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Zhang L, Jia X, Zhang Z, Yu T, Geng Z, Yuan L. ceRNA Network Analysis Reveals Potential Key miRNAs and Target Genes in COVID-19-Related Chronic Obstructive Pulmonary Disease. Appl Biochem Biotechnol 2024; 196:4303-4316. [PMID: 37947947 DOI: 10.1007/s12010-023-04773-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
The continued spread of SARS-CoV-2 has presented unprecedented obstacles to the worldwide public health system. Especially, individuals with chronic obstructive pulmonary disease (COPD) are at a heightened risk of contracting SARS-CoV-2 infection due to their pre-existing respiratory symptoms that are not well-managed. However, the viral mechanism of affecting the expression of host genes, COPD progression, and prognosis is not clear yet.This study integrated the differential expression information of COPD patients and then calculated the correlation between mRNAs and miRNAs to construct a COPD-specific ceRNA network. The DEGs of individuals with SARS-CoV-2 infection and anticipated miRNAs and their targets were analyzed in 9 SARS-CoV-2 sequences from different geographic locations. Furthermore, combining the experimentally validated miRNAs and genes, the regulatory miRNA-mRNA relationships were identified. All the regulatory relationships were integrated into the COPD-specific network and the network modules were explored to get insight into the functional mechanism of SARS-CoV-2 infection in COPD patients.A higher proportion of DEGs compete with the same miRNA suggesting a higher expression of genes in the COPD-specific ceRNA network. Hsa-miR-21-3p is the largest connected point in the network, but the proportion of genes upregulated by hsa-miR-21-3p is low (P = 0.1406). This indicates that the regulatory relationship of competitive inhibition has little effect on has-miR-21, and the high expression pattern is a poor prognostic factor in COPD. Hsa-miR-15a-5p is the most significant miRNA with the highest proportion of DEGs. And ANXA2P3 is the only gene in the COPD ceRNA network that interferes with hsa-miR-15a-5p. In addition, we found that has-miR-1184- and has-miR-99-cored modules were significant, and genes ZDHHC18, PCGF3, and KIAA0319L interacting with them were all associated with COPD prognosis, and high expression of these genes could lead to poor prognosis in COPD.The key regulators such as miR-21, miR-15a, ANXA2P3, ZDHHC18, PCGF3, and KIAA0319L can be used as prognostic biomarkers for early intervention in COPD with SARS-CoV-2 infection.
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Affiliation(s)
- Lihai Zhang
- Department of Respiratory and Critical Care, The First Hospital of Hebei Medical University, No.89, Donggang Road, Shijiazhuang City, 050000, Hebei Province, China
| | - Xiaodong Jia
- Joint Laboratory of Translational Medicine, Liaocheng People's Hospital, No.67, Dongchang West Road, Liaocheng City, 252000, China
| | - Zhipeng Zhang
- Respiratory Medicine, Jiyang District People's Hospital, No.9, Xinyuan Street, Jiyang District, Jinan, 251400, Shandong Province, China
| | - Tong Yu
- Department of Respiratory and Critical Care Medicine, Liaocheng People's Hospital, No.67, Dongchang West Road, Liaocheng City, 252000, China
| | - Zhangyan Geng
- Department of Geriatrics, First Hospital of Hebei Medical University, No.89, Donggang Road, Shijiazhuang City, 050000, Hebei Province, China
| | - Lindong Yuan
- Department of Respiratory and Critical Care Medicine, Liaocheng People's Hospital, No.67, Dongchang West Road, Liaocheng City, 252000, China.
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2
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Wang Y, Kulkarni VV, Pantaleón García J, Leiva-Juárez MM, Goldblatt DL, Gulraiz F, Vila Ellis L, Chen J, Longmire MK, Donepudi SR, Lorenzi PL, Wang H, Wong LJ, Tuvim MJ, Evans SE. Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial immunometabolic modulation. PLoS Pathog 2023; 19:e1011138. [PMID: 37695784 PMCID: PMC10522048 DOI: 10.1371/journal.ppat.1011138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 09/26/2023] [Accepted: 08/01/2023] [Indexed: 09/13/2023] Open
Abstract
Pneumonia is a worldwide threat, making discovery of novel means to combat lower respiratory tract infection an urgent need. Manipulating the lungs' intrinsic host defenses by therapeutic delivery of certain pathogen-associated molecular patterns protects mice against pneumonia in a reactive oxygen species (ROS)-dependent manner. Here we show that antimicrobial ROS are induced from lung epithelial cells by interactions of CpG oligodeoxynucleotides (ODN) with mitochondrial voltage-dependent anion channel 1 (VDAC1). The ODN-VDAC1 interaction alters cellular ATP/ADP/AMP localization, increases delivery of electrons to the electron transport chain (ETC), increases mitochondrial membrane potential (ΔΨm), differentially modulates ETC complex activities and consequently results in leak of electrons from ETC complex III and superoxide formation. The ODN-induced mitochondrial ROS yield protective antibacterial effects. Together, these studies identify a therapeutic metabolic manipulation strategy to broadly protect against pneumonia without reliance on antibiotics.
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Affiliation(s)
- Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Vikram V. Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
| | - Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Miguel M. Leiva-Juárez
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - David L. Goldblatt
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Fahad Gulraiz
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lisandra Vila Ellis
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jichao Chen
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Michael K. Longmire
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
| | - Sri Ramya Donepudi
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Hao Wang
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lee-Jun Wong
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael J. Tuvim
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Scott E. Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
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3
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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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4
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Wang Y, Kulkarni VV, Pantaleón García J, Leiva-Juárez MM, Goldblatt DL, Gulraiz F, Chen J, Donepudi SR, Lorenzi PL, Wang H, Wong LJ, Tuvim MJ, Evans SE. Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial metabolic reprogramming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524841. [PMID: 36711510 PMCID: PMC9882263 DOI: 10.1101/2023.01.19.524841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pneumonia is a worldwide threat, making discovery of novel means to combat lower respiratory tract infections an urgent need. We have previously shown that manipulating the lungs' intrinsic host defenses by therapeutic delivery of a unique dyad of pathogen-associated molecular patterns protects mice against pneumonia in a reactive oxygen species (ROS)-dependent manner. Here we show that antimicrobial ROS are induced from lung epithelial cells by interactions of CpG oligodeoxynucleotides (ODNs) with mitochondrial voltage-dependent anion channel 1 (VDAC1) without dependence on Toll-like receptor 9 (TLR9). The ODN-VDAC1 interaction alters cellular ATP/ADP/AMP localization, increases delivery of electrons to the electron transport chain (ETC), enhances mitochondrial membrane potential (Δ Ψm ), and differentially modulates ETC complex activities. These combined effects promote leak of electrons from ETC complex III, resulting in superoxide formation. The ODN-induced mitochondrial ROS yield protective antibacterial effects. Together, these studies identify a therapeutic metabolic manipulation strategy that has the potential to broadly protect patients against pneumonia during periods of peak vulnerability without reliance on currently available antibiotics. Author Summary Pneumonia is a major cause of death worldwide. Increasing antibiotic resistance and expanding immunocompromised populations continue to enhance the clinical urgency to find new strategies to prevent and treat pneumonia. We have identified a novel inhaled therapeutic that stimulates lung epithelial defenses to protect mice against pneumonia in a manner that depends on production of reactive oxygen species (ROS). Here, we report that the induction of protective ROS from lung epithelial mitochondria occurs following the interaction of one component of the treatment, an oligodeoxynucleotide, with the mitochondrial voltage-dependent anion channel 1. This interaction alters energy transfer between the mitochondria and the cytosol, resulting in metabolic reprogramming that drives more electrons into the electron transport chain, then causes electrons to leak from the electron transport chain to form protective ROS. While antioxidant therapies are endorsed in many other disease states, we present here an example of therapeutic induction of ROS that is associated with broad protection against pneumonia without reliance on administration of antibiotics.
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Affiliation(s)
- Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vikram V. Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Miguel M. Leiva-Juárez
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David L. Goldblatt
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fahad Gulraiz
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sri Ramya Donepudi
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Philip L. Lorenzi
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Hao Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lee-Jun Wong
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael J. Tuvim
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott E. Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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5
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Czechtizky W, Su W, Ripa L, Schiesser S, Höijer A, Cox RJ. Advances in the design of new types of inhaled medicines. PROGRESS IN MEDICINAL CHEMISTRY 2022; 61:93-162. [PMID: 35753716 DOI: 10.1016/bs.pmch.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Inhalation of small molecule drugs has proven very efficacious for the treatment of respiratory diseases due to enhanced efficacy and a favourable therapeutic index compared with other dosing routes. It enables targeted delivery to the lung with rapid onset of therapeutic action, low systemic drug exposure, and thereby reduced systemic side effects. An increasing number of pharmaceutical companies and biotechs are investing in new modalities-for this review defined as therapeutic molecules with a molecular weight >800Da and therefore beyond usual inhaled small molecule drug-like space. However, our experience with inhaled administration of PROTACs, peptides, oligonucleotides (antisense oligonucleotides, siRNAs, miRs and antagomirs), diverse protein scaffolds, antibodies and antibody fragments is still limited. Investigating the retention and metabolism of these types of molecules in lung tissue and fluid will contribute to understanding which are best suited for inhalation. Nonetheless, the first such therapeutic molecules have already reached the clinic. This review will provide information on the physiology of healthy and diseased lungs and their capacity for drug metabolism. It will outline the stability, aggregation and immunogenicity aspects of new modalities, as well as recap on formulation and delivery aspects. It concludes by summarising clinical trial outcomes with inhaled new modalities based on information available at the end of 2021.
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Affiliation(s)
- Werngard Czechtizky
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden.
| | - Wu Su
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Lena Ripa
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Andreas Höijer
- Cardiovascular, Renal & Metabolism CMC Projects, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rhona J Cox
- Department of Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal & Metabolism, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
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6
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Pantaleón García J, Kulkarni VV, Reese TC, Wali S, Wase SJ, Zhang J, Singh R, Caetano MS, Kadara H, Moghaddam S, Johnson FM, Wang J, Wang Y, Evans S. OBIF: an omics-based interaction framework to reveal molecular drivers of synergy. NAR Genom Bioinform 2022; 4:lqac028. [PMID: 35387383 PMCID: PMC8982434 DOI: 10.1093/nargab/lqac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/08/2023] Open
Abstract
Bioactive molecule library screening may empirically identify effective combination therapies, but molecular mechanisms underlying favorable drug–drug interactions often remain unclear, precluding further rational design. In the absence of an accepted systems theory to interrogate synergistic responses, we introduce Omics-Based Interaction Framework (OBIF) to reveal molecular drivers of synergy through integration of statistical and biological interactions in synergistic biological responses. OBIF performs full factorial analysis of feature expression data from single versus dual exposures to identify molecular clusters that reveal synergy-mediating pathways, functions and regulators. As a practical demonstration, OBIF analyzed transcriptomic and proteomic data of a dyad of immunostimulatory molecules that induces synergistic protection against influenza A and revealed unanticipated NF-κB/AP-1 cooperation that is required for antiviral protection. To demonstrate generalizability, OBIF analyzed data from a diverse array of Omics platforms and experimental conditions, successfully identifying the molecular clusters driving their synergistic responses. Hence, unlike existing synergy quantification and prediction methods, OBIF is a phenotype-driven systems model that supports multiplatform interrogation of synergy mechanisms.
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Affiliation(s)
- Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Vikram V Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Tanner C Reese
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- Rice University, Houston, TX 77005, USA
| | - Shradha Wali
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Saima J Wase
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ratnakar Singh
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Mauricio S Caetano
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Faye M Johnson
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Banerjee S, Banerjee D, Singh A, Saharan VA. A Comprehensive Investigation Regarding the Differentiation of the Procurable COVID-19 Vaccines. AAPS PharmSciTech 2022; 23:95. [PMID: 35314902 PMCID: PMC8936379 DOI: 10.1208/s12249-022-02247-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/06/2022] [Indexed: 11/30/2022] Open
Abstract
COVID-19 caused by coronavirus SARS-CoV-2 became a serious threat to humankind for the past couple of years. The development of vaccine and its immediate application might be the only to escape from the grasp of this demoniac pandemic. Approximately 343 clinical trials on COVID-19 vaccines are ongoing currently, and almost all countries are motivating ongoing researches at warp speed for the development of vaccines against COVID-19. This review explores the progress in the development of the vaccines, their current status of ongoing clinical research, mechanisms, and regulatory approvals. Many pharmaceutical companies are already in the endgame for manufacturing various vaccines of which some are already being marketed across the globe, while others are yet to get approval for marketing. The primary aim of this review is to compare regulatory accepted vaccines in terms of their composition, doses, regulatory status, and efficacy. The study is conducted by grouping into approved and unapproved vaccines for marketing. Different routes of administration of vaccines along with the efficacy of the routes are also presented in the review. A wide range of database and clinical trial data is reviewed for sorting out the information on different vaccines. Unfortunately, many mutations (alpha, beta, gamma, delta, kappa, omicron etc.) of SARS-CoV-2 have attacked people in very short time, which is the great challenge for investigational vaccines. Moreover, some vaccines like Pfizer's BNT162, Oxford's ChAdOx1, Moderna's mRNA-1273, and Bharat Biotech's Covaxin have got regulatory approval in some countries for its distribution which may prove to stand tall against the pandemic.
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Affiliation(s)
- Surojit Banerjee
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India.
| | - Debadri Banerjee
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
| | - Anupama Singh
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
| | - Vikas Anand Saharan
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
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8
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Mabrey FL, Morrell ED, Wurfel MM. TLRs in COVID-19: How they drive immunopathology and the rationale for modulation. Innate Immun 2021; 27:503-513. [PMID: 34806446 PMCID: PMC8762091 DOI: 10.1177/17534259211051364] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is both a viral illness and a disease of immunopathology. Proximal events within the innate immune system drive the balance between deleterious inflammation and viral clearance. We hypothesize that a divergence between the generation of excessive inflammation through over activation of the TLR associated myeloid differentiation primary response (MyD88) pathway relative to the TIR-domain-containing adaptor-inducing IFN-β (TRIF) pathway plays a key role in COVID-19 severity. Both viral elements and damage associated host molecules act as TLR ligands in this process. In this review, we detail the mechanism for this imbalance in COVID-19 based on available evidence, and we discuss how modulation of critical elements may be important in reducing severity of disease.
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Affiliation(s)
- F Linzee Mabrey
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, 7284University of Washington, USA
| | - Eric D Morrell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, 7284University of Washington, USA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, 7284University of Washington, USA
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9
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Khemani RG, Lee JT, Wu D, Schenck EJ, Hayes MM, Kritek PA, Mutlu GM, Gershengorn HB, Coudroy R. Update in Critical Care 2020. Am J Respir Crit Care Med 2021; 203:1088-1098. [PMID: 33734938 DOI: 10.1164/rccm.202102-0336up] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Robinder G Khemani
- Pediatric ICU, Department of Anesthesiology and Critical Care Medicine, Children's Hospital Los Angeles, Los Angeles, California.,Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jessica T Lee
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Wu
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Edward J Schenck
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.,NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Margaret M Hayes
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Patricia A Kritek
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Washington Seattle, Washington
| | - Gökhan M Mutlu
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Hayley B Gershengorn
- Division of Pulmonary, Critical Care, and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, Florida.,Division of Critical Care Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Rémi Coudroy
- Institut National de la Santé et de la Recherche Médicale, Poitiers, France; and.,Médecine Intensive Réanimation, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
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10
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Chotirmall SH, Leither LM, Çoruh B, Chan LLY, Joudi AM, Brown SM, Singer BD, Seam N. Update in COVID-19 2020. Am J Respir Crit Care Med 2021; 203:1462-1471. [PMID: 33835905 PMCID: PMC8483226 DOI: 10.1164/rccm.202102-0415up] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lindsay M Leither
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Başak Çoruh
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Anthony M Joudi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Samuel M Brown
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Biochemistry and Molecular Genetics, and.,Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Nitin Seam
- Critical Care Medicine Department, NIH, Bethesda, Maryland
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11
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Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. Comput Biol Med 2021; 135:104570. [PMID: 34157472 PMCID: PMC8197616 DOI: 10.1016/j.compbiomed.2021.104570] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
Background The spread of a novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has affected both the public health and the global economy. The current study was aimed at analysing the genetic sequence of this highly contagious corona virus from an evolutionary perspective, comparing the genetic variation features of different geographic strains, and identifying the key miRNAs as well as their gene targets from the transcriptome data of infected lung tissues. Methods A multilevel robust computational analysis was undertaken for viral genetic sequence alignment, phylogram construction, genome-wide transcriptome data interpretation of virus-infected lung tissues, miRNA mapping, and functional biology networking. Results Our findings show both genetic similarities as well as notable differences in the S protein length among SARS-CoV-1, SARS-CoV-2 and MERS viruses. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). The infected lung tissues demonstrated the upregulation of 282 (56.51%) antiviral defensive response pathway genes and downregulation of 217 (43.48%) genes involved in autophagy and lung repair pathways. By miRNA mapping, 4 key miRNAs (hsa-miR-342-5p, hsa-miR-432-5p, hsa-miR-98-5p and hsa-miR-17-5p), targeting multiple host genes (MYC, IL6, ICAM1 and VEGFA) as well as SARS-CoV2 gene (ORF1ab) were identified. Conclusion Systems biology methods offer a new perspective in understanding the molecular basis for the faster spread of SARS-CoV-2 infection. The antiviral miRNAs identified in this study may aid in the ongoing search for novel personalized therapeutic avenues for COVID patients.
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12
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Han K, Blair RV, Iwanaga N, Liu F, Russell-Lodrigue KE, Qin Z, Midkiff CC, Golden NA, Doyle-Meyers LA, Kabir ME, Chandler KE, Cutrera KL, Ren M, Monjure CJ, Lehmicke G, Fischer T, Beddingfield B, Wanek AG, Birnbaum A, Maness NJ, Roy CJ, Datta PK, Rappaport J, Kolls JK, Qin X. Lung Expression of Human Angiotensin-Converting Enzyme 2 Sensitizes the Mouse to SARS-CoV-2 Infection. Am J Respir Cell Mol Biol 2021; 64:79-88. [PMID: 32991819 PMCID: PMC7781002 DOI: 10.1165/rcmb.2020-0354oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Preclinical mouse models that recapitulate some characteristics of coronavirus disease (COVID-19) will facilitate focused study of pathogenesis and virus-host responses. Human agniotensin-converting enzyme 2 (hACE2) serves as an entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to infect people via binding to envelope spike proteins. Herein we report development and characterization of a rapidly deployable COVID-19 mouse model. C57BL/6J (B6) mice expressing hACE2 in the lung were transduced by oropharyngeal delivery of the recombinant human adenovirus type 5 that expresses hACE2 (Ad5-hACE2). Mice were infected with SARS-CoV-2 at Day 4 after transduction and developed interstitial pneumonia associated with perivascular inflammation, accompanied by significantly higher viral load in lungs at Days 3, 6, and 12 after infection compared with Ad5-empty control group. SARS-CoV-2 was detected in pneumocytes in alveolar septa. Transcriptomic analysis of lungs demonstrated that the infected Ad5-hACE mice had a significant increase in IFN-dependent chemokines Cxcl9 and Cxcl10, and genes associated with effector T-cell populations including Cd3 g, Cd8a, and Gzmb. Pathway analysis showed that several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the data set, including cytokine-cytokine receptor interaction, the chemokine signaling pathway, the NOD-like receptor signaling pathway, the measles pathway, and the IL-17 signaling pathway. This response is correlative to clinical response in lungs of patients with COVID-19. These results demonstrate that expression of hACE2 via adenovirus delivery system sensitized the mouse to SARS-CoV-2 infection and resulted in the development of a mild COVID-19 phenotype, highlighting the immune and inflammatory host responses to SARS-CoV-2 infection. This rapidly deployable COVID-19 mouse model is useful for preclinical and pathogenesis studies of COVID-19.
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Affiliation(s)
- Kun Han
- Tulane National Primate Research Center, Covington, Louisiana; and
| | - Robert V. Blair
- Tulane National Primate Research Center, Covington, Louisiana; and
| | - Naoki Iwanaga
- Department of Medicine and Department of Pediatrics, Center for Translational Research in Infection and Inflammation, and
| | - Fengming Liu
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Zhongnan Qin
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Nadia A. Golden
- Tulane National Primate Research Center, Covington, Louisiana; and
| | | | - Mohammad E. Kabir
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | | | | | - Mi Ren
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Gabrielle Lehmicke
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tracy Fischer
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Alanna G. Wanek
- Department of Medicine and Department of Pediatrics, Center for Translational Research in Infection and Inflammation, and
| | - Angela Birnbaum
- Tulane National Primate Research Center, Covington, Louisiana; and
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Chad J. Roy
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Prasun K. Datta
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jay K. Kolls
- Department of Medicine and Department of Pediatrics, Center for Translational Research in Infection and Inflammation, and
| | - Xuebin Qin
- Tulane National Primate Research Center, Covington, Louisiana; and
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana
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13
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Wali S, Flores JR, Jaramillo AM, Goldblatt DL, Pantaleón García J, Tuvim MJ, Dickey BF, Evans SE. Immune Modulation to Improve Survival of Viral Pneumonia in Mice. Am J Respir Cell Mol Biol 2020; 63:758-766. [PMID: 32853024 PMCID: PMC7790135 DOI: 10.1165/rcmb.2020-0241oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022] Open
Abstract
Viral pneumonias remain global health threats, as exemplified in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, requiring novel treatment strategies both early and late in the disease process. We have reported that mice treated before or soon after infection with a combination of inhaled Toll-like receptor (TLR) 2/6 and 9 agonists (Pam2-ODN) are broadly protected against microbial pathogens including respiratory viruses, but the mechanisms remain incompletely understood. The objective of this study was to validate strategies for immune modulation in a preclinical model of viral pneumonia and determine their mechanisms. Mice were challenged with the Sendai paramyxovirus in the presence or absence of Pam2-ODN treatment. Virus burden and host immune responses were assessed to elucidate Pam2-ODN mechanisms of action and to identify additional opportunities for therapeutic intervention. Enhanced survival of Sendai virus pneumonia with Pam2-ODN treatment was associated with reductions in lung virus burden and with virus inactivation before internalization. We noted that mortality in sham-treated mice corresponded with CD8+ T-cell lung inflammation on days 11-12 after virus challenge, after the viral burden had declined. Pam2-ODN blocked this injurious inflammation by minimizing virus burden. As an alternative intervention, depleting CD8+ T cells 8 days after viral challenge also decreased mortality. Stimulation of local innate immunity within the lungs by TLR agonists early in disease or suppression of adaptive immunity by systemic CD8+ T-cell depletion late in disease improves outcomes of viral pneumonia in mice. These data reveal opportunities for targeted immunomodulation to protect susceptible human subjects.
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Affiliation(s)
- Shradha Wali
- UTHealth Graduate School of Biomedical Sciences and
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jose R. Flores
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ana M. Jaramillo
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David L. Goldblatt
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Michael J. Tuvim
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Burton F. Dickey
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott E. Evans
- UTHealth Graduate School of Biomedical Sciences and
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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