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Valderrábano RJ, Wipper B, Pencina KM, Migaud M, Shang YV, Latham NK, Montano M, Cunningham JM, Wilson L, Peng L, Memish-Beleva Y, Bhargava A, Swain PM, Lehman P, Lavu S, Livingston DJ, Bhasin S. Dysregulated nicotinamide adenine dinucleotide metabolome in patients hospitalized with COVID-19. Aging Cell 2024:e14326. [PMID: 39354697 DOI: 10.1111/acel.14326] [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: 03/14/2024] [Revised: 07/08/2024] [Accepted: 08/01/2024] [Indexed: 10/03/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) depletion has been postulated as a contributor to the severity of COVID-19; however, no study has prospectively characterized NAD+ and its metabolites in relation to disease severity in patients with COVID-19. We measured NAD+ and its metabolites in 56 hospitalized patients with COVID-19 and in two control groups without COVID-19: (1) 31 age- and sex-matched adults with comorbidities, and (2) 30 adults without comorbidities. Blood NAD+ concentrations in COVID-19 group were only slightly lower than in the control groups (p < 0.05); however, plasma 1-methylnicotinamide concentrations were significantly higher in patients with COVID-19 (439.7 ng/mL, 95% CI: 234.0, 645.4 ng/mL) than in age- and sex-matched controls (44.5 ng/mL, 95% CI: 15.6, 73.4) and in healthy controls (18.1 ng/mL, 95% CI 15.4, 20.8; p < 0.001 for each comparison). Plasma nicotinamide concentrations were also higher in COVID-19 group and in controls with comorbidities than in healthy control group. Plasma concentrations of 2-methyl-2-pyridone-5-carboxamide (2-PY), but not NAD+, were significantly associated with increased risk of death (HR = 3.65; 95% CI 1.09, 12.2; p = 0.036) and escalation in level of care (HR = 2.90, 95% CI 1.01, 8.38, p = 0.049). RNAseq and RTqPCR analyses of PBMC mRNA found upregulation of multiple genes involved in NAD+ synthesis as well as degradation, and dysregulation of NAD+-dependent processes including immune response, DNA repair, metabolism, apoptosis/autophagy, redox reactions, and mitochondrial function. Blood NAD+ concentrations are modestly reduced in COVID-19; however, NAD+ turnover is substantially increased with upregulation of genes involved in both NAD+ biosynthesis and degradation, supporting the rationale for NAD+ augmentation to attenuate disease severity.
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Affiliation(s)
- Rodrigo J Valderrábano
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin Wipper
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Karol Mateusz Pencina
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marie Migaud
- Department of Pharmacology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Yili Valentine Shang
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nancy K Latham
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Monty Montano
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James M Cunningham
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren Wilson
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Liming Peng
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yusnie Memish-Beleva
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avantika Bhargava
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela M Swain
- Metro International Biotech, Worcester, Massachusetts, USA
| | - Phoebe Lehman
- Metro International Biotech, Worcester, Massachusetts, USA
| | - Siva Lavu
- Metro International Biotech, Worcester, Massachusetts, USA
| | | | - Shalender Bhasin
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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2
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Wong SN, Li S, Low KH, Chan HW, Zhang X, Chow S, Hui B, Chow PCY, Chow SF. Development of favipiravir dry powders for intranasal delivery: An integrated cocrystal and particle engineering approach via spray freeze drying. Int J Pharm 2024; 653:123896. [PMID: 38346602 DOI: 10.1016/j.ijpharm.2024.123896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
The therapeutic potential of pharmaceutical cocrystals in intranasal applications remains largely unexplored despite progressive advancements in cocrystal research. We present the application of spray freeze drying (SFD) in successful fabrication of a favipiravir-pyridinecarboxamide cocrystal nasal powder formulation for potential treatment of broad-spectrum antiviral infections. Preliminary screening via mechanochemistry revealed that favipiravir (FAV) can cocrystallize with isonicotinamide (INA), but not nicotinamide (NCT) and picolinamide (PIC) notwithstanding their structural similarity. The cocrystal formation was characterized by differential scanning calorimetry, Fourier-transform infrared spectroscopy, and unit cell determination through Rietveld refinement of powder X-ray analysis. FAV-INA crystalized in a monoclinic space group P21/c with a unit cell volume of 1223.54(3) Å3, accommodating one FAV molecule and one INA molecule in the asymmetric unit. The cocrystal was further reproduced as intranasal dry powders by SFD, of which the morphology, particle size, in vitro drug release, and nasal deposition were assessed. The non-porous flake shaped FAV-INA powders exhibited a mean particle size of 19.79 ± 2.61 μm, rendering its suitability for intranasal delivery. Compared with raw FAV, FAV-INA displayed a 3-fold higher cumulative fraction of drug permeated in Franz diffusion cells at 45 min (p = 0.001). Dose fraction of FAV-INA deposited in the nasal fraction of a customized 3D-printed nasal cast reached over 80 %, whereas the fine particle fraction remained below 6 % at a flow rate of 15 L/min, suggesting high nasal deposition whilst minimal lung deposition. FAV-INA was safe in RPMI 2650 nasal and SH-SY5Y neuroblastoma cells without any in vitro cytotoxicity observed. This study demonstrated that combining the merits of cocrystallization and particle engineering via SFD can propel the development of advanced dry powder formulations for intranasal drug delivery.
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Affiliation(s)
- Si Nga Wong
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region
| | - Si Li
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region
| | - Kam-Hung Low
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Ho Wan Chan
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Xinyue Zhang
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Stephanie Chow
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Bo Hui
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Philip C Y Chow
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Shing Fung Chow
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region.
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3
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Li J, Wang J, Wang H. Emerging Landscape of Preclinical Models for Studying COVID-19 Neurologic Diseases. ACS Pharmacol Transl Sci 2023; 6:1323-1339. [PMID: 37854617 PMCID: PMC10580392 DOI: 10.1021/acsptsci.3c00127] [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: 06/21/2023] [Indexed: 10/20/2023]
Abstract
COVID-19 (Coronavirus Disease 2019) is an infectious disease caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and has globally infected 768 million people and caused over 6 million deaths. COVID-19 primarily affects the respiratory system but increasing reports of neurologic symptoms associated with COVID-19 have been reported in the literature. The exact mechanism behind COVID-19 neurologic pathophysiology remains poorly understood due to difficulty quantifying clinical neurologic symptoms in humans and correlating them to findings in human post-mortem samples and animal models. Thus, robust preclinical experimental models for COVID-19 neurologic manifestations are urgently needed. Here, we review recent advances in in vitro, in vivo, and other models and technologies for studying COVID-19 including primary cell cultures, pluripotent stem cell-derived neurons and organoids, rodents, nonhuman primates, 3D bioprinting, artificial intelligence, and multiomics. We specifically focus our discussion on the contribution, recent advancements, and limitations these preclinical models have on furthering our understanding of COVID-19's neuropathic physiology. We also discuss these models' roles in the screening and development of therapeutics, vaccines, antiviral drugs, and herbal medicine, and on future opportunities for COVID-19 neurologic research and clinical management.
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Affiliation(s)
- Jason Li
- Department
of Neurology, Indiana University School
of Medicine, Indianapolis, Indiana 46202, United States
| | - Jing Wang
- Department
of Cellular and Molecular Medicine, University
of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Hu Wang
- Institute
of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore 21215, United States
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4
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Thi Hong Nguyen N, Ou TY, Huy LD, Shih CL, Chang YM, Phan TP, Huang CC. A global analysis of COVID-19 infection fatality rate and its associated factors during the Delta and Omicron variant periods: an ecological study. Front Public Health 2023; 11:1145138. [PMID: 37333556 PMCID: PMC10274323 DOI: 10.3389/fpubh.2023.1145138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/28/2023] [Indexed: 06/20/2023] Open
Abstract
Background The Omicron variant of SARS-CoV-2 is more highly infectious and transmissible than prior variants of concern. It was unclear which factors might have contributed to the alteration of COVID-19 cases and deaths during the Delta and Omicron variant periods. This study aimed to compare the COVID-19 average weekly infection fatality rate (AWIFR), investigate factors associated with COVID-19 AWIFR, and explore the factors linked to the increase in COVID-19 AWIFR between two periods of Delta and Omicron variants. Materials and methods An ecological study has been conducted among 110 countries over the first 12 weeks during two periods of Delta and Omicron variant dominance using open publicly available datasets. Our analysis included 102 countries in the Delta period and 107 countries in the Omicron period. Linear mixed-effects models and linear regression models were used to explore factors associated with the variation of AWIFR over Delta and Omicron periods. Findings During the Delta period, the lower AWIFR was witnessed in countries with better government effectiveness index [β = -0.762, 95% CI (-1.238)-(-0.287)] and higher proportion of the people fully vaccinated [β = -0.385, 95% CI (-0.629)-(-0.141)]. In contrast, a higher burden of cardiovascular diseases was positively associated with AWIFR (β = 0.517, 95% CI 0.102-0.932). Over the Omicron period, while years lived with disability (YLD) caused by metabolism disorders (β = 0.843, 95% CI 0.486-1.2), the proportion of the population aged older than 65 years (β = 0.737, 95% CI 0.237-1.238) was positively associated with poorer AWIFR, and the high proportion of the population vaccinated with a booster dose [β = -0.321, 95% CI (-0.624)-(-0.018)] was linked with the better outcome. Over two periods of Delta and Omicron, the increase in government effectiveness index was associated with a decrease in AWIFR [β = -0.438, 95% CI (-0.750)-(-0.126)]; whereas, higher death rates caused by diabetes and kidney (β = 0.472, 95% CI 0.089-0.855) and percentage of population aged older than 65 years (β = 0.407, 95% CI 0.013-0.802) were associated with a significant increase in AWIFR. Conclusion The COVID-19 infection fatality rates were strongly linked with the coverage of vaccination rate, effectiveness of government, and health burden related to chronic diseases. Therefore, proper policies for the improvement of vaccination coverage and support of vulnerable groups could substantially mitigate the burden of COVID-19.
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Affiliation(s)
- Nhi Thi Hong Nguyen
- School of Health Care Administration, College of Management, Taipei Medical University, Taipei, Taiwan
- Health Personnel Training Institute, University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Tsong-Yih Ou
- Division of Infectious Diseases, Department of Internal Medicine, Taipei Municipal Wanfang Hospital-Managed by Taipei Medical University, Taipei, Taiwan
- Department of Nursing, Cardinal Tien Junior College of Healthcare and Management, Taipei, Taiwan
- Department of Medical Quality, Taipei Municipal Wanfang Hospital-Managed by Taipei Medical University, Taipei, Taiwan
| | - Le Duc Huy
- Health Personnel Training Institute, University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Chung-Liang Shih
- National Health Insurance Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yao-Mao Chang
- School of Health Care Administration, College of Management, Taipei Medical University, Taipei, Taiwan
- Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Thanh-Phuc Phan
- School of Health Care Administration, College of Management, Taipei Medical University, Taipei, Taiwan
- International Ph.D. Program in Biotech and Healthcare Management, College of Management, Taipei Medical University, Taipei, Taiwan
- University of Medical Center, Ho Chi Minh City, Vietnam
| | - Chung-Chien Huang
- School of Health Care Administration, College of Management, Taipei Medical University, Taipei, Taiwan
- Department of Medical Quality, Taipei Municipal Wanfang Hospital-Managed by Taipei Medical University, Taipei, Taiwan
- International Ph.D. Program in Biotech and Healthcare Management, College of Management, Taipei Medical University, Taipei, Taiwan
- Department of Long-Term Care, School of Gerontology Health Management, College of Nursing, Taipei Medical University, Taipei, Taiwan
- Department and School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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5
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Murali R, Wanjari UR, Mukherjee AG, Gopalakrishnan AV, Kannampuzha S, Namachivayam A, Madhyastha H, Renu K, Ganesan R. Crosstalk between COVID-19 Infection and Kidney Diseases: A Review on the Metabolomic Approaches. Vaccines (Basel) 2023; 11:vaccines11020489. [PMID: 36851366 PMCID: PMC9959335 DOI: 10.3390/vaccines11020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a respiratory disorder. Various organ injuries have been reported in response to this virus, including kidney injury and, in particular, kidney tubular injury. It has been discovered that infection with the virus does not only cause new kidney disease but also increases treatment difficulty and mortality rates in people with kidney diseases. In individuals hospitalized with COVID-19, urinary metabolites from several metabolic pathways are used to distinguish between patients with acute kidney injury (AKI) and those without. This review summarizes the pathogenesis, pathophysiology, treatment strategies, and role of metabolomics in relation to AKI in COVID-19 patients. Metabolomics is likely to play a greater role in predicting outcomes for patients with kidney disease and COVID-19 with varying levels of severity in the near future as data on metabolic profiles expand rapidly. Here, we also discuss the correlation between COVID-19 and kidney diseases and the available metabolomics approaches.
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Affiliation(s)
- Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Correspondence: (A.V.G.); (R.G.)
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kaviyarasi Renu
- Center of Molecular Medicine and Diagnostics (COMMAND), Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Correspondence: (A.V.G.); (R.G.)
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6
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Spectroscopic methods for COVID-19 detection and early diagnosis. Virol J 2022; 19:152. [PMID: 36138463 PMCID: PMC9502632 DOI: 10.1186/s12985-022-01867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
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7
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Baros-Steyl SS, Al Heialy S, Semreen AH, Semreen MH, Blackburn JM, Soares NC. A review of mass spectrometry-based analyses to understand COVID-19 convalescent plasma mechanisms of action. Proteomics 2022; 22:e2200118. [PMID: 35809024 PMCID: PMC9349457 DOI: 10.1002/pmic.202200118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/08/2023]
Abstract
The spread of coronavirus disease 2019 (COVID‐19) viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become a worldwide pandemic claiming several thousands of lives worldwide. During this pandemic, several studies reported the use of COVID‐19 convalescent plasma (CCP) from recovered patients to treat severely or critically ill patients. Although this historical and empirical treatment holds immense potential as a first line of response against eventual future unforeseen viral epidemics, there are several concerns regarding the efficacy and safety of this approach. This critical review aims to pinpoint the possible role of mass spectrometry‐based analysis in the identification of unique molecular component proteins, peptides, and metabolites of CCP that explains the therapeutic mechanism of action against COVID‐19. Additionally, the text critically reviews the potential application of mass spectrometry approaches in the search for novel plasma biomarkers that may enable a rapid and accurate assessment of the safety and efficacy of CCP. Considering the relative low‐cost value involved in the CCP therapy, this proposed line of research represents a tangible scientific challenge that will be translated into clinical practice and help save several thousand lives around the world, specifically in low‐ and middle‐income countries.
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Affiliation(s)
- Seanantha S Baros-Steyl
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakin-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Ahlam H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy-Department of Medicinal Chemistry, University of Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
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8
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Gu M, Pan H, Yuan Y, Zhou X, Chen L, Wang X, Fang F, Hu L, Xie Y, Shen C. Sera Metabolomics Characterization of Patients at Different Stages in Wuhan Identifies Critical Biomarkers of COVID-19. Front Cell Infect Microbiol 2022; 12:882661. [PMID: 35586248 PMCID: PMC9108257 DOI: 10.3389/fcimb.2022.882661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
We have witnessed the 2-year-long global rampage of COVID-19 caused by the wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, knowledge about biomarkers of the entire COVID-19 process is limited. Identification of the systemic features of COVID-19 will lead to critical biomarkers and therapeutic targets for early intervention and clinical disease course prediction. Here, we performed a comprehensive analysis of clinical measurements and serum metabolomics in 199 patients with different stages of COVID-19. In particular, our study is the first serum metabolomic analysis of critical rehabilitation patients and critical death patients. We found many differential metabolites in the comparison of metabolomic results between ordinary, severe, and critical patients and uninfected patients. Through the metabolomic results of COVID-19 patients in various stages, and critical rehabilitation patients and critical death patients, we identified a series of differential metabolites as biomarkers, a separate queue and precise distinction, and predicted COVID-19 verification. These differentially expressed metabolites, included 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate, propylparaben, 20-hydroxyeicosatetraenoic acid, triethanolamine, chavicol, disialosyl galactosyl globoside, 1-arachidonoylglycerophosphoinositol, and alpha-methylstyrene, all of which have been identified for the first time as biomarkers in COVID-19 progression. These biomarkers are involved in many pathological and physiological pathways of COVID-19, for example, immune responses, platelet degranulation, and metabolism which might result in pathogenesis. Our results showed valuable information about metabolites obviously altered in COVID-19 patients with different stages, which could shed light on the pathogenesis as well as serve as potential therapeutic agents of COVID-19.
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Affiliation(s)
- Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Huaqin Pan
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University; Clinical Research Center of Hubei Critical Care Medicine, Wuhan, China
| | - Yuncong Yuan
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Xuemin Zhou
- Shanghai BIOTREE Biological Technology Co., Ltd, Shanghai, China
| | - Luojia Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xingran Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Fang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liu Hu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaxuan Xie
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Chao Shen
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
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9
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Treatment of SARS-CoV-2-induced pneumonia with NAD + and NMN in two mouse models. Cell Discov 2022; 8:38. [PMID: 35487885 PMCID: PMC9053567 DOI: 10.1038/s41421-022-00409-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/02/2022] [Indexed: 12/14/2022] Open
Abstract
The global COVID-19 epidemic has spread rapidly around the world and caused the death of more than 5 million people. It is urgent to develop effective strategies to treat COVID-19 patients. Here, we revealed that SARS-CoV-2 infection resulted in the dysregulation of genes associated with NAD+ metabolism, immune response, and cell death in mice, similar to that in COVID-19 patients. We therefore investigated the effect of treatment with NAD+ and its intermediate (NMN) and found that the pneumonia phenotypes, including excessive inflammatory cell infiltration, hemolysis, and embolization in SARS-CoV-2-infected lungs were significantly rescued. Cell death was suppressed substantially by NAD+ and NMN supplementation. More strikingly, NMN supplementation can protect 30% of aged mice infected with the lethal mouse-adapted SARS-CoV-2 from death. Mechanically, we found that NAD+ or NMN supplementation partially rescued the disturbed gene expression and metabolism caused by SARS-CoV-2 infection. Thus, our in vivo mouse study supports trials for treating COVID-19 patients by targeting the NAD+ pathway.
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10
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Novak Kujundžić R. COVID-19: Are We Facing Secondary Pellagra Which Cannot Simply Be Cured by Vitamin B3? Int J Mol Sci 2022; 23:ijms23084309. [PMID: 35457123 PMCID: PMC9032523 DOI: 10.3390/ijms23084309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Immune response to SARS-CoV-2 and ensuing inflammation pose a huge challenge to the host’s nicotinamide adenine dinucleotide (NAD+) metabolism. Humans depend on vitamin B3 for biosynthesis of NAD+, indispensable for many metabolic and NAD+-consuming signaling reactions. The balance between its utilization and resynthesis is vitally important. Many extra-pulmonary symptoms of COVID-19 strikingly resemble those of pellagra, vitamin B3 deficiency (e.g., diarrhoea, dermatitis, oral cavity and tongue manifestations, loss of smell and taste, mental confusion). In most developed countries, pellagra is successfully eradicated by vitamin B3 fortification programs. Thus, conceivably, it has not been suspected as a cause of COVID-19 symptoms. Here, the deregulation of the NAD+ metabolism in response to the SARS-CoV-2 infection is reviewed, with special emphasis on the differences in the NAD+ biosynthetic pathway’s efficiency in conditions predisposing for the development of serious COVID-19. SARS-CoV-2 infection-induced NAD+ depletion and the elevated levels of its metabolites contribute to the development of a systemic disease. Acute liberation of nicotinamide (NAM) in antiviral NAD+-consuming reactions potentiates “NAM drain”, cooperatively mediated by nicotinamide N-methyltransferase and aldehyde oxidase. “NAM drain” compromises the NAD+ salvage pathway’s fail-safe function. The robustness of the host’s NAD+ salvage pathway, prior to the SARS-CoV-2 infection, is an important determinant of COVID-19 severity and persistence of certain symptoms upon resolution of infection.
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Affiliation(s)
- Renata Novak Kujundžić
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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11
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Roberts I, Wright Muelas M, Taylor JM, Davison AS, Xu Y, Grixti JM, Gotts N, Sorokin A, Goodacre R, Kell DB. Untargeted metabolomics of COVID-19 patient serum reveals potential prognostic markers of both severity and outcome. Metabolomics 2021; 18:6. [PMID: 34928464 PMCID: PMC8686810 DOI: 10.1007/s11306-021-01859-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The diagnosis of COVID-19 is normally based on the qualitative detection of viral nucleic acid sequences. Properties of the host response are not measured but are key in determining outcome. Although metabolic profiles are well suited to capture host state, most metabolomics studies are either underpowered, measure only a restricted subset of metabolites, compare infected individuals against uninfected control cohorts that are not suitably matched, or do not provide a compact predictive model. OBJECTIVES Here we provide a well-powered, untargeted metabolomics assessment of 120 COVID-19 patient samples acquired at hospital admission. The study aims to predict the patient's infection severity (i.e., mild or severe) and potential outcome (i.e., discharged or deceased). METHODS High resolution untargeted UHPLC-MS/MS analysis was performed on patient serum using both positive and negative ionization modes. A subset of 20 intermediary metabolites predictive of severity or outcome were selected based on univariate statistical significance and a multiple predictor Bayesian logistic regression model was created. RESULTS The predictors were selected for their relevant biological function and include deoxycytidine and ureidopropionate (indirectly reflecting viral load), kynurenine (reflecting host inflammatory response), and multiple short chain acylcarnitines (energy metabolism) among others. Currently, this approach predicts outcome and severity with a Monte Carlo cross validated area under the ROC curve of 0.792 (SD 0.09) and 0.793 (SD 0.08), respectively. A blind validation study on an additional 90 patients predicted outcome and severity at ROC AUC of 0.83 (CI 0.74-0.91) and 0.76 (CI 0.67-0.86). CONCLUSION Prognostic tests based on the markers discussed in this paper could allow improvement in the planning of COVID-19 patient treatment.
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Affiliation(s)
- Ivayla Roberts
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Joseph M Taylor
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Andrew S Davison
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Justine M Grixti
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nigel Gotts
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anatolii Sorokin
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Douglas B Kell
- Department of Biochemistry and Systems Biology, 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.
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12
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Hartsell EM, Gillespie MN, Langley RJ. Does acute and persistent metabolic dysregulation in COVID19 point to novel biomarkers and future therapeutic strategies? Eur Respir J 2021; 59:13993003.02417-2021. [PMID: 34675049 PMCID: PMC8542864 DOI: 10.1183/13993003.02417-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/09/2021] [Indexed: 12/15/2022]
Abstract
When the coronavirus disease 2019 (COVID-19) pandemic first appeared in December of 2019, the pathophysiological underpinnings of the disease were largely unknown. Scientists, physicians and government institutions from around the globe took an “all-hands on deck” approach with the hope of identifying potential therapies to treat as well as understand the pathophysiology of the disease [1]. Currently, more than 4800 clinical trials listed on clinicaltrials.gov have been performed or proposed around the world, many with subjects from vastly different ethnic and racial backgrounds, as well as different standard-of-care strategies [2]. Despite this effort, apart from monoclonal antibodies, few therapies have emerged as effective treatments of COVID-19; vaccines remain the best approach to control and mitigate the pandemic [3]. Metabolomics changes in COVID-19 predict acute patient outcomes and suggest a role for a bioenergetic crisis. Thus, metabolomics changes in COVID-19 may serve as a biomarker and provide insight into pathogenic mechanisms and pharmacologic targets.https://bit.ly/2XkJeU8
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Affiliation(s)
- Emily M Hartsell
- Department of Pharmacology, University of South Alabama College of Medicine, Mobile, AL, USA
| | - Mark N Gillespie
- Department of Pharmacology, University of South Alabama College of Medicine, Mobile, AL, USA
| | - Raymond J Langley
- Department of Pharmacology, University of South Alabama College of Medicine, Mobile, AL, USA
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13
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SARS-CoV2 Infection Alters Tryptophan Catabolism and Phospholipid Metabolism. Metabolites 2021; 11:metabo11100659. [PMID: 34677374 PMCID: PMC8538244 DOI: 10.3390/metabo11100659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has so far infected hundreds of million individuals, with several million deaths worldwide. The lack of understanding of the disease pathophysiology and the host’s immune response has resulted in this rapid spread of the disease on a global scale. In this respect, we employed UPLC-MS to compare the metabolites in the serum from COVID-19-positive patients and COVID-19-recovered subjects to determine the metabolic changes responsible for an infection. Our investigations revealed significant increase in the levels of serum phospholipids including sphingomyelins, phosphatidylcholines and arachidonic acid in the serum of COVID-19-positive patients as compared to COVID-19-recovered individuals. We further show increased levels of tryptophan and its metabolites in the serum of COVID-19-positive patients thus emphasizing the role of tryptophan metabolism in the disease pathogenesis of COVID-19. Future studies are required to determine the changes in the lipid and tryptophan metabolism at various stages of COVID-19 disease development, progression and recovery to better understand the host–pathogen interaction and the long-term effects of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection in humans.
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14
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Tan A, Doig CL. NAD + Degrading Enzymes, Evidence for Roles During Infection. Front Mol Biosci 2021; 8:697359. [PMID: 34485381 PMCID: PMC8415550 DOI: 10.3389/fmolb.2021.697359] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Declines in cellular nicotinamide adenine dinucleotide (NAD) contribute to metabolic dysfunction, increase susceptibility to disease, and occur as a result of pathogenic infection. The enzymatic cleavage of NAD+ transfers ADP-ribose (ADPr) to substrate proteins generating mono-ADP-ribose (MAR), poly-ADP-ribose (PAR) or O-acetyl-ADP-ribose (OAADPr). These important post-translational modifications have roles in both immune response activation and the advancement of infection. In particular, emergent data show viral infection stimulates activation of poly (ADP-ribose) polymerase (PARP) mediated NAD+ depletion and stimulates hydrolysis of existing ADP-ribosylation modifications. These studies are important for us to better understand the value of NAD+ maintenance upon the biology of infection. This review focuses specifically upon the NAD+ utilising enzymes, discusses existing knowledge surrounding their roles in infection, their NAD+ depletion capability and their influence within pathogenic infection.
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Affiliation(s)
- Arnold Tan
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Craig L Doig
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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15
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Sindelar M, Stancliffe E, Schwaiger-Haber M, Anbukumar DS, Adkins-Travis K, Goss CW, O’Halloran JA, Mudd PA, Liu WC, Albrecht RA, García-Sastre A, Shriver LP, Patti GJ. Longitudinal metabolomics of human plasma reveals prognostic markers of COVID-19 disease severity. Cell Rep Med 2021; 2:100369. [PMID: 34308390 PMCID: PMC8292035 DOI: 10.1016/j.xcrm.2021.100369] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/01/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we perform untargeted metabolomics on plasma from 339 patients, with samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we build a predictive model of disease severity. We discover that a panel of metabolites measured at the time of study entry successfully determines disease severity. Through analysis of longitudinal samples, we confirm that most of these markers are directly related to disease progression and that their levels return to baseline upon disease recovery. Finally, we validate that these metabolites are also altered in a hamster model of COVID-19.
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Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Ethan Stancliffe
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Dhanalakshmi S. Anbukumar
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | | | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Philip A. Mudd
- Department of Emergency Medicine, Washington University, St. Louis, MO, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah P. Shriver
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO, USA
- Department of Medicine, Washington University, St. Louis, MO, USA
- Siteman Cancer Center, Washington University, St. Louis, MO, USA
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16
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Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review. Food Sci Biotechnol 2021; 30:881-890. [PMID: 34395019 PMCID: PMC8302692 DOI: 10.1007/s10068-021-00917-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022] Open
Abstract
Metabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.
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17
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Yuan ZC, Hu B. Mass Spectrometry-Based Human Breath Analysis: Towards COVID-19 Diagnosis and Research. JOURNAL OF ANALYSIS AND TESTING 2021; 5:287-297. [PMID: 34422436 PMCID: PMC8364943 DOI: 10.1007/s41664-021-00194-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
COVID-19 is a highly contagious respiratory disease that can be infected through human exhaled breath. Human breath analysis is an attractive strategy for rapid diagnosis of COVID-19 in a non-invasive way by monitoring breath biomarkers. Mass spectrometry (MS)-based approaches offer a promising analytical platform for human breath analysis due to their high speed, specificity, sensitivity, reproducibility, and broad coverage, as well as its versatile coupling methods with different chromatographic separation, and thus can lead to a better understanding of the clinical and biochemical processes of COVID-19. Herein, we try to review the developments and applications of MS-based approaches for multidimensional analysis of COVID-19 breath samples, including metabolites, proteins, microorganisms, and elements. New features of breath sampling and analysis are highlighted. Prospects and challenges on MS-based breath analysis related to COVID-19 diagnosis and study are discussed.
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Affiliation(s)
- Zi-Cheng Yuan
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
| | - Bin Hu
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
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18
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Stevens RP, Paudel SS, Johnson SC, Stevens T, Lee JY. Endothelial metabolism in pulmonary vascular homeostasis and acute respiratory distress syndrome. Am J Physiol Lung Cell Mol Physiol 2021; 321:L358-L376. [PMID: 34159794 PMCID: PMC8384476 DOI: 10.1152/ajplung.00131.2021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Capillary endothelial cells possess a specialized metabolism necessary to adapt to the unique alveolar-capillary environment. Here, we highlight how endothelial metabolism preserves the integrity of the pulmonary circulation by controlling vascular permeability, defending against oxidative stress, facilitating rapid migration and angiogenesis in response to injury, and regulating the epigenetic landscape of endothelial cells. Recent reports on single-cell RNA-sequencing reveal subpopulations of pulmonary capillary endothelial cells with distinctive reparative capacities, which potentially offer new insight into their metabolic signature. Lastly, we discuss broad implications of pulmonary vascular metabolism on acute respiratory distress syndrome, touching on emerging findings of endotheliitis in coronavirus disease 2019 (COVID-19) lungs.
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Affiliation(s)
- Reece P Stevens
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, Alabama
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Sunita S Paudel
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, Alabama
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Santina C Johnson
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, Alabama
- Department of Biomolecular Engineering, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Troy Stevens
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, Alabama
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Ji Young Lee
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, Alabama
- Department of Internal Medicine, College of Medicine, University of South Alabama, Mobile, Alabama
- Division of Pulmonary and Critical Care Medicine, College of Medicine, University of South Alabama, Mobile, Alabama
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, Alabama
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19
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Mussap M, Fanos V. Could metabolomics drive the fate of COVID-19 pandemic? A narrative review on lights and shadows. Clin Chem Lab Med 2021; 59:1891-1905. [PMID: 34332518 DOI: 10.1515/cclm-2021-0414] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
Human Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection activates a complex interaction host/virus, leading to the reprogramming of the host metabolism aimed at the energy supply for viral replication. Alterations of the host metabolic homeostasis strongly influence the immune response to SARS-CoV-2, forming the basis of a wide range of outcomes, from the asymptomatic infection to the onset of COVID-19 and up to life-threatening acute respiratory distress syndrome, vascular dysfunction, multiple organ failure, and death. Deciphering the molecular mechanisms associated with the individual susceptibility to SARS-CoV-2 infection calls for a system biology approach; this strategy can address multiple goals, including which patients will respond effectively to the therapeutic treatment. The power of metabolomics lies in the ability to recognize endogenous and exogenous metabolites within a biological sample, measuring their concentration, and identifying perturbations of biochemical pathways associated with qualitative and quantitative metabolic changes. Over the last year, a limited number of metabolomics- and lipidomics-based clinical studies in COVID-19 patients have been published and are discussed in this review. Remarkable alterations in the lipid and amino acid metabolism depict the molecular phenotype of subjects infected by SARS-CoV-2; notably, structural and functional data on the lipids-virus interaction may open new perspectives on targeted therapeutic interventions. Several limitations affect most metabolomics-based studies, slowing the routine application of metabolomics. However, moving metabolomics from bench to bedside cannot imply the mere determination of a given metabolite panel; rather, slotting metabolomics into clinical practice requires the conversion of metabolic patient-specific data into actionable clinical applications.
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Affiliation(s)
- Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, School of Medicine, University of Cagliari, Monserrato, Italy
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20
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Khemani RG, Lee JT, Wu D, Schenck EJ, Hayes MM, Kritek PA, Mutlu GM, Gershengorn HB, Coudroy R. Update in Critical Care 2020. Am J Respir Crit Care Med 2021; 203:1088-1098. [PMID: 33734938 DOI: 10.1164/rccm.202102-0336up] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Robinder G Khemani
- Pediatric ICU, Department of Anesthesiology and Critical Care Medicine, Children's Hospital Los Angeles, Los Angeles, California.,Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jessica T Lee
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Wu
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Edward J Schenck
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.,NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Margaret M Hayes
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Patricia A Kritek
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Washington Seattle, Washington
| | - Gökhan M Mutlu
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Hayley B Gershengorn
- Division of Pulmonary, Critical Care, and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, Florida.,Division of Critical Care Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Rémi Coudroy
- Institut National de la Santé et de la Recherche Médicale, Poitiers, France; and.,Médecine Intensive Réanimation, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
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21
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Chotirmall SH, Leither LM, Çoruh B, Chan LLY, Joudi AM, Brown SM, Singer BD, Seam N. Update in COVID-19 2020. Am J Respir Crit Care Med 2021; 203:1462-1471. [PMID: 33835905 PMCID: PMC8483226 DOI: 10.1164/rccm.202102-0415up] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lindsay M Leither
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Başak Çoruh
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Anthony M Joudi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Samuel M Brown
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Biochemistry and Molecular Genetics, and.,Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Nitin Seam
- Critical Care Medicine Department, NIH, Bethesda, Maryland
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22
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Satterfield BA, Dikilitas O, Kullo IJ. Leveraging the Electronic Health Record to Address the COVID-19 Pandemic. Mayo Clin Proc 2021; 96:1592-1608. [PMID: 34088418 PMCID: PMC8059945 DOI: 10.1016/j.mayocp.2021.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/17/2021] [Accepted: 04/08/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic continues its global spread. Coordinated effort on a vast scale is required to halt its progression and to save lives. Electronic health record (EHR) data are a valuable resource to mitigate the COVID-19 pandemic. We review how the EHR could be used for disease surveillance and contact tracing. When linked to "omics" data, the EHR could facilitate identification of genetic susceptibility variants, leading to insights into risk factors, disease complications, and drug repurposing. Real-time monitoring of patients could enable early detection of potential complications, informing appropriate interventions and therapy. We reviewed relevant articles from PubMed, MEDLINE, and Google Scholar searches as well as preprint servers, given the rapidly evolving understanding of the COVID-19 pandemic.
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Affiliation(s)
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN; Gonda Vascular Center, Mayo Clinic, Rochester, MN.
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23
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Chen T, Philip M, Lê Cao KA, Tyagi S. A multi-modal data harmonisation approach for discovery of COVID-19 drug targets. Brief Bioinform 2021; 22:6279836. [PMID: 34036326 PMCID: PMC8194516 DOI: 10.1093/bib/bbab185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/09/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Despite the volume of experiments performed and data available, the complex biology of coronavirus SARS-COV-2 is not yet fully understood. Existing molecular profiling studies have focused on analysing functional omics data of a single type, which captures changes in a small subset of the molecular perturbations caused by the virus. As the logical next step, results from multiple such omics analysis may be aggregated to comprehensively interpret the molecular mechanisms of SARS-CoV-2. An alternative approach is to integrate data simultaneously in a parallel fashion to highlight the inter-relationships of disease-driving biomolecules, in contrast to comparing processed information from each omics level separately. We demonstrate that valuable information may be masked by using the former fragmented views in analysis, and biomarkers resulting from such an approach cannot provide a systematic understanding of the disease aetiology. Hence, we present a generic, reproducible and flexible open-access data harmonisation framework that can be scaled out to future multi-omics analysis to study a phenotype in a holistic manner. The pipeline source code, detailed documentation and automated version as a R package are accessible. To demonstrate the effectiveness of our pipeline, we applied it to a drug screening task. We integrated multi-omics data to find the lowest level of statistical associations between data features in two case studies. Strongly correlated features within each of these two datasets were used for drug-target analysis, resulting in a list of 84 drug-target candidates. Further computational docking and toxicity analyses revealed seven high-confidence targets, amsacrine, bosutinib, ceritinib, crizotinib, nintedanib and sunitinib as potential starting points for drug therapy and development.
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Affiliation(s)
- Tyrone Chen
- School of Biological Sciences, Monash University, 25 Rainforest Walk, 3800, VIC, Australia
| | - Melcy Philip
- School of Biological Sciences, Monash University, 25 Rainforest Walk, 3800, VIC, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, University of Melbourne, Building 184, Royal Parade, 3010, VIC, Australia.,School of Mathematics and Statistics, University of Melbourne, 813 Swanston Street, 3010, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, 25 Rainforest Walk, 3800, VIC, Australia.,Monash eResearch Centre, Monash University, 15 Innovation Walk, 3800, VIC, Australia.,Department of Infectious Disease, Monash University, 85 Commercial Road, 3004, VIC, Australia
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24
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Langley RJ, Migaud ME, Flores L, Thompson JW, Kean EA, Mostellar MM, Mowry M, Luckett P, Purcell LD, Lovato J, Gandotra S, Benton R, Files DC, Harrod KS, Gillespie MN, Morris PE. A metabolomic endotype of bioenergetic dysfunction predicts mortality in critically ill patients with acute respiratory failure. Sci Rep 2021; 11:10515. [PMID: 34006901 PMCID: PMC8131588 DOI: 10.1038/s41598-021-89716-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/05/2021] [Indexed: 12/25/2022] Open
Abstract
Acute respiratory failure (ARF) requiring mechanical ventilation, a complicating factor in sepsis and other disorders, is associated with high morbidity and mortality. Despite its severity and prevalence, treatment options are limited. In light of accumulating evidence that mitochondrial abnormalities are common in ARF, here we applied broad spectrum quantitative and semiquantitative metabolomic analyses of serum from ARF patients to detect bioenergetic dysfunction and determine its association with survival. Plasma samples from surviving and non-surviving patients (N = 15/group) were taken at day 1 and day 3 after admission to the medical intensive care unit and, in survivors, at hospital discharge. Significant differences between survivors and non-survivors (ANOVA, 5% FDR) include bioenergetically relevant intermediates of redox cofactors nicotinamide adenine dinucleotide (NAD) and NAD phosphate (NADP), increased acyl-carnitines, bile acids, and decreased acyl-glycerophosphocholines. Many metabolites associated with poor outcomes are substrates of NAD(P)-dependent enzymatic processes, while alterations in NAD cofactors rely on bioavailability of dietary B-vitamins thiamine, riboflavin and pyridoxine. Changes in the efficiency of the nicotinamide-derived cofactors' biosynthetic pathways also associate with alterations in glutathione-dependent drug metabolism characterized by substantial differences observed in the acetaminophen metabolome. Based on these findings, a four-feature model developed with semi-quantitative and quantitative metabolomic results predicted patient outcomes with high accuracy (AUROC = 0.91). Collectively, this metabolomic endotype points to a close association between mitochondrial and bioenergetic dysfunction and mortality in human ARF, thus pointing to new pharmacologic targets to reduce mortality in this condition.
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Affiliation(s)
| | - Marie E Migaud
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Lori Flores
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - J Will Thompson
- Duke University Center for Genomic and Computational Biology, Durham, NC, USA
| | - Elizabeth A Kean
- University of South Alabama College of Medicine, Mobile, AL, USA
| | | | - Matthew Mowry
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Patrick Luckett
- Washington University in Saint Louis, Saint Louis, MO, USA
- University of South Alabama School of Computing, Mobile, AL, USA
| | - Lina D Purcell
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - James Lovato
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Sheetal Gandotra
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
- University of Alabama-Birmingham College of Medicine, Birmingham, AL, USA
| | - Ryan Benton
- University of South Alabama School of Computing, Mobile, AL, USA
| | - D Clark Files
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Kevin S Harrod
- University of Alabama-Birmingham College of Medicine, Birmingham, AL, USA
| | - Mark N Gillespie
- University of South Alabama College of Medicine, Mobile, AL, USA
| | - Peter E Morris
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kentucky Health Care, 206E Mathews Building, Lexington, KY, 40506-0047, USA.
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25
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The Ability to Normalise Energy Metabolism in Advanced COVID-19 Disease Seems to Be One of the Key Factors Determining the Disease Progression—A Metabolomic NMR Study on Blood Plasma. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11094231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: COVID-19 represents a severe inflammatory condition. Our work was designed to monitor the longitudinal dynamics of the metabolomic response of blood plasma and to reveal presumable discrimination in patients with positive and negative outcomes of COVID-19 respiratory symptoms. Methods: Blood plasma from patients, divided into subgroups with positive (survivors) and negative (worsening condition, non-survivors) outcomes, on Days 1, 3, and 7 after admission to hospital, was measured by NMR spectroscopy. Results: We observed changes in energy metabolism in both groups of COVID-19 patients; initial hyperglycaemia, indicating lowered glucose utilisation, was balanced with increased production of 3-hydroxybutyrate as an alternative energy source and accompanied by accelerated protein catabolism manifested by an increase in BCAA levels. These changes were normalised in patients with positive outcome by the seventh day, but still persisted one week after hospitalisation in patients with negative outcome. The initially decreased glutamine plasma level normalised faster in patients with positive outcome. Patients with negative outcome showed a more pronounced Phe/Tyr ratio, which is related to exacerbated and generalised inflammatory processes. Almost ideal discrimination from controls was proved. Conclusions: Distinct metabolomic responses to severe inflammation initiated by SARS-CoV-2 infection may serve towards complementary personalised pharmacological and nutritional support to improve patient outcomes.
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26
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Lee JY, Stevens RP, Migaud M, Stevens T. Salvaging the endothelium in acute respiratory distress syndrome: a druggable intersection between TLR4 and NAD + signalling. Eur Respir J 2021; 57:57/5/2004588. [PMID: 33958376 DOI: 10.1183/13993003.04588-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/17/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Ji Young Lee
- Dept of Physiology and Cell Biology, University of South Alabama, Mobile, AL, USA.,Dept of Internal Medicine, University of South Alabama, Mobile, AL, USA.,The Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - Reece P Stevens
- Dept of Physiology and Cell Biology, University of South Alabama, Mobile, AL, USA.,The Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - Marie Migaud
- Dept of Pharmacology, University of South Alabama, Mobile, AL, USA.,The Mitchell Cancer Institute, the University of South Alabama, Mobile, AL, USA
| | - Troy Stevens
- Dept of Physiology and Cell Biology, University of South Alabama, Mobile, AL, USA.,Dept of Internal Medicine, University of South Alabama, Mobile, AL, USA.,The Center for Lung Biology, University of South Alabama, Mobile, AL, USA
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27
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Mahrooz A, Muscogiuri G, Buzzetti R, Maddaloni E. The complex combination of COVID-19 and diabetes: pleiotropic changes in glucose metabolism. Endocrine 2021; 72:317-325. [PMID: 33886062 PMCID: PMC8060688 DOI: 10.1007/s12020-021-02729-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/09/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE Angiotensin converting enzyme 2 (ACE2) is the door for SARS-CoV-2, expressed in critical metabolic tissues. So, it is rational that the new virus causes pleiotropic alterations in glucose metabolism, resulting in the complication of pre-existing diabetes's pathophysiology or creating new disease mechanisms. However, it seems that less attention has been paid to this issue. This review aimed to highlight the importance of long-term consequences and pleiotropic alterations in glucose metabolism following COVID-19 and emphasize the need for basic and clinical research in metabolism and endocrinology. RESULTS SARS-CoV-2 shifts cellular metabolism from oxidative phosphorylation to glycolysis, which leads to a decrease in ATP generation. Together with metabolic imbalance, the impaired immune system elevates the susceptibility of patients with diabetes to this deadly virus. SARS-CoV-2-induced metabolic alterations in immune cells can result in hyper inflammation and a cytokine storm. Metabolic dysfunction may affect therapies against SARS-CoV-2 infection. The effective control of metabolic complications could prove useful therapeutic targets for combating COVID-19. It is also necessary to understand the long-term consequences that will affect patients with diabetes who survived COVID-19. CONCLUSIONS Since the pathophysiology of COVID-19 is still mostly unknown, identifying the metabolic mechanisms contributing to its progression is essential to provide specific ways to prevent and improve this dangerous virus's detrimental effects. The findings show that the new virus may induce new-onset diabetes with uncertain metabolic and clinical features, supporting a potential role of COVID-19 in the development of diabetes.
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Affiliation(s)
- Abdolkarim Mahrooz
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
- Diabetes Research Center, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Giovanna Muscogiuri
- Sezione di Endocrinologia, Dipartimento di Medicina Clinica e Chirurgia, Università Federico II Napoli, Napoli, Italy
| | - Raffaella Buzzetti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Ernesto Maddaloni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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28
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Mussap M, Noto A, Piras C, Atzori L, Fanos V. Slotting metabolomics into routine precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021. [DOI: 10.1080/23808993.2021.1911639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michele Mussap
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
| | - Antonio Noto
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato, Italy
| | - Cristina Piras
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Luigi Atzori
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
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29
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Zheng H, Jin S, Li T, Ying W, Ying B, Chen D, Ning J, Zheng C, Li Y, Li C, Chen C, Li X, Gao H. Metabolomics reveals sex-specific metabolic shifts and predicts the duration from positive to negative in non-severe COVID-19 patients during recovery process. Comput Struct Biotechnol J 2021; 19:1863-1873. [PMID: 33841749 PMCID: PMC8021501 DOI: 10.1016/j.csbj.2021.03.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
Metabolic profiling in COVID-19 patients has been associated with disease severity, but there is no report on sex-specific metabolic changes in discharged survivors. Herein we used an integrated approach of LC-MS-and GC-MS-based untargeted metabolomics to analyze plasma metabolic characteristics in men and women with non-severe COVID-19 at both acute period and 30 days after discharge. The results demonstrate that metabolic alterations in plasma of COVID-19 patients during the recovery and rehabilitation process were presented in a sex specific manner. Overall, the levels of most metabolites were increased in COVID-19 patients after the cure relative to acute period. The major plasma metabolic changes were identified including fatty acids in men and glycerophosphocholines and carbohydrates in women. In addition, we found that women had shorter length of hospitalization than men and metabolic characteristics may contribute to predict the duration from positive to negative in non-severe COVID-19 patients. Collectively, this study shed light on sex-specific metabolic shifts in non-severe COVID-19 patients during the recovery process, suggesting a sex bias in prognostic and therapeutic evaluations based on metabolic profiling.
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Key Words
- ALT, Alanine aminotransferase
- AP, Acute period (AP)
- APTT, Activated partial thromboplastin time
- BCAAs, Branched‐chain amino acids
- BP, Blood platelet
- CA, Carbamide
- COVID-19
- COVID-19, Novel coronavirus disease 2019
- CRP, C-reactive protein
- DAA, Dehydroascorbic acid
- DD, D-dimer
- DP, Diastolic pressure
- FIB, Fibrinogen
- FP, Follow-up period
- Fatty acid
- GPCs, Glycerophosphocholines
- HGB, Hemoglobin
- LY, Lymphocyte
- Metabolism
- NG, Neutrophilic granulocyte
- NK, Natural killer
- PCT, Procalcitonin
- PLS-DA, Partial least squares-discriminant analysis
- PLSR, Partial least squares regression
- PT, Prothrombin time
- PTC, Phosphatidylcholine
- RDW, Red cell distribution width
- RR, Respiratory rate
- S1P, Sphingosine-1-phosphate
- SARS-CoV
- Sex difference
- TBL, Total B lymphocyte
- TTL, Total T lymphocyte
- WBC, White blood cell
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Affiliation(s)
- Hong Zheng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Shengwei Jin
- Department of Anesthesia and Critical Care, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Ting Li
- Clinical Research Unit, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Weiyang Ying
- Department of Pain Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Binyu Ying
- Department of Critical Care Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Dong Chen
- Wenzhou Central Hospital, Wenzhou 325015, China
| | - Jie Ning
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Chanfan Zheng
- Clinical Research Unit, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Chen Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Chengshui Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Xiaokun Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hongchang Gao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
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30
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High-throughput approaches of diagnosis and therapies for COVID-19: antibody panels, proteomics and metabolomics. FUTURE DRUG DISCOVERY 2021. [PMCID: PMC7714045 DOI: 10.4155/fdd-2020-0027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The urgent need for diagnostics and therapeutics against the COVID-19 pandemic has shown the great potential of antibodies, proteomics and metabolomics in this direction. Several clinical trials are underway using antibodies from COVID-19 patients that show very specific and strong binding to viral proteins leading to neutralization. On the other hand, proteomic and metabolomic profiles of COVID-19 patients present novel diagnostic biomarkers to predict patient outcomes and enable the development of personalized therapeutics to target the dysregulated pathways, as revealed by those profiles. Here, we discuss how studies based on antibodies, proteomics and metabolomics contribute to the development of diagnostics and therapeutics against COVID-19. The elegant technology can extend to high-throughput, rapid and reliable drug discovery strategies of the future. In order to prevent and treat the ongoing COVID-19 pandemic, several groups around the world are focused on a detailed understanding of the biology of SARS-CoV-2 infection, the biological events occurring inside the patients and the response of the patients to the infection. SARS-CoV-2 is the coronavirus that causes COVID-19. Some of the approaches to combat the pandemic have provided important results that can help toward therapeutic developments against COVID-19. This review discusses three such areas – antibody treatment to prevent COVID-19 infection, analysis of changes in protein profiles of COVID-19 patients, and analysis of metabolism or energy-related changes in COVID-19 patients. Antibodies are molecules produced in the host’s body as a defense response to infection. Antibodies extracted from patients who recovered from COVID-19 have been used to successfully manufacture large amounts of antibodies to treat COVID-19 patients. The analysis of protein and metabolism profiles of COVID-19 patients has shown that several proteins and metabolism-related entities in the body are either upregulated or downregulated in COVID-19. These abnormal levels can either be attenuated by medical intervention or can be monitored as indicators of COVID-19 diagnosis. Overall, antibodies, protein and metabolism profiles are three important tools, among several others, that are helpful in combating the COVID-19 pandemic.
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31
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Amer B, Baidoo EEK. Omics-Driven Biotechnology for Industrial Applications. Front Bioeng Biotechnol 2021; 9:613307. [PMID: 33708762 PMCID: PMC7940536 DOI: 10.3389/fbioe.2021.613307] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
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Affiliation(s)
- Bashar Amer
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Edward E. K. Baidoo
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- U.S. Department of Energy, Agile BioFoundry, Emeryville, CA, United States
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32
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Sindelar M, Stancliffe E, Schwaiger-Haber M, Anbukumar DS, Albrecht RA, Liu WC, Travis KA, García-Sastre A, Shriver LP, Patti GJ. Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.05.21251173. [PMID: 33564793 PMCID: PMC7872388 DOI: 10.1101/2021.02.05.21251173] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that scarce medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we performed untargeted metabolomics profiling of 341 patients with plasma samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we then built a predictive model of disease severity. We determined that the levels of 25 metabolites measured at the time of hospital admission successfully predict future disease severity. Through analysis of longitudinal samples, we confirmed that these prognostic markers are directly related to disease progression and that their levels are restored to baseline upon disease recovery. Finally, we validated that these metabolites are also altered in a hamster model of COVID-19. Our results indicate that metabolic changes associated with COVID-19 severity can be effectively used to stratify patients and inform resource allocation during the pandemic.
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Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Ethan Stancliffe
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Dhanalakshmi S. Anbukumar
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- These authors contributed equally
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
- Current affiliation: Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Leah P. Shriver
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO
- Department of Medicine, Washington University, St. Louis, MO
- Siteman Cancer Center, Washington University, St. Louis, MO
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33
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Hartog N, Faber W, Frisch A, Bauss J, Bupp CP, Rajasekaran S, Prokop JW. SARS-CoV-2 infection: molecular mechanisms of severe outcomes to suggest therapeutics. Expert Rev Proteomics 2021; 18:105-118. [PMID: 33779460 PMCID: PMC8022340 DOI: 10.1080/14789450.2021.1908894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Introduction:The year 2020 was defined by the 29,903 base pairs of RNA that codes for the SARS-CoV-2 genome. SARS-CoV-2 infects humans to cause COVID-19, spreading from patient-to-patient yet impacts patients very divergently.Areas covered: Within this review, we address the known molecular mechanisms and supporting data for COVID-19 clinical course and pathology, clinical risk factors and molecular signatures, therapeutics of severe COVID-19, and reinfection/vaccination. Literature and published datasets were reviewed using PubMed, Google Scholar, and NCBI SRA tools. The combination of exaggerated cytokine signaling, pneumonia, NETosis, pyroptosis, thrombocytopathy, endotheliopathy, multiple organ dysfunction syndrome (MODS), and acute respiratory distress syndrome (ARDS) create a positive feedback loop of severe damage in patients with COVID-19 that impacts the entire body and may persist for months following infection. Understanding the molecular pathways of severe COVID-19 opens the door for novel therapeutic design. We summarize the current insights into pathology, risk factors, secondary infections, genetics, omics, and drugs being tested to treat severe COVID-19.Expert opinion: A growing level of support suggests the need for stronger integration of biomarkers and precision medicine to guide treatment strategies of severe COVID-19, where each patient has unique outcomes and thus require guided treatment.
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Affiliation(s)
- Nicholas Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, USA
| | - William Faber
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Chemistry, Grand Rapids Community College, Grand Rapids, MI, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, USA
- Office of Research, Office of Research, Spectrum Health, Grand Rapids, MI, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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34
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Overmyer KA, Shishkova E, Miller IJ, Balnis J, Bernstein MN, Peters-Clarke TM, Meyer JG, Quan Q, Muehlbauer LK, Trujillo EA, He Y, Chopra A, Chieng HC, Tiwari A, Judson MA, Paulson B, Brademan DR, Zhu Y, Serrano LR, Linke V, Drake LA, Adam AP, Schwartz BS, Singer HA, Swanson S, Mosher DF, Stewart R, Coon JJ, Jaitovich A. Large-Scale Multi-omic Analysis of COVID-19 Severity. Cell Syst 2021; 12:23-40.e7. [PMID: 33096026 PMCID: PMC7543711 DOI: 10.1016/j.cels.2020.10.003] [Citation(s) in RCA: 360] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
We performed RNA-seq and high-resolution mass spectrometry on 128 blood samples from COVID-19-positive and COVID-19-negative patients with diverse disease severities and outcomes. Quantified transcripts, proteins, metabolites, and lipids were associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many of which were involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a machine learning approach for prediction of COVID-19 severity.
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Affiliation(s)
- Katherine A Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Morgridge Institute for Research, Madison, WI 53562, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Ian J Miller
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | | | - Trenton M Peters-Clarke
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Jesse G Meyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Qiuwen Quan
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Laura K Muehlbauer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Edna A Trujillo
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Yuchen He
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Division of Sleep Medicine, Albany Medical Center, Albany, NY 12208, USA
| | - Marc A Judson
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA
| | - Brett Paulson
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Dain R Brademan
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Yunyun Zhu
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Lia R Serrano
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Vanessa Linke
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Alejandro P Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA; Department of Ophthalmology, Albany Medical College, Albany, NY 12208, USA
| | | | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Joshua J Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Morgridge Institute for Research, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA.
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA.
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Asim M, Sathian B, Banerjee I, Robinson J. A contemporary insight of metabolomics approach for COVID-19: Potential for novel therapeutic and diagnostic targets. Nepal J Epidemiol 2020; 10:923-927. [PMID: 33495710 PMCID: PMC7812325 DOI: 10.3126/nje.v10i4.33964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by rapidly spreading pathogenic virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that affects vast majority of population worldwide. Although, around 80% of the cases had mild infection but still remaining 20% had developed respiratory failure and dysfunction of other organs that necessitate urgent oxygen therapy or specific interventions. Therefore, it is imperative to establish novel prognostic approaches to screen patients at high-risk of developing severe complications. The primary focus of current research for COVID-19 is to discover safe and efficacious vaccine for prevention and effective treatment for better management of the patients to overcome the pandemic. To achieve this goal, it is imperative to have better understanding of the molecular pathways involved in the pathophysiology and progression of severe COVID-19. The surge for reliable diagnostics and therapeutics targets for COVID-19 highlighted the great potential of high-throughput approach like metabolomics which may enable the development of personalized medicine.
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Affiliation(s)
- Mohammad Asim
- Surgery Department, Trauma Surgery, Hamad General Hospital, Doha, Qatar
| | - Brijesh Sathian
- Geriatrics and long term care Department, Rumailah Hospital, Hamad Medical Corporation, Doha, Qatar
- Centre for Midwifery, Maternal and Perinatal Health, Bournemouth University, Bournemouth, England, United Kingdom
| | | | - Jared Robinson
- Sir Seewoosagur Ramgoolam Medical College, Belle Rive, Mauritius
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36
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Mahmud I, Garrett TJ. Mass Spectrometry Techniques in Emerging Pathogens Studies: COVID-19 Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2013-2024. [PMID: 32880453 PMCID: PMC7496948 DOI: 10.1021/jasms.0c00238] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 05/04/2023]
Abstract
As corona virus disease 2019 (COVID-19) is a rapidly growing public health crisis across the world, our knowledge of meaningful diagnostic tests and treatment for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is still evolving. This novel coronavirus disease COVID-19 can be diagnosed using RT-PCR, but inadequate access to reagents, equipment, and a nonspecific target has slowed disease detection and management. Precision medicine, individualized patient care, requires suitable diagnostics approaches to tackle the challenging aspects of viral outbreaks where many tests are needed in a rapid and deployable approach. Mass spectrometry (MS)-based technologies such as proteomics, glycomics, lipidomics, and metabolomics have been applied in disease outbreaks for identification of infectious disease agents such as virus and bacteria and the molecular phenomena associated with pathogenesis. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is widely used in clinical diagnostics in the United States and Europe for bacterial pathogen identification. Paper spray ionization mass spectrometry (PSI-MS), a rapid ambient MS technique, has recently open a new opportunity for future clinical investigation to diagnose pathogens. Ultra-high-pressure liquid chromatography coupled high-resolution mass spectrometry (UHPLC-HRMS)-based metabolomics and lipidomics have been employed in large-scale biomedical research to discriminate infectious pathogens and uncover biomarkers associated with pathogenesis. PCR-MS has emerged as a new technology with the capability to directly identify known pathogens from the clinical specimens and the potential to identify genetic evidence of undiscovered pathogens. Moreover, miniaturized MS offers possible applications with relatively fast, highly sensitive, and potentially portable ways to analyze for viral compounds. However, beneficial aspects of these rapidly growing MS technologies in pandemics like COVID-19 outbreaks has been limited. Hence, this perspective gives a brief of the existing knowledge, current challenges, and opportunities for MS-based techniques as a promising avenue in studying emerging pathogen outbreaks such as COVID-19.
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Affiliation(s)
- Iqbal Mahmud
- Department of Pathology, Immunology,
and Laboratory Medicine, University of
Florida, College of Medicine, Gainesville, Florida
32610, United States
- Southeast Center for Integrated
Metabolomics (SECIM), Clinical and Translational Science Institute,
University of Florida, Gainesville,
Florida 32610, United States
- University of Florida Health,
University of Florida, Gainesville,
Florida 32610, United States
| | - Timothy J. Garrett
- Department of Pathology, Immunology,
and Laboratory Medicine, University of
Florida, College of Medicine, Gainesville, Florida
32610, United States
- Southeast Center for Integrated
Metabolomics (SECIM), Clinical and Translational Science Institute,
University of Florida, Gainesville,
Florida 32610, United States
- University of Florida Health,
University of Florida, Gainesville,
Florida 32610, United States
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37
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Overmyer KA, Shishkova E, Miller IJ, Balnis J, Bernstein MN, Peters-Clarke TM, Meyer JG, Quan Q, Muehlbauer LK, Trujillo EA, He Y, Chopra A, Chieng HC, Tiwari A, Judson MA, Paulson B, Brademan DR, Zhu Y, Serrano LR, Linke V, Drake LA, Adam AP, Schwartz BS, Singer HA, Swanson S, Mosher DF, Stewart R, Coon JJ, Jaitovich A. Large-scale Multi-omic Analysis of COVID-19 Severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.17.20156513. [PMID: 32743614 PMCID: PMC7388490 DOI: 10.1101/2020.07.17.20156513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We performed RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities. Over 17,000 transcripts, proteins, metabolites, and lipids were quantified and associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a comparative analysis with published data and a machine learning approach for prediction of COVID-19 severity.
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Affiliation(s)
- Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Ian J. Miller
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | | | - Trenton M. Peters-Clarke
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Jesse G. Meyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Qiuwen Quan
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Laura K. Muehlbauer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Edna A. Trujillo
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Yuchen He
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Hau C. Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Division of Sleep Medicine, Albany Medical Center, Albany, NY, USA
| | - Marc A. Judson
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Brett Paulson
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Dain R. Brademan
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Yunyun Zhu
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Lia R. Serrano
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Vanessa Linke
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Lisa A. Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Alejandro P. Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
- Department of Ophthalmology, Albany Medical College, Albany, NY, USA
| | | | - Harold A. Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Deane F. Mosher
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA
- Morgridge Institute for Research, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53562, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53562, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
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