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Song MS, Lee DK, Lee CY, Park SC, Yang J. Host Subcellular Organelles: Targets of Viral Manipulation. Int J Mol Sci 2024; 25:1638. [PMID: 38338917 PMCID: PMC10855258 DOI: 10.3390/ijms25031638] [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: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.
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Affiliation(s)
- Min Seok Song
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Sang-Cheol Park
- Artificial Intelligence and Robotics Laboratory, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Jinsung Yang
- Department of Biochemistry and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
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Tripathi A, Iyer K, Mitra D. HIV-1 replication requires optimal activation of the unfolded protein response. FEBS Lett 2023; 597:2908-2930. [PMID: 37984889 DOI: 10.1002/1873-3468.14772] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/16/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Several human diseases including viral infections activate the unfolded protein response (UPR) due to abnormal accumulation of unfolded/misfolded proteins. However, UPR modulation and its functional relevance in HIV-1 infection lack comprehensive elucidation. This study reveals that HIV-1 activates IRE1, PERK, and ATF6 signaling pathways of UPR. The knockdown of PERK and ATF6 reduces HIV-1 long terminal repeat (LTR)-driven gene expression, whereas the endoplasmic reticulum (ER) chaperone HSPA5 prevents proteasomal degradation of HIV-1 p24 through its chaperone activity. Interestingly, overstimulation of UPR by a chemical inducer leads to anti-HIV activity through an enhanced type-1 interferon response. Also, treatment with a chemical ER stress inhibitor reduces HIV-1 replication. These findings suggest that an optimal UPR activation is crucial for effective viral replication, as either overstimulating UPR or inhibiting ER stress leads to viral suppression.
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Rose R, McGrath MS. HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105514. [PMID: 37832752 PMCID: PMC10842591 DOI: 10.1016/j.meegid.2023.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. METHODS 2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. RESULTS In validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. CONCLUSIONS Recent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.
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Affiliation(s)
| | | | - Enoch S Liu
- Natural Selection, San Diego, California, USA
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Ghaly M, Proulx J, Borgmann K, Park IW. Novel role of HIV-1 Nef in regulating the ubiquitination of cellular proteins. Front Cell Infect Microbiol 2023; 13:1106591. [PMID: 36968110 PMCID: PMC10031067 DOI: 10.3389/fcimb.2023.1106591] [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: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 03/10/2023] Open
Abstract
Our recent data established that HIV-1 Nef is pivotal in determining the fate of cellular proteins by modulating ubiquitination. However, it is unknown which proteins are ubiquitinated in the presence of Nef, a question critical for understanding the proliferation/restriction strategies of HIV-1 in infected cells. To identify cellular proteins ubiquitinated by Nef, we conducted a proteomic analysis of cellular proteins in the presence and absence of Nef. Proteomic analysis in HEK293T cells indicated that 93 proteins were upregulated and 232 were downregulated in their ubiquitination status by Nef. Computational analysis classified these proteins based on molecular function, biological process, subcellular localization, and biological pathway. Of those proteins, we found a majority of molecular functions to be involved in binding and catalytic activity. With respect to biological processes, a significant portion of the proteins identified were related to cellular and metabolic processes. Subcellular localization analysis showed the bulk of proteins to be localized to the cytosol and cytosolic compartments, which is consistent with the known function and location of Nef during HIV-1 infection. As for biological pathways, the wide range of affected proteins was denoted by the multiple modes to fulfill function, as distinguished from a strictly singular means, which was not detected. Among these ubiquitinated proteins, six were found to directly interact with Nef, wherein two were upregulated and four downregulated. We also identified 14 proteins involved in protein stability through directly participating in the Ubiquitin Proteasome System (UPS)-mediated proteasomal degradation pathway. Of those proteins, we found six upregulated and eight downregulated. Taken together, these analyses indicate that HIV-1 Nef is integral to regulating the stability of various cellular proteins via modulating ubiquitination. The molecular mechanisms directing Nef-triggered regulation of cellular protein ubiquitination are currently under investigation.
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Sviridov D, Miller YI, Bukrinsky MI. Trained Immunity and HIV Infection. Front Immunol 2022; 13:903884. [PMID: 35874772 PMCID: PMC9304701 DOI: 10.3389/fimmu.2022.903884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Findings that certain infections induce immunity not only against the causing agent, but also against an unrelated pathogen have intrigued investigators for many years. Recently, underlying mechanisms of this phenomenon have started to come to light. It was found that the key cells responsible for heterologous protection are innate immune cells such as natural killer cells (NKs), dendritic cells, and monocytes/macrophages. These cells are 'primed' by initial infection, allowing them to provide enhanced response to subsequent infection by the same or unrelated agent. This phenomenon of innate immune memory was termed 'trained immunity'. The proposed mechanism for trained immunity involves activation by the first stimulus of metabolic pathways that lead to epigenetic changes, which maintain the cell in a "trained" state, allowing enhanced responses to a subsequent stimulus. Innate immune memory can lead either to enhanced responses or to suppression of subsequent responses ('tolerance'), depending on the strength and length of the initial stimulation of the immune cells. In the context of HIV infection, innate memory induced by infection is not well understood. In this Hypothesis and Theory article, we discuss evidence for HIV-induced trained immunity in human monocytes, its possible mechanisms, and implications for HIV-associated co-morbidities.
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Affiliation(s)
- Dmitri Sviridov
- Laboratory of Lipoproteins and Atherosclerosis, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Yury I. Miller
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Michael I. Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
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Paolini A, Baldassarre A, Bruno SP, Felli C, Muzi C, Ahmadi Badi S, Siadat SD, Sarshar M, Masotti A. Improving the Diagnostic Potential of Extracellular miRNAs Coupled to Multiomics Data by Exploiting the Power of Artificial Intelligence. Front Microbiol 2022; 13:888414. [PMID: 35756065 PMCID: PMC9218639 DOI: 10.3389/fmicb.2022.888414] [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: 03/02/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
In recent years, the clinical use of extracellular miRNAs as potential biomarkers of disease has increasingly emerged as a new and powerful tool. Serum, urine, saliva and stool contain miRNAs that can exert regulatory effects not only in surrounding epithelial cells but can also modulate bacterial gene expression, thus acting as a “master regulator” of many biological processes. We think that in order to have a holistic picture of the health status of an individual, we have to consider comprehensively many “omics” data, such as miRNAs profiling form different parts of the body and their interactions with cells and bacteria. Moreover, Artificial Intelligence (AI) and Machine Learning (ML) algorithms coupled to other multiomics data (i.e., big data) could help researchers to classify better the patient’s molecular characteristics and drive clinicians to identify personalized therapeutic strategies. Here, we highlight how the integration of “multiomic” data (i.e., miRNAs profiling and microbiota signature) with other omics (i.e., metabolomics, exposomics) analyzed by AI algorithms could improve the diagnostic and prognostic potential of specific biomarkers of disease.
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Affiliation(s)
- Alessandro Paolini
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | | | - Stefania Paola Bruno
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy.,Department of Science, University Roma Tre, Rome, Italy
| | - Cristina Felli
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Chantal Muzi
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Sara Ahmadi Badi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Meysam Sarshar
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
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Namazi F, Davoodi S, Bolhassani A. Comparison of the efficacy of HIV-1 Nef-Tat-Gp160-p24 polyepitope vaccine candidate with Nef protein in different immunization strategies. Curr Drug Deliv 2021; 19:142-156. [PMID: 33655833 DOI: 10.2174/1567201818666210224101144] [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: 10/04/2020] [Revised: 12/23/2020] [Accepted: 01/25/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVES One of the promising strategies for effective HIV-1 vaccine design involves finding the polyepitope immunogens using T cell epitopes. METHODS Herein, an HIV-1 polyepitope construct (i.e., Nef-Tat-Gp160-P24) comprising of several epitopes from Nef, Tat, Gp160, and P24 proteins was designed. To improve its immunogenicity in BALB/c mice, cell-penetrating peptides (HR9 & MPG for DNA delivery, and LDP-NLS & CyLoP-1 for protein transfer), Montanide adjuvant, and heterologous DNA prime/polypeptide boost strategy were used. To compare the immunogenicity, Nef was utilized as a vaccine candidate. The levels of total IgG and its subclasses, cytokines, and Granzyme B were assessed using ELISA. RESULTS Immunological studies showed that heterologous prime-boost regimens for both antigens could considerably augment the levels of IgG2a, IgG2b, IFN-γ, and Granzyme B directed toward Th1 and CTL immune responses in comparison with homologous prime-boost strategies. The levels of IFN-γ, IL-10, total IgG, IgG1, and IgG2b were drastically higher in groups immunized with Nef-Tat-Gp160-P24 in heterologous prime-boost regimens than those in groups immunized with Nef. CONCLUSIONS The use of the Nef-Tat-Gp160-P24 polyepitope immunogen in heterologous prime-boost strategy could generate the mixture of Th1 and Th2 responses directed further toward Th1 response as a hopeful method for improvement of HIV-1 vaccine.
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Affiliation(s)
- Fatemeh Namazi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran. Iran
| | - Saba Davoodi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran. Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran. Iran
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Bello-Morales R, Ripa I, López-Guerrero JA. Extracellular Vesicles in Viral Spread and Antiviral Response. Viruses 2020; 12:E623. [PMID: 32521696 PMCID: PMC7354624 DOI: 10.3390/v12060623] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
Viral spread by both enveloped and non-enveloped viruses may be mediated by extracellular vesicles (EVs), including microvesicles (MVs) and exosomes. These secreted vesicles have been demonstrated to be an efficient mechanism that viruses can use to enter host cells, enhance spread or evade the host immune response. However, the complex interplay between viruses and EVs gives rise to antagonistic biological tasks-to benefit the viruses, enhancing infection and interfering with the immune system or to benefit the host, by mediating anti-viral responses. Exosomes from cells infected with herpes simplex type 1 (HSV-1) may transport viral and host transcripts, proteins and innate immune components. This virus may also use MVs to expand its tropism and evade the host immune response. This review aims to describe the current knowledge about EVs and their participation in viral infection, with a specific focus on the role of exosomes and MVs in herpesvirus infections, particularly that of HSV-1.
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Affiliation(s)
- Raquel Bello-Morales
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Inés Ripa
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - José Antonio López-Guerrero
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
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Namazi F, Bolhassani A, Sadat SM, Irani S. Delivery of HIV-1 Polyepitope Constructs Using Cationic and Amphipathic Cell Penetrating Peptides into Mammalian Cells. Curr HIV Res 2020; 17:408-428. [DOI: 10.2174/1570162x17666191121114522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Background:
An effective vaccine against human immunodeficiency virus 1 (HIV-1) is
an important global health priority. Despite many efforts in the development of the HIV-1 vaccine,
no effective vaccine has been approved yet. Recently, polyepitope vaccines including several immunogenic
and conserved epitopes of HIV-1 proteins have received special attention.
Methods:
In this study, HIV-1 Nef, Tat, Gp160 and P24 proteins were considered for selection of
immunodominant and conserved epitopes due to their critical roles in the viral life cycle and pathogenesis.
At first, the Nef60-84-Nef126-144-Tat29-49-Gp16030-53-Gp160308-323-P248-151 DNA construct was
designed using in silico studies. Then, the DNA construct was subcloned in pEGFP-N1 and pET-
24a (+) expression vectors and the rNef-Tat-Gp160-P24 polyepitope peptide was generated in E.coli
expression system for in vitro delivery using novel cell-penetrating peptides (CPPs), LDP-NLS and
CyLoP-1, in a non-covalent manner. Also, the HR9 and MPG CPPs were used to transfer the DNA
construct.
Results:
Our results showed that the recombinant polyepitope peptide generated in Rosetta strain
migrated as a clear band of ~31 kDa in SDS-PAGE. The SEM data confirmed the formation of stable
nanoparticles with a size below 250 nm. MTT assay revealed that the complexes did not represent
any considerable cytotoxic effect compared to untreated cells. The results of fluorescence microscopy,
flow cytometry and western blotting indicated that these CPPs successfully delivered polyepitope
constructs into HEK-293T cell line.
Conclusion:
These data suggested that these CPPs can be used as a promising approach for the development
of the HIV-1 vaccine.
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Affiliation(s)
- Fatemeh Namazi
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Shiva Irani
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Vistro WA, Huang Y, Bai X, Yang P, Haseeb A, Chen H, Liu Y, Yue Z, Tarique I, Chen Q. In Vivo Multivesicular Body and Exosome Secretion in the Intestinal Epithelial Cells of Turtles During Hibernation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2019; 25:1341-1351. [PMID: 31656212 DOI: 10.1017/s1431927619015071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The present study was designed to investigate the in vivo biological processes of multivesicular bodies (MVBs) and exosomes in mitochondria-rich cells (MRCs), goblet cells (GCs), and absorptive cells (ACs) in turtle intestines during hibernation. The exosome markers, cluster of differentiation 63 (CD63) and tumor susceptibility gene 101 (TSG101), were positively expressed in intestinal villi during turtle hibernation. The distribution and formation processes of MVBs and exosomes in turtle MRCs, GCs, and ACs were further confirmed by transmission electron microscopy. During hibernation, abundantly secreted early endosomes (ees) were localized in the luminal and basal cytoplasm of the MRCs and ACs, and late endosomes (les) were dispersed with the supranuclear parts of the MRCs and ACs. Many "heterogeneous" MVBs were identified throughout the cytoplasm of the MRCs and ACs. Interestingly, the ees, les, and MVBs were detected in the cytoplasm of the GCs during hibernation; however, they were absent during nonhibernation. Furthermore, the exocytosis pathways of exosomes and autophagic vacuoles were observed in the MRCs, GCs, and ACs during hibernation. In addition, the number of different MVBs with intraluminal vesicles (ILVs) and heterogeneous endosome-MVB-exosome complexes was significantly increased in the MRCs, GCs, and ACs during hibernation. All these findings indicate that intestinal epithelial cells potentially perform a role in the secretion of MVBs and exosomes, which are essential for mucosal immunity, during hibernation.
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Affiliation(s)
- Waseem Ali Vistro
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Yufei Huang
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Xuebing Bai
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Ping Yang
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Abdul Haseeb
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Hong Chen
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Yifei Liu
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Zhang Yue
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Imran Tarique
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
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Namazi F, Bolhassani A, Sadat SM, Irani S. In vitro Delivery of HIV-1 Nef Antigen by Histidine-rich nona-arginine and Latarcin 1 peptide. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2019. [DOI: 10.29252/jommid.7.4.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Slonchak A, Clarke B, Mackenzie J, Amarilla AA, Setoh YX, Khromykh AA. West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles. BMC Genomics 2019; 20:474. [PMID: 31182021 PMCID: PMC6558756 DOI: 10.1186/s12864-019-5835-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of pro-inflammatory cytokines has been shown to alter molecular composition of EV content. Transfer of antiviral proteins by EVs is thought to contribute to the development of inflammation and antiviral state. Altered incorporation of selected host RNAs into EVs in response to infection has also been demonstrated for several viruses, but not for WNV. Considering the medical significance of flaviviruses and the importance of deeper knowledge about the mechanisms of flavivirus-host interactions we assessed the ability of West Nile virus (WNV) and type I interferon (IFN), the main cytokine regulating antiviral response to WNV, to alter the composition of EV RNA cargo. RESULTS We employed next generation sequencing to perform transcriptome-wide profiling of RNA cargo in EVs produced by cells infected with WNV or exposed to IFN-alpha. RNA profile of EVs secreted by uninfected cells was also determined and used as a reference. We found that WNV infection significantly changed the levels of certain host microRNAs (miRNAs), small noncoding RNAs (sncRNAs) and mRNAs incorporated into EVs. Treatment with IFN-alpha also altered miRNA and mRNA profiles in EV but had less profound effect on sncRNAs. Functional classification of RNAs differentially incorporated into EVs upon infection and in response to IFN-alpha treatment demonstrated association of enriched in EVs mRNAs and miRNAs with viral processes and pro-inflammatory pathways. Further analysis revealed that WNV infection and IFN-alpha treatment changed the levels of common and unique mRNAs and miRNAs in EVs and that IFN-dependent and IFN-independent processes are involved in regulation of RNA sorting into EVs during infection. CONCLUSIONS WNV infection and IFN-alpha treatment alter the spectrum and the levels of mRNAs, miRNAs and sncRNAs in EVs. Differentially incorporated mRNAs and miRNAs in EVs produced in response to WNV infection and to IFN-alpha treatment are associated with viral processes and host response to infection. WNV infection affects composition of RNA cargo in EVs via IFN-dependent and IFN-independent mechanisms.
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Affiliation(s)
- Andrii Slonchak
- The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia
| | - Brian Clarke
- The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia
- The Pirbright Institute, Ash Rd, Pirbright, Surrey, GU24 GNF, UK
| | - Jason Mackenzie
- The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
| | - Alberto Anastacio Amarilla
- The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia
| | - Yin Xiang Setoh
- The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia
| | - Alexander A Khromykh
- The Australian Infectious Diseases Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, MBS building 76, Cooper Rd, St Lucia, QLD, 4072, Australia.
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Bai X, Guo Y, Shi Y, Lin J, Tarique I, Wang X, Vistro WA, Huang Y, Chen H, Haseeb A, Yang P, Chen Q. In vivo multivesicular bodies and their exosomes in the absorptive cells of the zebrafish (Danio Rerio) gut. FISH & SHELLFISH IMMUNOLOGY 2019; 88:578-586. [PMID: 30885742 DOI: 10.1016/j.fsi.2019.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/21/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
Intercellular communication of gut epithelial cells is critical to gut mucosal homeostasis. Exosomes are important intercellular mediators in communication between cell to cell. Although many literature focus on the immunologic roles in the gut by the exosomes, the biological process of exosomes in the absorptive cells remains unknown. Uncovering the distribution, classification and formation process of multivesicular bodies (MVBs) and their exosomes in the absorptive cells of the zebrafish gut, is urgently needed to establish a platform for immunological research of fish gut exosomes. The expression levels of CD63 and TSG101 were different among the three segments of the gut, and they were enriched at the apex of the mid gut villi. The characteristics of MVBs and their exosomes in the absorptive cells were further revealed by transmission electron microscopy (TEM). Early endosomes (ee) were mainly present in the apical and basal cytoplasm of absorptive cells. Late endosomes (le) were mostly distributed with the supranuclear part of these cells. "Heterogeneous" MVBs were detected underlying the apical membranes of absorptive cells. Many exosomes with some MVB-like structures occurred in the lumen, indicating that the release process was mainly through apical secretion. Various MVBs with exosomes and the endosome-heterogeneous MVB-exosome complex existed widely in the mid gut absorptive cells, concluding that zebrafish as a potential model for in vivo MVBs and their exosomes research. All the results were summarized in a schematic diagram illustrating the morphological characteristics of gut MVBs and their exosomes in zebrafish.
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Affiliation(s)
- Xuebing Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yanna Guo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yonghong Shi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Jinxing Lin
- Shanghai Laboratory Animal Research Center, Shanghai, 201203, China
| | - Imran Tarique
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Xindong Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Waseem Ali Vistro
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yufei Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Hong Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Abdul Haseeb
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ping Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China.
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14
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Chen J, Jin L, Yan M, Yang Z, Wang H, Geng S, Gong Z, Liu G. Serum Exosomes from Newborn Piglets Restrict Porcine Epidemic Diarrhea Virus Infection. J Proteome Res 2019; 18:1939-1947. [PMID: 30983354 DOI: 10.1021/acs.jproteome.9b00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Exosomes are vehicles in the body fluid that participate in many biological processes, especially immune responses. In this study, we employed comparative proteome analysis to investigate the roles of serum exosomes during viral infection in neonates using porcine epidemic diarrhea virus (PEDV), a devastating enteric virus in newborn piglets, as a model virus. Serum exosomes were first isolated from newborn piglets infected with PEDV or mock-infected newborn piglets, followed by label-free LC-MS/MS-based comparative quantitative proteomic analysis. Among the 441 detected proteins, 10 complement proteins were found in the serum exosomes, and significantly decreased expression levels of the C3, C6, and CFB complements were measured in PEDV-infected serum exosomes compared to those in mock-infected serum exosomes. After confirmation by Western blot, we then investigated the function of these exosomes in PEDV infection and discovered that exosomes from mock-infected newborn piglets restricted PEDV infection. However, this inhibition disappeared after the exosomes were heat-inactivated, suggesting that complements are key antiviral molecules. Our findings improve the understanding of antiviral responses mediated by exosomes in neonatal piglets and facilitate the discovery of novel antiviral drugs.
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Affiliation(s)
- Jianing Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
| | - Li Jin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
| | - Miaomiao Yan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
| | - Ze Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China.,The First Affiliated Hospital of Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Haiwen Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
| | - Shuxian Geng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China.,School of Veterinary Medicine , Gansu Agricultural University , Lanzhou , Gansu 730070 , China
| | - Zhenli Gong
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
| | - Guangliang Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Lanzhou , Gansu 730046 , China
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15
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Patters BJ, Kumar S. The role of exosomal transport of viral agents in persistent HIV pathogenesis. Retrovirology 2018; 15:79. [PMID: 30577804 PMCID: PMC6303896 DOI: 10.1186/s12977-018-0462-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection, despite great advances in antiretroviral therapy, remains a lifelong affliction. Though current treatment regimens can effectively suppress viral load to undetectable levels and preserve healthy immune function, they cannot fully alleviate all symptoms caused by the presence of the virus, such as HIV-associated neurocognitive disorders. Exosomes are small vesicles that transport cellular proteins, RNA, and small molecules between cells as a mechanism of intercellular communication. Recent research has shown that HIV proteins and RNA can be packaged into exosomes and transported between cells, to pathogenic effect. This review summarizes the current knowledge on the diverse mechanisms involved in the sorting of viral elements into exosomes and the damage those exosomal agents can inflict. In addition, potential therapeutic options to counteract exosome-mediated HIV pathogenesis are reviewed and considered.
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Affiliation(s)
- Benjamin J Patters
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Santosh Kumar
- Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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