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Mujalli A, Alghamdi KS, Nasser KK, Al-Rayes N, Banaganapalli B, Shaik NA, Elango R. Bioinformatics insights into the genes and pathways on severe COVID-19 pathology in patients with comorbidities. Front Physiol 2022; 13:1045469. [PMID: 36589459 PMCID: PMC9795193 DOI: 10.3389/fphys.2022.1045469] [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: 09/15/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Coronavirus disease (COVID-19) infection is known for its severe clinical pathogenesis among individuals with pre-existing comorbidities. However, the molecular basis of this observation remains elusive. Thus, this study aimed to map key genes and pathway alterations in patients with COVID-19 and comorbidities using robust systems biology approaches. Methods: The publicly available genome-wide transcriptomic datasets from 120 COVID-19 patients, 281 patients suffering from different comorbidities (like cardiovascular diseases, atherosclerosis, diabetes, and obesity), and 252 patients with different infectious diseases of the lung (respiratory syncytial virus, influenza, and MERS) were studied using a range of systems biology approaches like differential gene expression, gene ontology (GO), pathway enrichment, functional similarity, mouse phenotypic analysis and drug target identification. Results: By cross-mapping the differentially expressed genes (DEGs) across different datasets, we mapped 274 shared genes to severe symptoms of COVID-19 patients or with comorbidities alone. GO terms and functional pathway analysis highlighted genes in dysregulated pathways of immune response, interleukin signaling, FCGR activation, regulation of cytokines, chemokines secretion, and leukocyte migration. Using network topology parameters, phenotype associations, and functional similarity analysis with ACE2 and TMPRSS2-two key receptors for this virus-we identified 17 genes with high connectivity (CXCL10, IDO1, LEPR, MME, PTAFR, PTGS2, MAOB, PDE4B, PLA2G2A, COL5A1, ICAM1, SERPINE1, ABCB1, IL1R1, ITGAL, NCAM1 and PRKD1) potentially contributing to the clinical severity of COVID-19 infection in patients with comorbidities. These genes are predicted to be tractable and/or with many existing approved inhibitors, modulators, and enzymes as drugs. Conclusion: By systemic implementation of computational methods, this study identified potential candidate genes and pathways likely to confer disease severity in COVID-19 patients with pre-existing comorbidities. Our findings pave the way to develop targeted repurposed therapies in COVID-19 patients.
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Affiliation(s)
- Abdulrahman Mujalli
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Abdulrahman Mujalli, ; Ramu Elango,
| | - Kawthar Saad Alghamdi
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Biology, Faculty of Science, University of Hafr Al Batin, Hafar Al-Batin, Saudi Arabia
| | - Khalidah Khalid Nasser
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Al-Rayes
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Abdulrahman Mujalli, ; Ramu Elango,
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Bardelčíková A, Miroššay A, Šoltýs J, Mojžiš J. Therapeutic and prophylactic effect of flavonoids in post-COVID-19 therapy. Phytother Res 2022; 36:2042-2060. [PMID: 35302260 PMCID: PMC9111001 DOI: 10.1002/ptr.7436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/17/2022]
Abstract
The high incidence of post-covid symptoms in humans confirms the need for effective treatment. Due to long-term complications across several disciplines, special treatment programs emerge for affected patients, emphasizing multidisciplinary care. For these reasons, we decided to look at current knowledge about possible long-term complications of COVID-19 disease and then present the effect of flavonoids, which could help alleviate or eliminate complications in humans after overcoming the COVID-19 infection. Based on articles published from 2003 to 2021, we summarize the flavonoids-based molecular mechanisms associated with the post-COVID-19 syndrome and simultaneously provide a complex view regarding their prophylactic and therapeutic potential. Review clearly sorts out the outcome of post-COVID-19 syndrome according particular body systems. The conclusion is that flavonoids play an important role in prevention of many diseases. We suggest that flavonoids as critical nutritional supplements, are suitable for the alleviation and shortening of the period associated with the post-COVID-19 syndrome. The most promising flavonoid with noteworthy therapeutic and prophylactic effect appears to be quercetin.
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Affiliation(s)
- Annamária Bardelčíková
- Department of Pharmacology, Medical Faculty of University of Pavol Jozef Šafárik in Košice, Košice, Slovak Republic
| | - Andrej Miroššay
- Department of Pharmacology, Medical Faculty of University of Pavol Jozef Šafárik in Košice, Košice, Slovak Republic
| | - Jindřich Šoltýs
- Institute of Parasitology, Slovak Academy of Science, Košice, Slovak Republic
| | - Ján Mojžiš
- Department of Pharmacology, Medical Faculty of University of Pavol Jozef Šafárik in Košice, Košice, Slovak Republic
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Abstract
The secretory phospholipase A2 (sPLA2) group of secreted enzymes hydrolyze phospholipids and lead to the production of multiple biologically active lipid mediators. sPLA2s and their products (e.g., eicosanoids) play a significant role in the pathophysiology of various inflammatory diseases, including life-threatening lung disorders such as acute lung injury (ALI) and the Acute Respiratory Distress Syndrome (ARDS). The ALI/ARDS spectrum of severe inflammatory conditions is caused by direct (such as bacterial or viral pneumonia) or indirect insults (sepsis) that are associated with high morbidity and mortality. Several sPLA2 isoforms are upregulated in patients with ARDS as well as in multiple ALI preclinical models, and individual sPLA2s exert unique roles in regulating ALI pathophysiology. This brief review will summarize the contributions of specific sPLA2 isoforms as markers and mediators in ALI, supporting a potential therapeutic role for targeting them in ARDS.
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Affiliation(s)
- Eleftheria Letsiou
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, IL, USA
| | - Yu Maw Htwe
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, IL, USA
| | - Steven M Dudek
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, IL, USA.
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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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Batsika CS, Gerogiannopoulou ADD, Mantzourani C, Vasilakaki S, Kokotos G. The design and discovery of phospholipase A 2 inhibitors for the treatment of inflammatory diseases. Expert Opin Drug Discov 2021; 16:1287-1305. [PMID: 34143707 DOI: 10.1080/17460441.2021.1942835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AREAS COVERED This review article summarizes the most important synthetic PLA2 inhibitors developed to target each one of the four major types of human PLA2 (cytosolic cPLA2, calcium-independent iPLA2, secreted sPLA2, and lipoprotein-associated Lp-PLA2), discussing their in vitro and in vivo activities as well as their recent applications and therapeutic properties. Recent findings on the role of PLA2 in the pathobiology of COVID-19 are also discussed. EXPERT OPINION Although a number of PLA2 inhibitors have entered clinical trials, none has reached the market yet. Lipoprotein-associated PLA2 is now considered a biomarker of vascular inflammation rather than a therapeutic target for inhibitors like darapladib. Inhibitors of cytosolic PLA2 may find topical applications for diseases like atopic dermatitis and psoriasis. Inhibitors of secreted PLA2, varespladib and varespladib methyl, are under investigation for repositioning in snakebite envenoming. A deeper understanding of PLA2 enzymes is needed for the development of novel selective inhibitors. Lipidomic technologies combined with medicinal chemistry approaches may be useful tools toward this goal.
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Affiliation(s)
| | | | - Christiana Mantzourani
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - Sofia Vasilakaki
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Greece
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