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Alshabrmi FM, Alatawi EA. Subtractive proteomics-guided vaccine targets identification and designing of multi-epitopes vaccine for immune response instigation against Burkholderia pseudomallei. Int J Biol Macromol 2024; 270:132105. [PMID: 38710251 DOI: 10.1016/j.ijbiomac.2024.132105] [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: 01/18/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
In this study, a methodical workflow using subtractive proteomics, vaccine designing, molecular simulation, and agent-based modeling approaches were used to annotate the whole proteome of Burkholderia pseudomallei (strain K96243) for vaccine designing. Among the total 5717 proteins in the whole proteome, 505 were observed to be essential for the pathogen's survival and pathogenesis predicted by the Database of Essential Genes. Among these, 23 vaccine targets were identified, of which fimbrial assembly chaperone (Q63UH5), Outer membrane protein (Q63UH1), and Hemolysin-like protein (Q63UE4) were selected for the subsequent analysis based on the systematic approaches. Using immunoinformatic approaches CTL (cytotoxic T lymphocytes), HTL (helper T lymphocytes), IFN-positive, and B cell epitopes were predicted for these targets. A total of 9 CTL epitopes were added using the GSS linker, 6 HTL epitopes using the GPGPG linker, and 6 B cell epitopes using the KK linker. An adjuvant was added for enhanced antigenicity, an HIV-TAT peptide for improved delivery, and a PADRE sequence was added to form a 466 amino acids long vaccine construct. The construct was classified as non-allergenic, highly antigenic, and experimentally feasible. Molecular docking results validated the robust interaction of MEVC with immune receptors such as TLR2/4. Furthermore, molecular simulation revealed stable dynamics and compact nature of the complexes. The binding free energy results further validated the robust binding. In silico cloning, results revealed GC contents of 50.73 % and a CIA value of 0.978 which shows proper downstream processing. Immune simulation results reported that after the three injections of the vaccine a robust secondary immune response, improved antigen clearance, and effective immune memory generation were observed highlighting its potential for effective and sustained immunity. Future directions should encompass experimental validations, animal model studies, and clinical trials to substantiate the vaccine's efficacy, safety, and immunogenicity.
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Affiliation(s)
- Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia.
| | - Eid A Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia.
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Ni F, Hu K, Li M, Yang M, Xiao Y, Fu M, Zhu Z, Liu Y, Hu Q. Tat-dependent conditionally replicating adenoviruses expressing diphtheria toxin A for specifically killing HIV-1-infected cells. Mol Ther 2024:S1525-0016(24)00317-4. [PMID: 38734901 DOI: 10.1016/j.ymthe.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
HIV-1 infection remains a public health problem with no cure. Although antiretroviral therapy (ART) is effective for suppressing HIV-1 replication, it requires lifelong drug administration due to a stable reservoir of latent proviruses and may cause serious side effects and drive the emergence of drug-resistant HIV-1 variants. Gene therapy represents an alternative approach to overcome the limitations of conventional treatments against HIV-1 infection. In this study, we constructed and investigated the antiviral effects of an HIV-1 Tat-dependent conditionally replicating adenovirus, which selectively replicates and expresses the diphtheria toxin A chain (Tat-CRAds-DTA) in HIV-1-infected cells both in vitro and in vivo. We found that Tat-CRAds-DTA could specifically induce cell death and inhibit virus replication in HIV-1-infected cells mediated by adenovirus proliferation and DTA expression. A low titer of progeny Tat-CRAds-DTA was also detected in HIV-1-infected cells. In addition, Tat-CRAds-DTA showed no apparent cytotoxicity to HIV-1-negative cells and demonstrated significant therapeutic efficacy against HIV-1 infection in a humanized mouse model. The findings in this study highlight the potential of Tat-CRAds-DTA as a new gene therapy for the treatment of HIV-1 infection.
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Affiliation(s)
- Fengfeng Ni
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Kai Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Miaomiao Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mengshi Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Yingying Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Ming Fu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Zhiyuan Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yalan Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Hubei Jiangxia Laboratory, Wuhan 430200, P.R. China.
| | - Qinxue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, P.R. China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China.
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3
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Chen Z, Xiong M, Tian J, Song D, Duan S, Zhang L. Encapsulation and assessment of therapeutic cargo in engineered exosomes: a systematic review. J Nanobiotechnology 2024; 22:18. [PMID: 38172932 PMCID: PMC10765779 DOI: 10.1186/s12951-023-02259-6] [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: 09/09/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Exosomes are nanoscale extracellular vesicles secreted by cells and enclosed by a lipid bilayer membrane containing various biologically active cargoes such as proteins, lipids, and nucleic acids. Engineered exosomes generated through genetic modification of parent cells show promise as drug delivery vehicles, and they have been demonstrated to have great therapeutic potential for treating cancer, cardiovascular, neurological, and immune diseases, but systematic knowledge is lacking regarding optimization of drug loading and assessment of delivery efficacy. This review summarizes current approaches for engineering exosomes and evaluating their drug delivery effects, and current techniques for assessing exosome drug loading and release kinetics, cell targeting, biodistribution, pharmacokinetics, and therapeutic outcomes are critically examined. Additionally, this review synthesizes the latest applications of exosome engineering and drug delivery in clinical translation. The knowledge compiled in this review provides a framework for the rational design and rigorous assessment of exosomes as therapeutics. Continued advancement of robust characterization methods and reporting standards will accelerate the development of exosome engineering technologies and pave the way for clinical studies.
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Affiliation(s)
- Zhen Chen
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250001, China
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Jinan, 250001, China
- School of Public Health, Weifang Medical University, Weifang, 261000, China
| | - Min Xiong
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, China
| | - Jiaqi Tian
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250001, China
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Jinan, 250001, China
| | - Dandan Song
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250001, China
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Jinan, 250001, China
| | - Shuyin Duan
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250001, China
| | - Lin Zhang
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250001, China.
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Jinan, 250001, China.
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Akkawi C, Feuillard J, Diaz FL, Belkhir K, Godefroy N, Peloponese JM, Mougel M, Laine S. Murine leukemia virus (MLV) P50 protein induces cell transformation via transcriptional regulatory function. Retrovirology 2023; 20:16. [PMID: 37700325 PMCID: PMC10496198 DOI: 10.1186/s12977-023-00631-w] [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: 04/10/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND The murine leukemia virus (MLV) has been a powerful model of pathogenesis for the discovery of genes involved in cancer. Its splice donor (SD')-associated retroelement (SDARE) is important for infectivity and tumorigenesis, but the mechanism remains poorly characterized. Here, we show for the first time that P50 protein, which is produced from SDARE, acts as an accessory protein that transregulates transcription and induces cell transformation. RESULTS By infecting cells with MLV particles containing SDARE transcript alone (lacking genomic RNA), we show that SDARE can spread to neighbouring cells as shown by the presence of P50 in infected cells. Furthermore, a role for P50 in cell transformation was demonstrated by CCK8, TUNEL and anchorage-independent growth assays. We identified the integrase domain of P50 as being responsible for transregulation of the MLV promoter using luciferase assay and RTqPCR with P50 deleted mutants. Transcriptomic analysis furthermore revealed that the expression of hundreds of cellular RNAs involved in cancerogenesis were deregulated in the presence of P50, suggesting that P50 induces carcinogenic processes via its transcriptional regulatory function. CONCLUSION We propose a novel SDARE-mediated mode of propagation of the P50 accessory protein in surrounding cells. Moreover, due to its transforming properties, P50 expression could lead to a cellular and tissue microenvironment that is conducive to cancer development.
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Affiliation(s)
- Charbel Akkawi
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Jerome Feuillard
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Felipe Leon Diaz
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Khalid Belkhir
- ISEM, CNRS, EPHE, Université Montpellier, IRD, Montpellier, France
| | - Nelly Godefroy
- ISEM, CNRS, EPHE, Université Montpellier, IRD, Montpellier, France
| | | | - Marylene Mougel
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France.
| | - Sebastien Laine
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France.
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Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 2022; 10:e13986. [PMID: 36275462 PMCID: PMC9586123 DOI: 10.7717/peerj.13986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A. Tikhomirova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Daria M. Potashnikova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra N. Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Eugene A. Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A. Shmakova
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Diego Germini
- UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Anastasia I. Kachalova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleena A. Saidova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Anastasia A. Zharikova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R. Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Andrey A. Mironov
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Institute for Information Transmission Problems, Moscow, Russia
| | - Yegor S. Vassetzky
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Eugene V. Sheval
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
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Roles of Interleukin-6-mediated immunometabolic reprogramming in COVID-19 and other viral infection-associated diseases. Int Immunopharmacol 2022; 110:109005. [PMID: 35780641 PMCID: PMC9236983 DOI: 10.1016/j.intimp.2022.109005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 01/08/2023]
Abstract
Interleukin-6 (IL-6) is a highly pleiotropic glycoprotein factor that can modulate innate and adaptive immunity as well as various aspects of metabolism, including glycolysis, fatty acid oxidation and oxidative phosphorylation. Recently, the expression and release of IL-6 is shown to be significantly increased in numerous diseases related to virus infection, and this increase is positively correlated with the disease severity. Immunity and metabolism are two highly integrated and interdependent systems, the balance between them plays a pivotal role in maintaining body homeostasis. IL-6-elicited inflammatory response is found to be closely associated with metabolic disorder in patients with viral infection. This brief review summarizes the regulatory role of IL-6 in immunometabolic reprogramming among seven viral infection-associated diseases.
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Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
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Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
- *Correspondence: Shringar Rao, ; Tokameh Mahmoudi,
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Role of Apoptosis in HIV Pathogenesis. Adv Virol 2022; 2022:8148119. [PMID: 35462964 PMCID: PMC9023228 DOI: 10.1155/2022/8148119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/08/2022] [Accepted: 03/28/2022] [Indexed: 11/18/2022] Open
Abstract
The apoptotic pathway is an important cell death pathway that contributes to the maintenance of homeostasis in living systems. However, variations in apoptosis have been linked to many diseases such as cancers and chronic infections. The HIV infection has contributed to increase mortality and morbidity worldwide, predominantly through the induction of gradual depletion of CD4+ T cells. The induction and mediation of both the intrinsic and extrinsic apoptotic pathways are crucial in HIV pathogenesis and intracellular survival. Consequently, a deep molecular understanding of how apoptosis is induced and modulated in HIV-mediated CD4+ T cell depletion is paramount, as this can lead to new portals of therapeutic intervention and control.
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