad de Concepción, Concepción, Chile
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Qld, 4102, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Flavio Carrión
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile.
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Qld, 4072, Australia.
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile.
| |
Collapse
|
48
|
Michaelis S, Zelzer S, Schneider C, Schnedl WJ, Baranyi A, Meinitzer A, Herrmann M, Enko D. The possible role of quinolinic acid as a predictive marker in patients with SARS-CoV-2. Clin Chim Acta 2023; 550:117583. [PMID: 37802207 DOI: 10.1016/j.cca.2023.117583] [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: 07/11/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND AND AIMS Quinolinic acid (QA) is a metabolite of the kynurenine pathway, which is activated by inflammatory stimuli during viral infection. We investigated the role of QA in patients infected with SARS-CoV-2, particularly its prognostic value for survival. METHODS Overall, 104 unvaccinated inpatients were included, divided into a survival (N = 80) and a deceased group (N = 24). Plasma levels of tryptophan, kynurenine, QA, C-reactive protein (CRP) and procalcitonin (PCT) were measured on admission and after seven days. The QA/TRP ratio and the relative differences between the measurements for QA (QA-Diff) and QA/TRP (Diff-QA/TRP) were calculated. RESULTS Among the kynurenine pathway markers, QA-Diff showed the highest discriminatory power for the survival prognosis (Youden index 0.467, cut-off -1.3 %, AUC 0.733, p < 0.001, sensitivity 0.79, specificity 0.675). Among the inflammatory markers, CRP showed the highest discriminatory power (Youden index 0.533, cut-off 25.0 mg/L, AUC 0.794, p < 0.001, sensitivity 0.958, specificity 0.575). A significant correlation between QA and PCT was found on admission and after one week (Spearman's rho 0.455 and 0.539, all p-values < 0.001). CONCLUSIONS QA may serve as prognostic marker for survival in patients with SARS-CoV-2. The repeated measurements during the first week of the disease may enhance the prognostic power.
Collapse
Affiliation(s)
- Simon Michaelis
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Hochsteiermark, Vordernberger Straße 42, 8700 Leoben, Austria.
| | - Sieglinde Zelzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Christopher Schneider
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Hochsteiermark, Vordernberger Straße 42, 8700 Leoben, Austria
| | - Wolfgang J Schnedl
- Practice for General Internal Medicine, Dr.-Theodor-Körner-Straße 19b, 8600 Bruck/Mur, Austria
| | - Andreas Baranyi
- Department of Psychiatry and Psychotherapeutic Medicine, Medical, University of Graz, Auenbruggerplatz 31, 8036 Graz, Austria
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Markus Herrmann
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Dietmar Enko
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Hochsteiermark, Vordernberger Straße 42, 8700 Leoben, Austria; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| |
Collapse
|
49
|
Fuller H, Zhu Y, Nicholas J, Chatelaine HA, Drzymalla EM, Sarvestani AK, Julián-Serrano S, Tahir UA, Sinnott-Armstrong N, Raffield LM, Rahnavard A, Hua X, Shutta KH, Darst BF. Metabolomic epidemiology offers insights into disease aetiology. Nat Metab 2023; 5:1656-1672. [PMID: 37872285 PMCID: PMC11164316 DOI: 10.1038/s42255-023-00903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Metabolomic epidemiology is the high-throughput study of the relationship between metabolites and health-related traits. This emerging and rapidly growing field has improved our understanding of disease aetiology and contributed to advances in precision medicine. As the field continues to develop, metabolomic epidemiology could lead to the discovery of diagnostic biomarkers predictive of disease risk, aiding in earlier disease detection and better prognosis. In this Review, we discuss key advances facilitated by the field of metabolomic epidemiology for a range of conditions, including cardiometabolic diseases, cancer, Alzheimer's disease and COVID-19, with a focus on potential clinical utility. Core principles in metabolomic epidemiology, including study design, causal inference methods and multi-omic integration, are briefly discussed. Future directions required for clinical translation of metabolomic epidemiology findings are summarized, emphasizing public health implications. Further work is needed to establish which metabolites reproducibly improve clinical risk prediction in diverse populations and are causally related to disease progression.
Collapse
Affiliation(s)
- Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yiwen Zhu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jayna Nicholas
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Haley A Chatelaine
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Emily M Drzymalla
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Afrand K Sarvestani
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | | | - Usman A Tahir
- Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Xinwei Hua
- Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
50
|
El-Derany MO, Hanna DMF, Youshia J, Elmowafy E, Farag MA, Azab SS. Metabolomics-directed nanotechnology in viral diseases management: COVID-19 a case study. Pharmacol Rep 2023; 75:1045-1065. [PMID: 37587394 PMCID: PMC10539420 DOI: 10.1007/s43440-023-00517-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently regarded as the twenty-first century's plague accounting for coronavirus disease 2019 (COVID-19). Besides its reported symptoms affecting the respiratory tract, it was found to alter several metabolic pathways inside the body. Nanoparticles proved to combat viral infections including COVID-19 to demonstrate great success in developing vaccines based on mRNA technology. However, various types of nanoparticles can affect the host metabolome. Considering the increasing proportion of nano-based vaccines, this review compiles and analyses how COVID-19 and nanoparticles affect lipids, amino acids, and carbohydrates metabolism. A search was conducted on PubMed, ScienceDirect, Web of Science for available information on the interrelationship between metabolomics and immunity in the context of SARS-CoV-2 infection and the effect of nanoparticles on metabolite levels. It was clear that SARS-CoV-2 disrupted several pathways to ensure a sufficient supply of its building blocks to facilitate its replication. Such information can help in developing treatment strategies against viral infections and COVID-19 based on interventions that overcome these metabolic changes. Furthermore, it showed that even drug-free nanoparticles can exert an influence on biological systems as evidenced by metabolomics.
Collapse
Affiliation(s)
- Marwa O El-Derany
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Diana M F Hanna
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt
| | - John Youshia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Enas Elmowafy
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr El-Aini St., P.B. 11562, Cairo, Egypt
| | - Samar S Azab
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt.
| |
Collapse
|