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Qing L, Wu W. The mechanism of geniposide in patients with COVID-19 and atherosclerosis: A pharmacological and bioinformatics analysis. Medicine (Baltimore) 2024; 103:e39065. [PMID: 39093733 PMCID: PMC11296471 DOI: 10.1097/md.0000000000039065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024] Open
Abstract
In patients with severe acute respiratory syndrome coronavirus 2 (which causes coronavirus disease 2019 [COVID-19]), oxidative stress (OS) is associated with disease severity and death. OS is also involved in the pathogenesis of atherosclerosis (AS). Previous studies have shown that geniposide has anti-inflammatory and anti-viral properties, and can protect cells against OS. However, the potential target(s) of geniposide in patients with COVID-19 and AS, as well as the mechanism it uses, are unclear. We combined pharmacology and bioinformatics analysis to obtain geniposide against COVID-19/AS targets, and build protein-protein interaction network to filter hub genes. The hub genes were performed an enrichment analysis by ClueGO, including Gene Ontology and KEGG. The Enrichr database and the target microRNAs (miRNAs) of hub genes were predicted through the MiRTarBase via Enrichr. The common miRNAs were used to construct the miRNAs-mRNAs regulated network, and the miRNAs' function was evaluated by mirPath v3.0 software. Two hundred forty-seven targets of geniposide were identified in patients with COVID-19/AS comorbidity by observing the overlap between the genes modulated by geniposide, COVID-19, and AS. A protein-protein interaction network of geniposide in patients with COVID-19/AS was constructed, and 27 hub genes were identified. The results of enrichment analysis suggested that geniposide may be involved in regulating the OS via the FoxO signaling pathway. MiRNA-mRNA network revealed that hsa-miR-34a-5p may play an important role in the therapeutic mechanism of geniposide in COVID-19/AS patients. Our study found that geniposide represents a promising therapy for patients with COVID-19 and AS comorbidity. Furthermore, the target genes and miRNAs that we identified may aid the development of new treatment strategies against COVID-19/AS.
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Affiliation(s)
- Lijin Qing
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Wei Wu
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
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Naidu AS, Wang CK, Rao P, Mancini F, Clemens RA, Wirakartakusumah A, Chiu HF, Yen CH, Porretta S, Mathai I, Naidu SAG. Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID. NPJ Sci Food 2024; 8:19. [PMID: 38555403 PMCID: PMC10981760 DOI: 10.1038/s41538-024-00261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.
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Affiliation(s)
- A Satyanarayan Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA.
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA.
| | - Chin-Kun Wang
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- School of Nutrition, Chung Shan Medical University, 110, Section 1, Jianguo North Road, Taichung, 40201, Taiwan
| | - Pingfan Rao
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- College of Food and Bioengineering, Fujian Polytechnic Normal University, No.1, Campus New Village, Longjiang Street, Fuqing City, Fujian, China
| | - Fabrizio Mancini
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President-Emeritus, Parker University, 2540 Walnut Hill Lane, Dallas, TX, 75229, USA
| | - Roger A Clemens
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- University of Southern California, Alfred E. Mann School of Pharmacy/D. K. Kim International Center for Regulatory & Quality Sciences, 1540 Alcazar St., CHP 140, Los Angeles, CA, 90089, USA
| | - Aman Wirakartakusumah
- International Union of Food Science and Technology (IUFoST), Guelph, ON, Canada
- IPMI International Business School Jakarta; South East Asian Food and Agriculture Science and Technology, IPB University, Bogor, Indonesia
| | - Hui-Fang Chiu
- Department of Chinese Medicine, Taichung Hospital, Ministry of Health & Well-being, Taichung, Taiwan
| | - Chi-Hua Yen
- Department of Family and Community Medicine, Chung Shan Medical University Hospital; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sebastiano Porretta
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President, Italian Association of Food Technology (AITA), Milan, Italy
- Experimental Station for the Food Preserving Industry, Department of Consumer Science, Viale Tanara 31/a, I-43121, Parma, Italy
| | - Issac Mathai
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- Soukya International Holistic Health Center, Whitefield, Bengaluru, India
| | - Sreus A G Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA
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Słomian D, Szyda J, Dobosz P, Stojak J, Michalska-Foryszewska A, Sypniewski M, Liu J, Kotlarz K, Suchocki T, Mroczek M, Stępień M, Sztromwasser P, Król ZJ. Better safe than sorry-Whole-genome sequencing indicates that missense variants are significant in susceptibility to COVID-19. PLoS One 2023; 18:e0279356. [PMID: 36662838 PMCID: PMC9858061 DOI: 10.1371/journal.pone.0279356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/06/2022] [Indexed: 01/22/2023] Open
Abstract
Undoubtedly, genetic factors play an important role in susceptibility and resistance to COVID-19. In this study, we conducted the GWAS analysis. Out of 15,489,173 SNPs, we identified 18,191 significant SNPs for severe and 11,799 SNPs for resistant phenotype, showing that a great number of loci were significant in different COVID-19 representations. The majority of variants were synonymous (60.56% for severe, 58.46% for resistant phenotype) or located in introns (55.77% for severe, 59.83% for resistant phenotype). We identified the most significant SNPs for a severe outcome (in AJAP1 intron) and for COVID resistance (in FIG4 intron). We found no missense variants with a potential causal function on resistance to COVID-19; however, two missense variants were determined as significant a severe phenotype (in PM20D1 and LRP4 exons). None of the aforementioned SNPs and missense variants found in this study have been previously associated with COVID-19.
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Affiliation(s)
- Dawid Słomian
- National Research Institute of Animal Production, Balice, Poland
| | - Joanna Szyda
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Haematology, Transplantation and Internal Medicine, University Clinical Centre of the Medical University of Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Magdalenka, Poland
| | | | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
- Department of Genetics and Animal Breedings, Poznan University of Life Sciences, Poznan, Poland
| | - Jakub Liu
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Krzysztof Kotlarz
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Tomasz Suchocki
- National Research Institute of Animal Production, Balice, Poland
- Department of Genetics, Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Maria Stępień
- Department of Infectious Diseases, Doctoral School, Medical University of Lublin, Lublin, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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Tsermpini EE, Glamočlija U, Ulucan-Karnak F, Redenšek Trampuž S, Dolžan V. Molecular Mechanisms Related to Responses to Oxidative Stress and Antioxidative Therapies in COVID-19: A Systematic Review. Antioxidants (Basel) 2022; 11:antiox11081609. [PMID: 36009328 PMCID: PMC9405444 DOI: 10.3390/antiox11081609] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic is a leading global health and economic challenge. What defines the disease’s progression is not entirely understood, but there are strong indications that oxidative stress and the defense against reactive oxygen species are crucial players. A big influx of immune cells to the site of infection is marked by the increase in reactive oxygen and nitrogen species. Our article aims to highlight the critical role of oxidative stress in the emergence and severity of COVID-19 and, more importantly, to shed light on the underlying molecular and genetic mechanisms. We have reviewed the available literature and clinical trials to extract the relevant genetic variants within the oxidative stress pathway associated with COVID-19 and the anti-oxidative therapies currently evaluated in the clinical trials for COVID-19 treatment, in particular clinical trials on glutathione and N-acetylcysteine.
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Affiliation(s)
- Evangelia Eirini Tsermpini
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Una Glamočlija
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
- School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
| | - Fulden Ulucan-Karnak
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, Bornova, 35100 İzmir, Turkey
| | - Sara Redenšek Trampuž
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Serpeloni JM, Lima Neto QA, Lucio LC, Ramão A, Carvalho de Oliveira J, Gradia DF, Malheiros D, Ferrasa A, Marchi R, Figueiredo DLA, Silva WA, Ribeiro EMSF, Cólus IMS, Cavalli LR. Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection. Immunobiology 2021; 226:152130. [PMID: 34425415 PMCID: PMC8378551 DOI: 10.1016/j.imbio.2021.152130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
In this review, we highlight the interaction of SARS-CoV-2 virus and host genomes, reporting the current studies on the sequence analysis of SARS-CoV-2 isolates and host genomes from diverse world populations. The main genetic variants that are present in both the virus and host genomes were particularly focused on the ACE2 and TMPRSS2 genes, and their impact on the patients' susceptibility to the virus infection and severity of the disease. Finally, the interaction of the virus and host non-coding RNAs is described in relation to their regulatory roles in target genes and/or signaling pathways critically associated with SARS-CoV-2 infection. Altogether, these studies provide a significant contribution to the knowledge of SARS-CoV-2 mechanisms of infection and COVID-19 pathogenesis. The described genetic variants and molecular factors involved in host/virus genome interactions have significantly contributed to defining patient risk groups, beyond those based on patients' age and comorbidities, and they are promising candidates to be potentially targeted in treatment strategies for COVID-19 and other viral infectious diseases.
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Affiliation(s)
- Juliana M Serpeloni
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Quirino Alves Lima Neto
- Departamento de Ciências Básicas da Saúde, CCS, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Léia Carolina Lucio
- Programa de Pós-graduação em Ciências Aplicadas à Saúde, CCS, Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
| | - Anelisa Ramão
- Departamento de Ciências Biológicas, Universidade Estadual do Centro-Oeste, Guarapuava, PR, Brazil
| | | | | | - Danielle Malheiros
- Departamento de Genética, SCB, Universidade Federal do Paraná, PR, Brazil
| | - Adriano Ferrasa
- Departamento de Informática, SECATE, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Marchi
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - David L A Figueiredo
- Departamento de Medicina, Universidade Estadual do Centro-Oeste, UNICENTRO e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | - Wilson A Silva
- Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, SP, e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | | | - Ilce M S Cólus
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Luciane R Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
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Qian Y, Li Y, Liu X, Yuan N, Ma J, Zheng Q, Liu F. Evidence for CAT gene being functionally involved in the susceptibility of COVID-19. FASEB J 2021; 35:e21384. [PMID: 33710662 PMCID: PMC8250337 DOI: 10.1096/fj.202100008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/27/2022]
Abstract
Novel coronary pneumonia (COVID-19) is a respiratory distress syndrome caused by a new type of coronavirus. Understanding the genetic basis of susceptibility and prognosis to COVID-19 is of great significance to disease prevention, molecular typing, prognosis, and treatment. However, so far, there have been only two genome-wide association studies (GWASs) on the susceptibility of COVID-19. Starting with these reported DNA variants, we found the genes regulated by these variants through cis-eQTL and cis-meQTL acting. We further did a series of bioinformatics analysis on these potential risk genes. The analysis shows that the genetic variants on EHF regulate the expression of its neighbor CAT gene via cis-eQTL. There was significant evidence that CAT and the SARS-CoV-2-related S protein binding protein ACE2 interact with each other. Intracellular localization results showed that CAT and ACE2 proteins both exists in the cell membrane and extracellular area and their interaction could have an impact on the cell invasion ability of S protein. In addition, the expression of these three genes showed a significant positive correlation in the lungs. Based on these results, we propose that CAT plays a crucial intermediary role in binding effectiveness of ACE2, thereby affecting the susceptibility to COVID-19.
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Affiliation(s)
- Yu Qian
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinjie Ma
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
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