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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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Almeida B, Dias TR, Cruz P, Sousa-Pimenta M, Teixeira AL, Pereira CE, Costa-Silva B, Oliveira J, Medeiros R, Dias F. Plasma EV-miRNAs as Potential Biomarkers of COVID-19 Vaccine Immune Response in Cancer Patients. Vaccines (Basel) 2024; 12:848. [PMID: 39203974 PMCID: PMC11359428 DOI: 10.3390/vaccines12080848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Cancer patients, prone to severe COVID-19, face immune challenges due to their disease and treatments. Identifying biomarkers, particularly extracellular vesicle (EV)-derived microRNAs (miRNAs), is vital for comprehending their response to COVID-19 vaccination. Therefore, this study aimed to investigate specific EV-miRNAs in the plasma of cancer patients under active treatment who received the COVID-19 booster vaccine. The selected miRNAs (EV-hsa-miR-7-5p, EV-hsa-miR-15b-5p, EV-hsa-miR-24-3p, EV-hsa-miR-145- 5p, and EV-hsa-miR-223-3p) are involved in regulating SARS-CoV-2 spike protein and cytokine release, making them potential biomarkers for vaccination response. The study involved 54 cancer patients. Plasma and serum samples were collected at pre-boost vaccination, and at 3 and 6 months post-boost vaccination. Anti-spike antibody levels were measured. Additionally, RNA was extracted from EVs isolated from plasma and the expression levels of miRNAs were assessed. The results showed a significantly positive antibody response after COVID-19 boost vaccination. The expression levels of EV-hsa-miR-7-5p, EV-hsa-miR-15b-5p, EV-hsa-miR-24-3p, and EV-hsa-miR-223-3p increased significantly after 6 months of COVID-19 booster vaccination. Interestingly, an increased expression of certain EV-hsa-miRNAs was positively correlated. Bioinformatic analysis revealed that these correlated miRNAs play a critical role in regulating the targets present in antiviral responses and cytokine production. These findings suggest that EV-hsa-miR-15b-5p, EV-hsa-miR-24-3p, and EV-hsa-miR-223-3p may be crucial in immune response induced by mRNA vaccines.
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Affiliation(s)
- Beatriz Almeida
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) & RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (B.A.); (T.R.D.); (A.L.T.); (R.M.)
- Research Department, Portuguese League Against Cancer Northern Branch (LPCC-NRN), 4200-172 Porto, Portugal
| | - Tânia R. Dias
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) & RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (B.A.); (T.R.D.); (A.L.T.); (R.M.)
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, 4050-523 Porto, Portugal
| | - Pedro Cruz
- Department of Oncology, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (P.C.); (J.O.)
| | - Mário Sousa-Pimenta
- Department of Onco-Hematology, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal;
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) & RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (B.A.); (T.R.D.); (A.L.T.); (R.M.)
| | - Catarina Esteves Pereira
- Systems Oncology Group, Champalimaud Research, Champalimaud Centre for the Unknown, Av. Brasília, 1400-038 Lisbon, Portugal; (C.E.P.); (B.C.-S.)
| | - Bruno Costa-Silva
- Systems Oncology Group, Champalimaud Research, Champalimaud Centre for the Unknown, Av. Brasília, 1400-038 Lisbon, Portugal; (C.E.P.); (B.C.-S.)
| | - Júlio Oliveira
- Department of Oncology, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (P.C.); (J.O.)
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) & RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (B.A.); (T.R.D.); (A.L.T.); (R.M.)
- Research Department, Portuguese League Against Cancer Northern Branch (LPCC-NRN), 4200-172 Porto, Portugal
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, 4050-523 Porto, Portugal
- Laboratory Medicine, Clinical Pathology Department, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal
- Biomedicine Research Center (CEBIMED), Research Innovation and Development Institute (FP-I3ID), 4249-004 Porto, Portugal
| | - Francisca Dias
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) & RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto. CCC), 4200-072 Porto, Portugal; (B.A.); (T.R.D.); (A.L.T.); (R.M.)
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de Antonellis P, Ferrucci V, Miceli M, Bibbo F, Asadzadeh F, Gorini F, Mattivi A, Boccia A, Russo R, Andolfo I, Lasorsa VA, Cantalupo S, Fusco G, Viscardi M, Brandi S, Cerino P, Monaco V, Choi DR, Cheong JH, Iolascon A, Amente S, Monti M, Fava LL, Capasso M, Kim HY, Zollo M. Targeting ATP2B1 impairs PI3K/Akt/FOXO signaling and reduces SARS-COV-2 infection and replication. EMBO Rep 2024; 25:2974-3007. [PMID: 38816514 PMCID: PMC11239940 DOI: 10.1038/s44319-024-00164-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
ATP2B1 is a known regulator of calcium (Ca2+) cellular export and homeostasis. Diminished levels of intracellular Ca2+ content have been suggested to impair SARS-CoV-2 replication. Here, we demonstrate that a nontoxic caloxin-derivative compound (PI-7) reduces intracellular Ca2+ levels and impairs SARS-CoV-2 infection. Furthermore, a rare homozygous intronic variant of ATP2B1 is shown to be associated with the severity of COVID-19. The mechanism of action during SARS-CoV-2 infection involves the PI3K/Akt signaling pathway activation, inactivation of FOXO3 transcription factor function, and subsequent transcriptional inhibition of the membrane and reticulum Ca2+ pumps ATP2B1 and ATP2A1, respectively. The pharmacological action of compound PI-7 on sustaining both ATP2B1 and ATP2A1 expression reduces the intracellular cytoplasmic Ca2+ pool and thus negatively influences SARS-CoV-2 replication and propagation. As compound PI-7 lacks toxicity in vitro, its prophylactic use as a therapeutic agent against COVID-19 is envisioned here.
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Affiliation(s)
- Pasqualino de Antonellis
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
- Elysium Cell Bio Ita SRL, Via Gaetano Salvatore 486, 80145, Naples, Italy
| | - Veronica Ferrucci
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
- Elysium Cell Bio Ita SRL, Via Gaetano Salvatore 486, 80145, Naples, Italy
| | - Marco Miceli
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
| | - Francesca Bibbo
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Fatemeh Asadzadeh
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
- European School of Molecular Medicine, SEMM, Naples, Italy
| | - Francesca Gorini
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Alessia Mattivi
- Armenise-Harvard Laboratory of Cell Division, Department of Cellular Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | | | - Roberta Russo
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Immacolata Andolfo
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | | | | | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, 80055, Italy
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, 80055, Italy
| | - Sergio Brandi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, 80055, Italy
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, 80055, Italy
| | - Vittoria Monaco
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Department of Chemical Sciences, University 'Federico II' University of Naples, Naples, 80125, Italy
| | - Dong-Rac Choi
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
- Elysiumbio Inc., #2007, Samsung Cheil B/D, 309, Teheran-ro, Gangnam-gu, Seoul, 06151, Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Stefano Amente
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Maria Monti
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Department of Chemical Sciences, University 'Federico II' University of Naples, Naples, 80125, Italy
| | - Luca L Fava
- Armenise-Harvard Laboratory of Cell Division, Department of Cellular Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy
| | - Hong-Yeoul Kim
- Elysiumbio Inc., #2007, Samsung Cheil B/D, 309, Teheran-ro, Gangnam-gu, Seoul, 06151, Korea
| | - Massimo Zollo
- CEINGE Biotecnologie Avanzate, Naples, 80145, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), 'Federico II' University of Naples, Naples, 80131, Italy.
- Elysium Cell Bio Ita SRL, Via Gaetano Salvatore 486, 80145, Naples, Italy.
- European School of Molecular Medicine, SEMM, Naples, Italy.
- DAI Medicina di Laboratorio e Trasfusionale, 'Federico II' University of Naples, 80131, Naples, Italy.
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Luebbert L, Sullivan DK, Carilli M, Hjörleifsson KE, Winnett AV, Chari T, Pachter L. Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.11.571168. [PMID: 38168363 PMCID: PMC10760059 DOI: 10.1101/2023.12.11.571168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infection is vital to understanding its impact on human health and to make accurate predictions to limit adverse effects, such as future epidemics. The increasing use of high-throughput sequencing methods in research, agriculture, and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus-disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on highly conserved amino acid domains, which enables the detection of RNA viruses covering up to 1012 virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We applied our method to identify putative novel viruses in rhesus macaque PBMC data that display cell type specificity and whose presence correlates with altered host gene expression.
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Affiliation(s)
- Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Delaney K. Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Maria Carilli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | | | - Alexander Viloria Winnett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California
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5
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Ma C, Zhang Y, Ding R, Chen H, Wu X, Xu L, Yu C. In search of the ratio of miRNA expression as robust biomarkers for constructing stable diagnostic models among multi-center data. Front Genet 2024; 15:1381917. [PMID: 38746057 PMCID: PMC11091382 DOI: 10.3389/fgene.2024.1381917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers for the early detection of disease, and many miRNA-based diagnostic models have been constructed to distinguish patients and healthy individuals. To thoroughly utilize the miRNA-profiling data across different sequencing platforms or multiple centers, the models accounting the batch effects were demanded for the generalization of medical application. We conducted transcription factor (TF)-mediated miRNA-miRNA interaction network analysis and adopted the within-sample expression ratios of miRNA pairs as predictive markers. The ratio of the expression values between each miRNA pair turned out to be stable across multiple data sources. A genetic algorithm-based classifier was constructed to quantify risk scores of the probability of disease and discriminate disease states from normal states in discovery, with a validation dataset for COVID-19, renal cell carcinoma, and lung adenocarcinoma. The predictive models based on the expression ratio of interacting miRNA pairs demonstrated good performances in the discovery and validation datasets, and the classifier may be used accurately for the early detection of disease.
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Affiliation(s)
- Cuidie Ma
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yonghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Rui Ding
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Han Chen
- Shenyang Medical College, Shenyang, China
| | - Xudong Wu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lida Xu
- Beijing Hotgen Biotech Co., Ltd., Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Mensah-Bonsu M, Doss C, Gloster C, Muganda P. Identification and Potential Roles of Human MicroRNAs in Ebola Virus Infection and Disease Pathogenesis. Genes (Basel) 2024; 15:403. [PMID: 38674337 PMCID: PMC11049046 DOI: 10.3390/genes15040403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Ebola virus (EBOV) is a highly pathogenic virus that causes a severe illness called Ebola virus disease (EVD). EVD has a high mortality rate and remains a significant threat to public health. Research on EVD pathogenesis has traditionally focused on host transcriptional responses. Limited recent studies, however, have revealed some information on the significance of cellular microRNAs (miRNAs) in EBOV infection and pathogenic mechanisms, but further studies are needed. Thus, this study aimed to identify and validate additional known and novel human miRNAs in EBOV-infected adult retinal pigment epithelial (ARPE) cells and predict their potential roles in EBOV infection and pathogenic mechanisms. We analyzed previously available small RNA-Seq data obtained from ARPE cells and identified 23 upregulated and seven downregulated miRNAs in the EBOV-infected cells; these included two novel miRNAs and 17 additional known miRNAs not previously identified in ARPE cells. In addition to pathways previously identified by others, these miRNAs are associated with pathways and biological processes that include WNT, FoxO, and phosphatidylinositol signaling; these pathways were not identified in the original study. This study thus confirms and expands on the previous study using the same datasets and demonstrates further the importance of human miRNAs in the host response and EVD pathogenesis during infection.
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Affiliation(s)
- Melvin Mensah-Bonsu
- Applied Science and Technology Ph.D. Program, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Christopher Doss
- Department of Electrical and Computer Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Clay Gloster
- Department of Computer Systems Technology, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Perpetua Muganda
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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Kole A, Bag AK, Pal AJ, De D. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology. BMC Bioinformatics 2024; 25:74. [PMID: 38365632 PMCID: PMC10874019 DOI: 10.1186/s12859-024-05690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
PURPOSE Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the graph coloring's effectiveness in computational network biology, more precisely in analyzing protein-protein interaction (PPI) networks to gain insights about the viral infections and its consequences on human health. Accordingly, we propose a generic model that can highlight important hub proteins of virus-associated disease manifestations, changes in disease-associated biological pathways, potential drug targets and respective drugs. We test our model on SARS-CoV-2 infection, a highly transmissible virus responsible for the COVID-19 pandemic. The pandemic took significant human lives, causing severe respiratory illnesses and exhibiting various symptoms ranging from fever and cough to gastrointestinal, cardiac, renal, neurological, and other manifestations. METHODS To investigate the underlying mechanisms of SARS-CoV-2 infection-induced dysregulation of human pathobiology, we construct a two-level PPI network and employed a differential evolution-based graph coloring (DEGCP) algorithm to identify critical hub proteins that might serve as potential targets for resolving the associated issues. Initially, we concentrate on the direct human interactors of SARS-CoV-2 proteins to construct the first-level PPI network and subsequently applied the DEGCP algorithm to identify essential hub proteins within this network. We then build a second-level PPI network by incorporating the next-level human interactors of the first-level hub proteins and use the DEGCP algorithm to predict the second level of hub proteins. RESULTS We first identify the potential crucial hub proteins associated with SARS-CoV-2 infection at different levels. Through comprehensive analysis, we then investigate the cellular localization, interactions with other viral families, involvement in biological pathways and processes, functional attributes, gene regulation capabilities as transcription factors, and their associations with disease-associated symptoms of these identified hub proteins. Our findings highlight the significance of these hub proteins and their intricate connections with disease pathophysiology. Furthermore, we predict potential drug targets among the hub proteins and identify specific drugs that hold promise in preventing or treating SARS-CoV-2 infection and its consequences. CONCLUSION Our generic model demonstrates the effectiveness of DEGCP algorithm in analyzing biological PPI networks, provides valuable insights into disease biology, and offers a basis for developing novel therapeutic strategies for other viral infections that may cause future pandemic.
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Affiliation(s)
- Arnab Kole
- Department of Computer Application, The Heritage Academy, Kolkata, W.B., 700107, India.
| | - Arup Kumar Bag
- Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Nadia, W.B., 741249, India
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Lai B, Jiang H, Liao T, Gao Y, Zhou X. Bioinformatics and system biology analysis revealed the crosstalk between COVID-19 and osteoarthritis. Immun Inflamm Dis 2023; 11:e1123. [PMID: 38156385 PMCID: PMC10739374 DOI: 10.1002/iid3.1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND The global coronavirus disease 2019 (COVID-19) outbreak has significantly impacted public health. Moreover, there has been an association between the incidence and severity of osteoarthritis (OA) and the onset of COVID-19. However, the optimal diagnosis and treatment strategies for patients with both diseases remain uncertain. Bioinformatics is a novel approach that may help find the common pathology between COVID-19 and OA. METHODS Differentially expressed genes (DEGs) were screened by R package "limma." Functional enrichment analyses were performed to find key biological functions. Protein-protein interaction (PPI) network was constructed by STRING database and then Cytoscape was used to select hub genes. External data sets and OA mouse model validated and identified the hub genes in both mRNA and protein levels. Related transcriptional factors (TF) and microRNAs (miRNAs) were predicted with miRTarBase and JASPR database. Candidate drugs were obtained from Drug Signatures database. The immune infiltration levels of COVID-19 and OA were evaluated by CIBERSORT and scRNA-seq. RESULTS A total of 74 common DEGs were identified between COVID-19 and OA. Receiver operating characteristic curves validated the effective diagnostic values (area under curve > 0.7) of four hub genes (matrix metalloproteinases 9, ATF3, CCL4, and RELA) in both the training and validation data sets of COVID-19 and OA. Quantitative polymerase chain reaction and Western Blot showed significantly higher hub gene expression in OA mice than in healthy controls. A total of 84 miRNAs and 28 TFs were identified to regulate the process of hub gene expression. The top 10 potential drugs were screened including "Simvastatin," "Hydrocortisone," and "Troglitazone" which have been proven by Food and Drug Administration. Correlated with hub gene expression, Macrophage M0 was highly expressed while Natural killer cells and Mast cells were low in both COVID-19 and OA. CONCLUSION Four hub genes, disease-related miRNAs, TFs, drugs, and immune infiltration help to understand the pathogenesis and perform further studies, providing a potential therapy target for COVID-19 and OA.
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Affiliation(s)
- Bowen Lai
- Department of OrthopedicsChangzheng Hospital, Second Military Medical UniversityShanghaiChina
| | - Heng Jiang
- Department of OrthopedicsChangzheng Hospital, Second Military Medical UniversityShanghaiChina
| | - Taotao Liao
- Department of OrthopedicsChangzheng Hospital, Second Military Medical UniversityShanghaiChina
| | - Yuan Gao
- Department of OrthopedicsChangzheng Hospital, Second Military Medical UniversityShanghaiChina
| | - Xuhui Zhou
- Department of OrthopedicsChangzheng Hospital, Second Military Medical UniversityShanghaiChina
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Maiese K. Cornerstone Cellular Pathways for Metabolic Disorders and Diabetes Mellitus: Non-Coding RNAs, Wnt Signaling, and AMPK. Cells 2023; 12:2595. [PMID: 37998330 PMCID: PMC10670256 DOI: 10.3390/cells12222595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Metabolic disorders and diabetes (DM) impact more than five hundred million individuals throughout the world and are insidious in onset, chronic in nature, and yield significant disability and death. Current therapies that address nutritional status, weight management, and pharmacological options may delay disability but cannot alter disease course or functional organ loss, such as dementia and degeneration of systemic bodily functions. Underlying these challenges are the onset of aging disorders associated with increased lifespan, telomere dysfunction, and oxidative stress generation that lead to multi-system dysfunction. These significant hurdles point to the urgent need to address underlying disease mechanisms with innovative applications. New treatment strategies involve non-coding RNA pathways with microRNAs (miRNAs) and circular ribonucleic acids (circRNAs), Wnt signaling, and Wnt1 inducible signaling pathway protein 1 (WISP1) that are dependent upon programmed cell death pathways, cellular metabolic pathways with AMP-activated protein kinase (AMPK) and nicotinamide, and growth factor applications. Non-coding RNAs, Wnt signaling, and AMPK are cornerstone mechanisms for overseeing complex metabolic pathways that offer innovative treatment avenues for metabolic disease and DM but will necessitate continued appreciation of the ability of each of these cellular mechanisms to independently and in unison influence clinical outcome.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, New York, NY 10022, USA
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10
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Maiese K. The impact of aging and oxidative stress in metabolic and nervous system disorders: programmed cell death and molecular signal transduction crosstalk. Front Immunol 2023; 14:1273570. [PMID: 38022638 PMCID: PMC10663950 DOI: 10.3389/fimmu.2023.1273570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Life expectancy is increasing throughout the world and coincides with a rise in non-communicable diseases (NCDs), especially for metabolic disease that includes diabetes mellitus (DM) and neurodegenerative disorders. The debilitating effects of metabolic disorders influence the entire body and significantly affect the nervous system impacting greater than one billion people with disability in the peripheral nervous system as well as with cognitive loss, now the seventh leading cause of death worldwide. Metabolic disorders, such as DM, and neurologic disease remain a significant challenge for the treatment and care of individuals since present therapies may limit symptoms but do not halt overall disease progression. These clinical challenges to address the interplay between metabolic and neurodegenerative disorders warrant innovative strategies that can focus upon the underlying mechanisms of aging-related disorders, oxidative stress, cell senescence, and cell death. Programmed cell death pathways that involve autophagy, apoptosis, ferroptosis, and pyroptosis can play a critical role in metabolic and neurodegenerative disorders and oversee processes that include insulin resistance, β-cell function, mitochondrial integrity, reactive oxygen species release, and inflammatory cell activation. The silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), AMP activated protein kinase (AMPK), and Wnt1 inducible signaling pathway protein 1 (WISP1) are novel targets that can oversee programmed cell death pathways tied to β-nicotinamide adenine dinucleotide (NAD+), nicotinamide, apolipoprotein E (APOE), severe acute respiratory syndrome (SARS-CoV-2) exposure with coronavirus disease 2019 (COVID-19), and trophic factors, such as erythropoietin (EPO). The pathways of programmed cell death, SIRT1, AMPK, and WISP1 offer exciting prospects for maintaining metabolic homeostasis and nervous system function that can be compromised during aging-related disorders and lead to cognitive impairment, but these pathways have dual roles in determining the ultimate fate of cells and organ systems that warrant thoughtful insight into complex autofeedback mechanisms.
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Affiliation(s)
- Kenneth Maiese
- Innovation and Commercialization, National Institutes of Health, Bethesda, MD, United States
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Cai X, Deng J, Shi W, Cai Y, Ma Z. Mining the potential therapeutic targets for COVID-19 infection in patients with severe burn injuries via bioinformatics analysis. Int Wound J 2023; 20:2742-2752. [PMID: 36924127 PMCID: PMC10410338 DOI: 10.1111/iwj.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
The Coronavirus Disease-19 (COVID-19) pandemic is posing a serious challenge to human health. Burn victims are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leading to delayed recovery and even profound debilitation. Nevertheless, the molecular mechanisms underlying COVID-19 and severe burn are yet to be elucidated. In our work, the differentially expressed genes (DEGs) were identified from GSE157852 and GSE19743, and the common DEGs between COVID-19 and severe burn were extracted. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interactions (PPI), gene coexpression network, and multifactor regulatory network analysis of hub genes were carried out. A total of 44 common DEGs were found between COVID-19 and severe burn. Functional analyses indicated that the pathways of immune regulation and cytokine response participated collectively in the development of severe burn and progression of COVID-19. Ten significant hub genes were identified, including MERTK, SIRPA, TLR3, ITGB1, DPP4, PTPRC, LY75, IFIT1, IL4R, and CD2. In addition, the gene coexpression network and regulatory network were constructed containing 42 microRNAs (miRNAs) and 2 transcription factors (TFs). Our study showed the shared pathogenic link between COVID-19 and severe burn. The identified common genes and pivotal pathways pave a new road for future mechanistic researches in severe burn injuries complicated with COVID-19.
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Affiliation(s)
- Xueyao Cai
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Jing Deng
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Wenjun Shi
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuchen Cai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhengzheng Ma
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
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12
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Maiese K. Innovative therapeutic strategies for cardiovascular disease. EXCLI JOURNAL 2023; 22:690-715. [PMID: 37593239 PMCID: PMC10427777 DOI: 10.17179/excli2023-6306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023]
Abstract
As a significant non-communicable disease, cardiovascular disease is the leading cause of death for both men and women, comprises almost twenty percent of deaths in most racial and ethnic groups, can affect greater than twenty-five million individuals worldwide over the age of twenty, and impacts global economies with far-reaching financial challenges. Multiple factors can affect the onset of cardiovascular disease that include high serum cholesterol levels, elevated blood pressure, tobacco consumption and secondhand smoke exposure, poor nutrition, physical inactivity, obesity, and concurrent diabetes mellitus. Yet, addressing any of these factors cannot completely eliminate the onset or progression of cardiovascular disorders. Novel strategies are necessary to target underlying cardiovascular disease mechanisms. The silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), a histone deacetylase, can limit cardiovascular injury, assist with stem cell development, oversee metabolic homeostasis through nicotinamide adenine dinucleotide (NAD+) pathways, foster trophic factor protection, and control cell senescence through the modulation of telomere function. Intimately tied to SIRT1 pathways are mammalian forkhead transcription factors (FoxOs) which can modulate cardiac disease to reduce oxidative stress, repair microcirculation disturbances, and reduce atherogenesis through pathways of autophagy, apoptosis, and ferroptosis. AMP activated protein kinase (AMPK) also is critical among these pathways for the oversight of cardiac cellular metabolism, insulin sensitivity, mitochondrial function, inflammation, and the susceptibility to viral infections such as severe acute respiratory syndrome coronavirus that can impact cardiovascular disease. Yet, the relationship among these pathways is both intricate and complex and requires detailed insight to successfully translate these pathways into clinical care for cardiovascular disorders.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, New York, New York 10022
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13
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Maiese K. Cognitive Impairment in Multiple Sclerosis. Bioengineering (Basel) 2023; 10:871. [PMID: 37508898 PMCID: PMC10376413 DOI: 10.3390/bioengineering10070871] [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: 06/20/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Almost three million individuals suffer from multiple sclerosis (MS) throughout the world, a demyelinating disease in the nervous system with increased prevalence over the last five decades, and is now being recognized as one significant etiology of cognitive loss and dementia. Presently, disease modifying therapies can limit the rate of relapse and potentially reduce brain volume loss in patients with MS, but unfortunately cannot prevent disease progression or the onset of cognitive disability. Innovative strategies are therefore required to address areas of inflammation, immune cell activation, and cell survival that involve novel pathways of programmed cell death, mammalian forkhead transcription factors (FoxOs), the mechanistic target of rapamycin (mTOR), AMP activated protein kinase (AMPK), the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), and associated pathways with the apolipoprotein E (APOE-ε4) gene and severe acute respiratory syndrome coronavirus (SARS-CoV-2). These pathways are intertwined at multiple levels and can involve metabolic oversight with cellular metabolism dependent upon nicotinamide adenine dinucleotide (NAD+). Insight into the mechanisms of these pathways can provide new avenues of discovery for the therapeutic treatment of dementia and loss in cognition that occurs during MS.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, New York, NY 10022, USA
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14
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Maiese K. Cellular Metabolism: A Fundamental Component of Degeneration in the Nervous System. Biomolecules 2023; 13:816. [PMID: 37238686 PMCID: PMC10216724 DOI: 10.3390/biom13050816] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
It is estimated that, at minimum, 500 million individuals suffer from cellular metabolic dysfunction, such as diabetes mellitus (DM), throughout the world. Even more concerning is the knowledge that metabolic disease is intimately tied to neurodegenerative disorders, affecting both the central and peripheral nervous systems as well as leading to dementia, the seventh leading cause of death. New and innovative therapeutic strategies that address cellular metabolism, apoptosis, autophagy, and pyroptosis, the mechanistic target of rapamycin (mTOR), AMP activated protein kinase (AMPK), growth factor signaling with erythropoietin (EPO), and risk factors such as the apolipoprotein E (APOE-ε4) gene and coronavirus disease 2019 (COVID-19) can offer valuable insights for the clinical care and treatment of neurodegenerative disorders impacted by cellular metabolic disease. Critical insight into and modulation of these complex pathways are required since mTOR signaling pathways, such as AMPK activation, can improve memory retention in Alzheimer's disease (AD) and DM, promote healthy aging, facilitate clearance of β-amyloid (Aß) and tau in the brain, and control inflammation, but also may lead to cognitive loss and long-COVID syndrome through mechanisms that can include oxidative stress, mitochondrial dysfunction, cytokine release, and APOE-ε4 if pathways such as autophagy and other mechanisms of programmed cell death are left unchecked.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, New York, NY 10022, USA
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15
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Redenšek Trampuž S, Vogrinc D, Goričar K, Dolžan V. Shared miRNA landscapes of COVID-19 and neurodegeneration confirm neuroinflammation as an important overlapping feature. Front Mol Neurosci 2023; 16:1123955. [PMID: 37008787 PMCID: PMC10064073 DOI: 10.3389/fnmol.2023.1123955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionDevelopment and worsening of most common neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis, have been associated with COVID-19 However, the mechanisms associated with neurological symptoms in COVID-19 patients and neurodegenerative sequelae are not clear. The interplay between gene expression and metabolite production in CNS is driven by miRNAs. These small non-coding molecules are dysregulated in most common neurodegenerative diseases and COVID-19.MethodsWe have performed a thorough literature screening and database mining to search for shared miRNA landscapes of SARS-CoV-2 infection and neurodegeneration. Differentially expressed miRNAs in COVID-19 patients were searched using PubMed, while differentially expressed miRNAs in patients with five most common neurodegenerative diseases (Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and multiple sclerosis) were searched using the Human microRNA Disease Database. Target genes of the overlapping miRNAs, identified with the miRTarBase, were used for the pathway enrichment analysis performed with Kyoto Encyclopedia of Genes and Genomes and Reactome.ResultsIn total, 98 common miRNAs were found. Additionally, two of them (hsa-miR-34a and hsa-miR-132) were highlighted as promising biomarkers of neurodegeneration, as they are dysregulated in all five most common neurodegenerative diseases and COVID-19. Additionally, hsa-miR-155 was upregulated in four COVID-19 studies and found to be dysregulated in neurodegeneration processes as well. Screening for miRNA targets identified 746 unique genes with strong evidence for interaction. Target enrichment analysis highlighted most significant KEGG and Reactome pathways being involved in signaling, cancer, transcription and infection. However, the more specific identified pathways confirmed neuroinflammation as being the most important shared feature.DiscussionOur pathway based approach has identified overlapping miRNAs in COVID-19 and neurodegenerative diseases that may have a valuable potential for neurodegeneration prediction in COVID-19 patients. Additionally, identified miRNAs can be further explored as potential drug targets or agents to modify signaling in shared pathways.Graphical AbstractShared miRNA molecules among the five investigated neurodegenerative diseases and COVID-19 were identified. The two overlapping miRNAs, hsa-miR-34a and has-miR-132, present potential biomarkers of neurodegenerative sequelae after COVID-19. Furthermore, 98 common miRNAs between all five neurodegenerative diseases together and COVID-19 were identified. A KEGG and Reactome pathway enrichment analyses was performed on the list of shared miRNA target genes and finally top 20 pathways were evaluated for their potential for identification of new drug targets. A common feature of identified overlapping miRNAs and pathways is neuroinflammation. AD, Alzheimer’s disease; ALS, amyotrophic lateral sclerosis; COVID-19, coronavirus disease 2019; HD, Huntington’s disease; KEGG, Kyoto Encyclopedia of Genes and Genomes; MS, multiple sclerosis; PD, Parkinson’s disease.
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Kato Y, Nishiyama K, Man Lee J, Ibuki Y, Imai Y, Noda T, Kamiya N, Kusakabe T, Kanda Y, Nishida M. TRPC3-Nox2 Protein Complex Formation Increases the Risk of SARS-CoV-2 Spike Protein-Induced Cardiomyocyte Dysfunction through ACE2 Upregulation. Int J Mol Sci 2022; 24:ijms24010102. [PMID: 36613540 PMCID: PMC9820218 DOI: 10.3390/ijms24010102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Myocardial damage caused by the newly emerged coronavirus (SARS-CoV-2) infection is one of the key determinants of COVID-19 severity and mortality. SARS-CoV-2 entry to host cells is initiated by binding with its receptor, angiotensin-converting enzyme (ACE) 2, and the ACE2 abundance is thought to reflect the susceptibility to infection. Here, we report that ibudilast, which we previously identified as a potent inhibitor of protein complex between transient receptor potential canonical (TRPC) 3 and NADPH oxidase (Nox) 2, attenuates the SARS-CoV-2 spike glycoprotein pseudovirus-evoked contractile and metabolic dysfunctions of neonatal rat cardiomyocytes (NRCMs). Epidemiologically reported risk factors of severe COVID-19, including cigarette sidestream smoke (CSS) and anti-cancer drug treatment, commonly upregulate ACE2 expression level, and these were suppressed by inhibiting TRPC3-Nox2 complex formation. Exposure of NRCMs to SARS-CoV-2 pseudovirus, as well as CSS and doxorubicin (Dox), induces ATP release through pannexin-1 hemi-channels, and this ATP release potentiates pseudovirus entry to NRCMs and human iPS cell-derived cardiomyocytes (hiPS-CMs). As the pseudovirus entry followed by production of reactive oxygen species was attenuated by inhibiting TRPC3-Nox2 complex in hiPS-CMs, we suggest that TRPC3-Nox2 complex formation triggered by panexin1-mediated ATP release participates in exacerbation of myocardial damage by amplifying ACE2-dependent SARS-CoV-2 entry.
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Affiliation(s)
- Yuri Kato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuhiro Nishiyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Jae Man Lee
- Laboratory of Creative Science for Insect Industries, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuko Ibuki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yumiko Imai
- Laboratory of Regulation for Intractable Infectious Diseases, Center for Vaccine and Adjuvant Research (CVAR), National Institutes of Biomedical Innovation Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Takamasa Noda
- Department of Psychiatry, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
- Department of Neuropsychopharmacology, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo 187-8553, Japan
- Department of Brain Bioregulatory Science, The Jikei University Graduate School of Medicine, Tokyo 105-8461, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Division of Biotechnology, Center for Future Chemistry, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences (NIHS), Kawasaki 210-9501, Japan
| | - Motohiro Nishida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- National Institute for Physiological Sciences, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Correspondence: ; Tel./Fax: +81-92-642-6556
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Al-kuraishy HM, Al-Buhadily AK, Al-Gareeb AI, Alorabi M, Hadi Al-Harcan NA, El-Bouseary MM, Batiha GES. Citicoline and COVID-19: vis-à-vis conjectured. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2022; 395:1463-1475. [PMID: 36063198 PMCID: PMC9442587 DOI: 10.1007/s00210-022-02284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a current pandemic disease caused by a novel severe acute respiratory syndrome coronavirus virus respiratory type 2 (SARS-CoV-2). SARS-CoV-2 infection is linked with various neurological manifestations due to cytokine-induced disruption of the blood brain barrier (BBB), neuroinflammation, and peripheral neuronal injury, or due to direct SARS-CoV-2 neurotropism. Of note, many repurposed agents were included in different therapeutic protocols in the management of COVID-19. These agents did not produce an effective therapeutic eradication of SARS-CoV-2, and continuing searching for novel anti-SARS-CoV-2 agents is a type of challenge nowadays. Therefore, this study aimed to review the potential anti-inflammatory and antioxidant effects of citicoline in the management of COVID-19.
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Affiliation(s)
- Hayder M. Al-kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Ali K. Al-Buhadily
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad, Iraq
| | - Mohammed Alorabi
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif, 21944 Saudi Arabia
| | - Nasser A. Hadi Al-Harcan
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Rasheed University College, Baghdad, Iraq
| | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, AlBeheira, Damanhour, 22511 Egypt
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Alkhayyat SS, Al-kuraishy HM, Al-Gareeb AI, El-Bouseary MM, AboKamer AM, Batiha GES, Simal-Gandara J. Fenofibrate for COVID-19 and related complications as an approach to improve treatment outcomes: the missed key for Holy Grail. Inflamm Res 2022; 71:1159-1167. [PMID: 35941297 PMCID: PMC9360649 DOI: 10.1007/s00011-022-01615-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Fenofibrate is an agonist of peroxisome proliferator activated receptor alpha (PPAR-α), that possesses anti-inflammatory, antioxidant, and anti-thrombotic properties. Fenofibrate is effective against a variety of viral infections and different inflammatory disorders. Therefore, the aim of critical review was to overview the potential role of fenofibrate in the pathogenesis of SARS-CoV-2 and related complications. RESULTS By destabilizing SARS-CoV-2 spike protein and preventing it from binding angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoV-2 entry, fenofibrate can reduce SARS-CoV-2 entry in human cells Fenofibrate also suppresses inflammatory signaling pathways, which decreases SARS-CoV-2 infection-related inflammatory alterations. In conclusion, fenofibrate anti-inflammatory, antioxidant, and antithrombotic capabilities may help to minimize the inflammatory and thrombotic consequences associated with SARSCoV-2 infection. Through attenuating the interaction between SARS-CoV-2 and ACE2, fenofibrate can directly reduce the risk of SARS-CoV-2 infection. CONCLUSIONS As a result, fenofibrate could be a potential treatment approach for COVID-19 control.
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Affiliation(s)
- Shadi Salem Alkhayyat
- Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Hayder M. Al-kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Amal M. AboKamer
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511 Al Beheira Egypt
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty Science, Universidade de Vigo, 32004 Ourense, Spain
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Al-Kuraishy HM, Al-Gareeb AI, Gabriela Bungau S, Radu AF, El-Saber Batiha G. The potential molecular implications of adiponectin in the evolution of SARS-CoV-2: Inbuilt tendency. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102347. [PMID: 36211634 PMCID: PMC9524222 DOI: 10.1016/j.jksus.2022.102347] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 12/16/2022]
Abstract
Adiponectin (APN) is an adipokine concerned in the regulation of glucose metabolism, insulin sensitivity and fatty acid oxidation. APN plays a critical role in viral infections by regulating the immune response through its anti-inflammatory/pro-inflammatory axis. Reduction of APN may augment the severity of viral infections because APN inhibits immune cells’ response via suppression of inflammatory signaling pathways and stimulation of adenosine monophosphate protein kinase (AMPK). Moreover, APN inhibits the stimulation of nuclear factor kappa B (NF-κB) and regulates the release of pro-inflammatory cytokines, such as tumor necrosis factor alpha (TNF-α) and interleukins (IL-18, IL-6). In COVID-19, abnormalities of the fatty tissue due to oxidative stress (OS) and hyperinflammation may inhibit the production and release of APN. APN has lung-protective effect and can prevent SARS-CoV-2-induced acute lung injury (ALI) through the amelioration of endoplasmic reticulum (ER) stress, endothelial dysfunction (ED) and stimulation of peroxisome proliferator-activated receptor-alpha (PPAR-α). It has been established that there is a potential correlation between inflammatory signal transduction pathways and APN that contributes to the development of SARS-CoV-2 infections. Deregulation of these molecular pathways affects the expression of APN and vice versa. In addition, the reduction of APN effect in SARS-CoV-2 infection could be a potential cause of the exacerbation of pro-inflammatory effects which are associated with the disease severity. In this context, exploratory, developmental, and extensive prospective studies are necessary.
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Babalghith AO, Al-kuraishy HM, Al-Gareeb AI, De Waard M, Sabatier JM, Saad HM, Batiha GES. The Potential Role of Growth Differentiation Factor 15 in COVID-19: A Corollary Subjective Effect or Not? Diagnostics (Basel) 2022; 12:diagnostics12092051. [PMID: 36140453 PMCID: PMC9497461 DOI: 10.3390/diagnostics12092051] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is primarily caused by various forms of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants. COVID-19 is characterized by hyperinflammation, oxidative stress, multi-organ injury (MOI)-like acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Different biomarkers are used in the assessment of COVID-19 severity including D-dimer, ferritin, lactate dehydrogenase (LDH), and hypoxia-inducible factor (HIF). Interestingly, growth differentiation factor 15 (GDF15) has recently become a potential biomarker correlated with the COVID-19 severity. Thus, this critical review aimed to determine the critical association between GDF15 and COVID-19. The perfect function of GDF15 remains not well-recognized; nevertheless, it plays a vital role in controlling cell growth, apoptosis and inflammatory activation. Furthermore, GDF15 may act as anti-inflammatory and pro-inflammatory signaling in diverse cardiovascular complications. Furthermore, the release of GDF15 is activated by various growth factors and cytokines including macrophage colony-stimulating factor (M-CSF), angiotensin II (AngII) and p53. Therefore, higher expression of GDF15 in COVID-19 might a compensatory mechanism to stabilize and counteract dysregulated inflammatory reactions. In conclusion, GDF15 is an anti-inflammatory cytokine that could be associated with the COVID-19 severity. Increased GDF15 could be a compensatory mechanism against hyperinflammation and exaggerated immune response in the COVID-19. Experimental, preclinical and large-scale clinical studies are warranted in this regard.
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Affiliation(s)
- Ahmad O. Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Mecca 24382, Saudi Arabia
| | - Hayder M. Al-kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad P.O. Box 14022, Iraq
| | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriya University, Baghdad P.O. Box 14022, Iraq
| | - Michel De Waard
- Smartox Biotechnology, 6 rue des Platanes, 38120 Saint-Egrève, France
- L’institut du Thorax, INSERM, CNRS, UNIV NANTES, F-44007 Nantes, France
- LabEx Ion Channels, Science & Therapeutics, Université de Nice Sophia-Antipolis, F-06560 Valbonne, France
| | - Jean-Marc Sabatier
- Institut de Neurophysiopathologie (INP), Aix-Marseille Université, CNRS UMR 7051, Faculté des Sciences Médicales et Paramédicales, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Hebatallah M. Saad
- Department of Pathology, Faculty of Veterinary Medicine, Matrouh University, Mersa Matruh 51744, Egypt
- Correspondence: (H.M.S.); (G.E.-S.B.)
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
- Correspondence: (H.M.S.); (G.E.-S.B.)
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21
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Zanganeh S, Goodarzi N, Doroudian M, Movahed E. Potential COVID-19 therapeutic approaches targeting angiotensin-converting enzyme 2; An updated review. Rev Med Virol 2021; 32:e2321. [PMID: 34958163 DOI: 10.1002/rmv.2321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 has spread swiftly throughout the world posing a global health emergency. The significant numbers of deaths attributed to this pandemic have researchers battling to understand this new, dangerous virus. Researchers are looking to find possible treatment regimens and develop effective therapies. This study aims to provide an overview of published scientific information on potential treatments, emphasizing angiotensin-converting enzyme II (ACE2) inhibitors as one of the most important drug targets. SARS-CoV-2 receptor-binding domain (RBD); as a viral attachment or entry inhibitor against SARS-CoV-2, human recombinant soluble ACE2; as a genetically modified soluble form of ACE2 to compete with membrane-bound ACE2, and microRNAs (miRNAs); as a negative regulator of the expression of ACE2/TMPRSS2 to inhibit SARS-CoV2 entry into cells, are the potential therapeutic approaches discussed thoroughly in this article. This review provides the groundwork for the ongoing development of therapeutic agents and effective treatments against SARS-COV-2.
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Affiliation(s)
- Saba Zanganeh
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nima Goodarzi
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Doroudian
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, New Year, USA
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22
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Maiese K. Neurodegeneration, memory loss, and dementia: the impact of biological clocks and circadian rhythm. FRONT BIOSCI-LANDMRK 2021; 26:614-627. [PMID: 34590471 PMCID: PMC8756734 DOI: 10.52586/4971] [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: 05/30/2021] [Revised: 07/26/2021] [Accepted: 08/10/2021] [Indexed: 11/23/2022]
Abstract
Introduction: Dementia and cognitive loss impact a significant proportion of the global population and present almost insurmountable challenges for treatment since they stem from multifactorial etiologies. Innovative avenues for treatment are highly warranted. Methods and results: Novel work with biological clock genes that oversee circadian rhythm may meet this critical need by focusing upon the pathways of the mechanistic target of rapamycin (mTOR), the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), mammalian forkhead transcription factors (FoxOs), the growth factor erythropoietin (EPO), and the wingless Wnt pathway. These pathways are complex in nature, intimately associated with autophagy that can maintain circadian rhythm, and have an intricate relationship that can lead to beneficial outcomes that may offer neuroprotection, metabolic homeostasis, and prevention of cognitive loss. However, biological clocks and alterations in circadian rhythm also have the potential to lead to devastating effects involving tumorigenesis in conjunction with pathways involving Wnt that oversee angiogenesis and stem cell proliferation. Conclusions: Current work with biological clocks and circadian rhythm pathways provide exciting possibilities for the treating dementia and cognitive loss, but also provide powerful arguments to further comprehend the intimate and complex relationship among these pathways to fully potentiate desired clinical outcomes.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, New York, NY 10022, USA
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