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Rojekar S, Gholap AD, Togre N, Bhoj P, Haeck C, Hatvate N, Singh N, Vitore J, Dhoble S, Kashid S, Patravale V. Current status of mannose receptor-targeted drug delivery for improved anti-HIV therapy. J Control Release 2024; 372:494-521. [PMID: 38849091 DOI: 10.1016/j.jconrel.2024.06.002] [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: 03/12/2024] [Revised: 05/22/2024] [Accepted: 06/01/2024] [Indexed: 06/09/2024]
Abstract
In the pursuit of achieving better therapeutic outcomes in the treatment of HIV, innovative drug delivery strategies have been extensively explored. Mannose receptors, which are primarily found on macrophages and dendritic cells, offer promising targets for drug delivery due to their involvement in HIV pathogenesis. This review article comprehensively evaluates recent drug delivery system advancements targeting the mannose receptor. We have systematically described recent developments in creating and utilizing drug delivery platforms, including nanoparticles, liposomes, micelles, noisomes, dendrimers, and other nanocarrier systems targeted at the mannose receptor. These strategies aim to enhance drug delivery specificity, bioavailability, and therapeutic efficacy while decreasing off-target effects and systemic toxicity. Furthermore, the article delves into how mannose receptors and HIV interact, highlighting the potential for exploiting this interaction to enhance drug delivery to infected cells. The review covers essential topics, such as the rational design of nanocarriers for mannose receptor recognition, the impact of physicochemical properties on drug delivery performance, and how targeted delivery affects the pharmacokinetics and pharmacodynamics of anti-HIV agents. The challenges of these novel strategies, including immunogenicity, stability, and scalability, and future research directions in this rapidly growing area are discussed. The knowledge synthesis presented in this review underscores the potential of mannose receptor-based targeted drug delivery as a promising avenue for advancing HIV treatment. By leveraging the unique properties of mannose receptors, researchers can design drug delivery systems that cater to individual needs, overcome existing limitations, and create more effective and patient-friendly treatments in the ongoing fight against HIV/AIDS.
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Affiliation(s)
- Satish Rojekar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Amol D Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar 401404, Maharashtra, India
| | - Namdev Togre
- Department of Pathology, Lewis Katz School of Medicine at Temple University, Philadelphia, USA
| | - Priyanka Bhoj
- Department of Pathology, Lewis Katz School of Medicine at Temple University, Philadelphia, USA
| | - Clement Haeck
- Population Council, , Center for Biomedical Research, 1230 York Avenue, New York, NY 10065, USA
| | - Navnath Hatvate
- Institute of Chemical Technology, Mumbai, Marathwada Campus, Jalna 431203, India
| | - Nidhi Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Kolkata 700054, India
| | - Jyotsna Vitore
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), Gujarat 382355, India
| | - Sagar Dhoble
- Department of Pharmacology and Toxicology, R. K. Coit College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Snehal Kashid
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), Gujarat 382355, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India.
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2
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Kilroy JM, Leal AA, Henderson AJ. Chronic HIV Transcription, Translation, and Persistent Inflammation. Viruses 2024; 16:751. [PMID: 38793632 PMCID: PMC11125830 DOI: 10.3390/v16050751] [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: 04/16/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
People with HIV exhibit persistent inflammation that correlates with HIV-associated comorbidities including accelerated aging, increased risk of cardiovascular disease, and neuroinflammation. Mechanisms that perpetuate chronic inflammation in people with HIV undergoing antiretroviral treatments are poorly understood. One hypothesis is that the persistent low-level expression of HIV proviruses, including RNAs generated from defective proviral genomes, drives the immune dysfunction that is responsible for chronic HIV pathogenesis. We explore factors during HIV infection that contribute to the generation of a pool of defective proviruses as well as how HIV-1 mRNA and proteins alter immune function in people living with HIV.
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Affiliation(s)
- Jonathan M. Kilroy
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew A. Leal
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew J. Henderson
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
- Department of Medicine and Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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3
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Xudong X, Heng L, Benchao C, Wenjie C, Bao L, Gaofeng L. Integrated RNA expression and alternative polyadenylation analysis identified CPSF1-CCDC137 oncogenic axis in lung adenocarcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2405-2416. [PMID: 38174951 DOI: 10.1002/tox.24105] [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: 09/06/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024]
Abstract
This study aims to analyze the RNA expression and alternative polyadenylation (APA) events and identify APA tuned genes with prognostic significance in lung adenocarcinoma (LUAD). Genome-wide RNA expression profile and APA events were acquired in LUAD cancer and normal samples in GSE197346. Comparative analysis screened common deregulated genes and transcripts. All 11 and 19 transcripts were up and down expressed and polyadenylated in cancer samples, respectively. Clinical analysis found eight genes with prognostic significance, such as coiled-coil domain containing 137 (CCDC137). Role of CCDC137 in LUAD was first reported in this study. The cellular and animal experiments indicated that downregulated CCDC137 suppressed the malignant tumor phenotype and tumor growth in LUAD. Then, to identify APA regulators for elevated CCDC137, we analyzed the expression of 26 APA regulators in GSE197346 and The Cancer Genome Atlas (TCGA), and found 4 differential regulators: CPSF1, CELF2, NUDT21, and ELAVL1. At last, the correlation of eight genes with four differential APA regulators was analyzed, and CPSF1 showed a strong positive correlation with CCDC137. Based on the above results, we propose an oncogenic axis of CPSF1-CCDC137 in LUAD. This study first constructed a polyadenylation tuned RNA expression map in LUAD, and the proposed oncogenic axis of CPSF1-CCDC137 would shed light on the pathogenesis of LUAD.
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Affiliation(s)
- Xiang Xudong
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Heng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Benchao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Wenjie
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lei Bao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Gaofeng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
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4
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Vanegas-Torres CA, Schindler M. HIV-1 Vpr Functions in Primary CD4 + T Cells. Viruses 2024; 16:420. [PMID: 38543785 PMCID: PMC10975730 DOI: 10.3390/v16030420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
HIV-1 encodes four accesory proteins in addition to its structural and regulatory genes. Uniquely amongst them, Vpr is abundantly present within virions, meaning it is poised to exert various biological effects on the host cell upon delivery. In this way, Vpr contributes towards the establishment of a successful infection, as evidenced by the extent to which HIV-1 depends on this factor to achieve full pathogenicity in vivo. Although HIV infects various cell types in the host organism, CD4+ T cells are preferentially targeted since they are highly permissive towards productive infection, concomitantly bringing about the hallmark immune dysfunction that accompanies HIV-1 spread. The last several decades have seen unprecedented progress in unraveling the activities Vpr possesses in the host cell at the molecular scale, increasingly underscoring the importance of this viral component. Nevertheless, it remains controversial whether some of these advances bear in vivo relevance, since commonly employed cellular models significantly differ from primary T lymphocytes. One prominent example is the "established" ability of Vpr to induce G2 cell cycle arrest, with enigmatic physiological relevance in infected primary T lymphocytes. The objective of this review is to present these discoveries in their biological context to illustrate the mechanisms whereby Vpr supports HIV-1 infection in CD4+ T cells, whilst identifying findings that require validation in physiologically relevant models.
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Affiliation(s)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany;
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5
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Kufera JT, Armstrong C, Wu F, Singhal A, Zhang H, Lai J, Wilkins HN, Simonetti FR, Siliciano JD, Siliciano RF. CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation. J Exp Med 2024; 221:e20231511. [PMID: 38270554 PMCID: PMC10818065 DOI: 10.1084/jem.20231511] [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: 08/24/2023] [Revised: 11/04/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy as a barrier to cure. The antigen-driven proliferation of infected cells is a major mechanism of reservoir persistence. However, activation through the T cell antigen receptor (TCR) can induce latent proviruses, leading to viral cytopathic effects and immune clearance. In single-cell studies, we show that, relative to uninfected cells or cells with a defective provirus, CD4+ T cells with an intact provirus have a profound proliferative defect in response to TCR stimulation. Virion production was observed in only 16.5% of cultures with an intact provirus, but proliferation was reduced even when no virion production was detected. Proliferation was inversely correlated with in vivo clone size. These results may reflect the effects of previous in vivo proliferation and do not support attempts to reduce the reservoir with antiproliferative agents, which may have greater effects on normal T cell responses.
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Affiliation(s)
- Joshua T. Kufera
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciara Armstrong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anushka Singhal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah N. Wilkins
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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6
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Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.21.533528. [PMID: 36993393 PMCID: PMC10055223 DOI: 10.1101/2023.03.21.533528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
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Sandoval C, Nisson K, Fregoso OI. HIV-1 Vpr-induced DNA damage activates NF-κB through ATM-NEMO independent of cell cycle arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.541990. [PMID: 37292767 PMCID: PMC10245860 DOI: 10.1101/2023.05.23.541990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lentiviral accessory genes enhance replication through diverse mechanisms. HIV-1 accessory protein Vpr modulates the host DNA damage response (DDR) at multiple steps through DNA damage, cell cycle arrest, the degradation of host proteins, and both the activation and repression of DDR signaling. Vpr also alters host and viral transcription; however, the connection between Vpr-mediated DDR modulation and transcriptional activation remains unclear. Here, we determined the cellular consequences of Vpr-induced DNA damage using Vpr mutants that allow us to separate the ability of Vpr to induce DNA damage from cell cycle arrest and other DDR phenotypes including host protein degradation and repression of DDR. RNA-sequencing of cells expressing Vpr or Vpr mutants identified that Vpr alters cellular transcription through mechanisms both dependent and independent of cell cycle arrest. In tissue-cultured U2OS cells and primary human monocyte-derived macrophages (MDMs), Vpr-induced DNA damage activates the ATM-NEMO pathway and alters cellular transcription via NF-κB/RelA signaling. HIV-1 infection of primary MDMs validated Vpr-dependent NF-κB transcriptional activation during infection. Both virion delivered and de novo expressed Vpr induced DNA damage and activated ATM-NEMO dependent NF-κB transcription, suggesting that engagement of the DDR and transcriptional reprogramming can occur during early and late stages of viral replication. Together, our data identifies a mechanism by which Vpr activates NF-κB through DNA damage and the ATM-NEMO pathway, which occur independent of cell cycle arrest. We propose this is essential to overcoming restrictive environments, such as in macrophages, to enhance viral transcription and replication.
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Affiliation(s)
- Carina Sandoval
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Karly Nisson
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Oliver I. Fregoso
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
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8
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Jackson-Jones KA, McKnight Á, Sloan RD. The innate immune factor RPRD2/REAF and its role in the Lv2 restriction of HIV. mBio 2023; 14:e0257221. [PMID: 37882563 PMCID: PMC10746242 DOI: 10.1128/mbio.02572-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
Intracellular innate immunity involves co-evolved antiviral restriction factors that specifically inhibit infecting viruses. Studying these restrictions has increased our understanding of viral replication, host-pathogen interactions, and pathogenesis, and represent potential targets for novel antiviral therapies. Lentiviral restriction 2 (Lv2) was identified as an unmapped early-phase restriction of HIV-2 and later shown to also restrict HIV-1 and simian immunodeficiency virus. The viral determinants of Lv2 susceptibility have been mapped to the envelope and capsid proteins in both HIV-1 and HIV-2, and also viral protein R (Vpr) in HIV-1, and appears dependent on cellular entry mechanism. A genome-wide screen identified several likely contributing host factors including members of the polymerase-associated factor 1 (PAF1) and human silencing hub (HUSH) complexes, and the newly characterized regulation of nuclear pre-mRNA domain containing 2 (RPRD2). Subsequently, RPRD2 (or RNA-associated early-stage antiviral factor) has been shown to be upregulated upon T cell activation, is highly expressed in myeloid cells, binds viral reverse transcripts, and potently restricts HIV-1 infection. RPRD2 is also bound by HIV-1 Vpr and targeted for degradation by the proteasome upon reverse transcription, suggesting RPRD2 impedes reverse transcription and Vpr targeting overcomes this block. RPRD2 is mainly localized to the nucleus and binds RNA, DNA, and DNA:RNA hybrids. More recently, RPRD2 has been shown to negatively regulate genome-wide transcription and interact with the HUSH and PAF1 complexes which repress HIV transcription and are implicated in maintenance of HIV latency. In this review, we examine Lv2 restriction and the antiviral role of RPRD2 and consider potential mechanism(s) of action.
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Affiliation(s)
- Kathryn A. Jackson-Jones
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- Division of Infectious Diseases & Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Áine McKnight
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Richard D. Sloan
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
- ZJU-UoE Institute, Zhejiang University, Haining, China
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9
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Williams ME, Williams AA, Naudé PJW. Viral protein R (Vpr)-induced neuroinflammation and its potential contribution to neuronal dysfunction: a scoping review. BMC Infect Dis 2023; 23:512. [PMID: 37545000 PMCID: PMC10405499 DOI: 10.1186/s12879-023-08495-3] [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: 03/01/2023] [Accepted: 07/30/2023] [Indexed: 08/08/2023] Open
Abstract
HIV-associated neurocognitive disorders (HAND) are the result of the activity of HIV-1 within the central nervous system (CNS). While the introduction of antiretroviral therapy (ART) has significantly reduced the occurrence of severe cases of HAND, milder cases still persist. The persistence of HAND in the modern ART era has been linked to a chronic dysregulated inflammatory profile. There is increasing evidence suggesting a potential role of Viral protein R (Vpr) in dysregulating the neuroinflammatory processes in people living with HIV (PLHIV), which may contribute to the development of HAND. Since the role of Vpr in neuroinflammatory mechanisms has not been clearly defined, we conducted a scoping review of fundamental research studies on this topic. The review aimed to assess the size and scope of available research literature on this topic and provide commentary on whether Vpr contributes to neuroinflammation, as highlighted in fundamental studies. Based on the specified selection criteria, 10 studies (6 of which were cell culture-based and 4 that included both animal and cell culture experiments) were eligible for inclusion. The main findings were that (1) Vpr can increase neuroinflammatory markers, with studies consistently reporting higher levels of TNF-α and IL-8, (2) Vpr induces (neuro)inflammation via specific pathways, including the PI3K/AKT, p38-MAPk, JNK-SAPK and Sur1-Trpm4 channels in astrocytes and the p38 and JNK-SAPK in myeloid cells, and (3) Vpr-specific protein amino acid signatures (73R, 77R and 80A) may play an important role in exacerbating neuroinflammation and the neuropathophysiology of HAND. Therefore, Vpr should be investigated for its potential contribution to neuroinflammation in the development of HAND.
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Affiliation(s)
| | | | - Petrus J W Naudé
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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10
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Tao S, Xie SJ, Diao LT, Lv G, Hou YR, Hu YX, Xu WY, Du B, Xiao ZD. RNA-binding protein CCDC137 activates AKT signaling and promotes hepatocellular carcinoma through a novel non-canonical role of DGCR8 in mRNA localization. J Exp Clin Cancer Res 2023; 42:194. [PMID: 37542342 PMCID: PMC10403887 DOI: 10.1186/s13046-023-02749-3] [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: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND RNA binding proteins (RBPs)-regulated gene expression play a vital role in various pathological processes, including the progression of cancer. However, the role of RBP in hepatocellular carcinoma (HCC) remains much unknown. In this study, we aimed to explore the contribution of RBP CCDC137 in HCC development. METHODS We analyzed the altered expression level and clinical significance of CCDC137 in database and HCC specimens. In vitro cell assays and in vivo spontaneous mouse models were used to assess the function of CCDC137. Finally, the molecular mechanisms of how CCDC137 regulates gene expression and promotes HCC was explored. RESULTS CCDC137 is aberrantly upregulated in HCC and correlates with poor clinical outcomes in HCC patients. CCDC137 markedly promoted HCC proliferation and progression in vitro and in vivo. Mechanistically, CCDC137 binds with FOXM1, JTV1, LASP1 and FLOT2 mRNAs, which was revealed by APOBEC1-mediated profiling, to increase their cytoplasmic localization and thus enhance their protein expressions. Upregulation of FOXM1, JTV1, LASP1 and FLOT2 subsequently synergistically activate AKT signaling and promote HCC. Interestingly, we found that CCDC137 binds with the microprocessor protein DGCR8 and DGCR8 has a novel non-canonical function in mRNA subcellular localization, which mediates the cytoplasmic distribution of mRNAs regulated by CCDC137. CONCLUSIONS Our results identify a critical proliferation-related role of CCDC137 and reveal a novel CCDC137/DGCR8/mRNA localization/AKT axis in HCC progression, which provide a potential target for HCC therapy.
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Affiliation(s)
- Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
- Present address: Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, P.R. China
| | - Shu-Juan Xie
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Guo Lv
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Bin Du
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, P.R. China.
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China.
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11
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McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature 2023; 620:1025-1030. [PMID: 37532928 PMCID: PMC10848312 DOI: 10.1038/s41586-023-06370-4] [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: 11/28/2018] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.
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Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - István Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Riley H Tough
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cher S Kiar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohana Prasad Sathya Moorthy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey F Tuff
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miriam Walter
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center and Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex H Kral
- Community Health Research Division, RTI International, Berkeley, CA, USA
| | - Olivier Lambotte
- Université Paris Saclay, Inserm UMR1184, CEA, Le Kremlin-Bicêtre, France
- APHP, Department of Clinical Immunology, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Therapeutics Laboratory, Medical and Scientific Affairs, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Javier Martinez-Picado
- University of Vic-Central University of Catalonia, Vic, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laurence Meyer
- INSERM U1018, Université Paris-Saclay, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'Épidémiologie, Le Kremlin Bicêtre, France
| | - José M Miro
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pravi Moodley
- National Health Laboratory Service, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kireem Nam
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ioannis Theodorou
- Laboratoire d'Immunologie, Hôpital Robert Debré Paris, Paris, France
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research and Cancer Innovative Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Judd F Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Deepti Gurdasani
- Queen Mary University of London, London, UK
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Harriet Groom
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Omnigen Biodata, Cambridge, UK.
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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12
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Borrmann H, Ulkar G, Kliszczak AE, Ismed D, Schilling M, Magri A, Harris JM, Balfe P, Vasudevan S, Borrow P, Zhuang X, McKeating JA. Molecular components of the circadian clock regulate HIV-1 replication. iScience 2023; 26:107007. [PMID: 37534138 PMCID: PMC10391662 DOI: 10.1016/j.isci.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 08/04/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading pathogens. Peripheral viral loads of HIV-1 infected patients show diurnal variation; however, the underlying mechanisms remain unknown. Here, we demonstrate a role for the cell-intrinsic clock to regulate rhythmic HIV-1 replication in circadian-synchronized systems. Silencing the circadian activator Bmal1 abolishes this phenotype, and we observe BMAL1 binding to the HIV-1 promoter. Importantly, we show differential binding of the nuclear receptors REV-ERB and ROR to the HIV-long terminal repeat at different circadian times, demonstrating a dynamic interplay in time-of-day regulation of HIV-1 transcription. Bioinformatic analysis shows circadian regulation of host factors that control HIV-1 replication, providing an additional mechanism for rhythmic viral replication. This study increases our understanding of the circadian regulation of HIV-1, which can ultimately inform new therapies.
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Affiliation(s)
- Helene Borrmann
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Görkem Ulkar
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anna E. Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dini Ismed
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mirjam Schilling
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jane A. McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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13
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Fu B, Zhou M, Song G, Zeng H, Gong Y, Jiang Y, Ke Y, Huang D, Peng H, Li Q. Comprehensive analysis reveals TSEN54 as a robust prognosis biomarker and promising immune-related therapeutic target for hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2734-2771. [PMID: 37059591 PMCID: PMC10120902 DOI: 10.18632/aging.204645] [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: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 04/16/2023]
Abstract
BACKGROUND Hepatocellular carcinoma represents the most common primary malignancy of all liver cancer types and its prognosis is usually unsatisfactory. TSEN54 encodes a protein constituting a subunit of the tRNA splicing endonuclease heterotetramer. Previous researches concentrated on the contribution of TSEN54 in pontocerebellar hypoplasia, but no studies have yet reported its role in HCC. METHODS TIMER, HCCDB, GEPIA, HPA, UALCAN, MEXPRESS, SMART, TargetScan, RNAinter, miRNet, starBase, Kaplan-Meier Plotter, cBioPortal, LinkedOmics, GSEA, TISCH, TISIDB, GeneMANIA, PDB, GSCALite were applied in this research. RESULTS We identified the upregulation of TSEN54 expression in HCC and related it to multiple clinicopathological features. Hypomethylation of TSEN54 was closely associated with its high expression. HCC sufferers who held high TSEN54 expression typically had shorter survival expectations. Enrichment analysis showed the involvement of TSEN54 in the cell cycle and metabolic processes. Afterward, we observed that TSEN54 expression level had a positive relationship to the infiltration level of multiple immune cells and the expression of several chemokines. We additionally identified that TSEN54 was related to the expression level of several immune checkpoints and TSEN54 was linked to several m6A-related regulators. CONCLUSIONS TSEN54 is a prognostic marker of HCC. TSEN54 could become a prospective candidate for HCC diagnosis and therapy.
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Affiliation(s)
- Bidong Fu
- Department of Pathology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Gelin Song
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Yun Ke
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
| | - Hong Peng
- Department of Colorectal Surgery, 908th Hospital of Chinese People’s Liberation Army Joint, Nanchang, Jiangxi Province, People’s Republic of China
| | - Qing Li
- Department of Pathology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, People’s Republic of China
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14
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Ode H, Saito A, Washizaki A, Seki Y, Yoshida T, Harada S, Ishii H, Shioda T, Yasutomi Y, Matano T, Miura T, Akari H, Iwatani Y. Development of a novel Macaque-Tropic HIV-1 adapted to cynomolgus macaques. J Gen Virol 2022; 103. [PMID: 36205476 DOI: 10.1099/jgv.0.001790] [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] [Indexed: 11/18/2022] Open
Abstract
Macaque-tropic HIV-1 (HIV-1mt) variants have been developed to establish preferable primate models that are advantageous in understanding HIV-1 infection pathogenesis and in assessing the preclinical efficacy of novel prevention/treatment strategies. We previously reported that a CXCR4-tropic HIV-1mt, MN4Rh-3, efficiently replicates in peripheral blood mononuclear cells (PBMCs) of cynomolgus macaques homozygous for TRIMCyp (CMsTC). However, the CMsTC challenged with MN4Rh-3 displayed low viral loads during the acute infection phase and subsequently exhibited short-term viremia. These virological phenotypes in vivo differed from those observed in most HIV-1-infected people. Therefore, further development of the HIV-1mt variant was needed. In this study, we first reconstructed the MN4Rh-3 clone to produce a CCR5-tropic HIV-1mt, AS38. In addition, serial in vivo passages allowed us to produce a highly adapted AS38-derived virus that exhibits high viral loads (up to approximately 106 copies ml-1) during the acute infection phase and prolonged periods of persistent viremia (lasting approximately 16 weeks postinfection) upon infection of CMsTC. Whole-genome sequencing of the viral genomes demonstrated that the emergence of a unique 15-nt deletion within the vif gene was associated with in vivo adaptation. The deletion resulted in a significant increase in Vpr protein expression but did not affect Vif-mediated antagonism of antiretroviral APOBEC3s, suggesting that Vpr is important for HIV-1mt adaptation to CMsTC. In summary, we developed a novel CCR5-tropic HIV-1mt that can induce high peak viral loads and long-term viremia and exhibits increased Vpr expression in CMsTC.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Akatsuki Saito
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Ayaka Washizaki
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Yohei Seki
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Takeshi Yoshida
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- Present address: Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan (A. S.), National Institute of Biomedical Innovation, Osaka, Japan (A. W.); National Institute of Infectious Diseases (Y.S. and T.Y.), Tokyo, Japan
| | - Shigeyoshi Harada
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hiroshi Ishii
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuhiro Yasutomi
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Tomoyuki Miura
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hirofumi Akari
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Ibaraki, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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15
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The KT Jeang Retrovirology prize 2022: Florence Margottin-Goguet. Retrovirology 2022; 19:20. [PMID: 36068604 PMCID: PMC9446835 DOI: 10.1186/s12977-022-00606-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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16
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Love M, Samora L, Barker D, Zukosky P, Kummet N, Ahmad A, Bernhardt D, Tripathi M, Klotz S, Ahmad N. Genetic Analysis of HIV-1 vpr Sequences from HIV-Infected Older Patients on Long-Term Antiretroviral Therapy. Curr HIV Res 2022; 20:309-320. [PMID: 35792120 DOI: 10.2174/1570162x20666220705124341] [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: 02/25/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Many HIV-infected individuals have achieved undetectable viral load and increased CD4 T cell counts due to the success of Antiretroviral Therapy (ART). However, HIV persists in resting T cells, monocytes/macrophages and other quiescent cells. Furthermore, the HIV- 1 vpr accessory gene may play an important role in the persistence of HIV in these infected patients. OBJECTIVES Therefore, we characterized the HIV-1 vpr gene from PBMC DNA of 14 HIV-infected older patients on long-term ART with mostly undetectable viral load and increased CD4 T cell counts. METHODS Peripheral Blood Mononuclear Cells (PBMC) were isolated from 14 HIV-infected individuals, followed by extraction of genomic DNA, amplification of HIV-1 vpr gene by polymerase chain reaction (PCR), cloning of vpr gene in TOPO vector and characterization of correct size recombinant inserts containing vpr genes. An average of 13 clones were sequenced from each patient, followed by sequence analysis by bioinformatic tools. RESULTS Phylogenetic analysis of 182 vpr sequences demonstrated that the vpr sequences of each patient were well separated and discriminated from other patients' sequences and formed distinct clusters. The vpr sequences showed a low degree of viral heterogeneity, lower estimates of genetic diversity and about half of the patients' sequences were under positive selection pressure. While the majority of the vpr deduced amino acid sequences from most patients contained intact open reading frames, several sequences, mostly from two patients, had stop codons. Numerous patient-specific and common amino acid motifs were found in deduced vpr sequences. The functional domains required for vpr activity, including virion incorporation, nuclear import of pre-integration complex and cell cycle arrest, were generally conserved in most vpr sequences. Several of the known Cytotoxic T-lymphocytes (CTL) epitopes in vpr showed variation in our patients' sequences. CONCLUSION In summary, a low degree of genetic variability, conservation of functional domains and variations in CTL epitopes were the features of vpr sequences from the 14 HIV-infected older patients with controlled viremia on long-term ART.
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Affiliation(s)
- Maria Love
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Luiza Samora
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Danae Barker
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Priya Zukosky
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Nathan Kummet
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Aasim Ahmad
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Dana Bernhardt
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Meghna Tripathi
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Stephen Klotz
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
| | - Nafees Ahmad
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85721, Arizona, USA
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17
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Sato H, Murakami T, Matsuura R, Abe M, Matsuoka S, Yashiroda Y, Yoshida M, Akari H, Nagasawa Y, Takei M, Aida Y. A Novel Class of HIV-1 Inhibitors Targeting the Vpr-Induced G2-Arrest in Macrophages by New Yeast- and Cell-Based High-Throughput Screening. Viruses 2022; 14:v14061321. [PMID: 35746791 PMCID: PMC9227106 DOI: 10.3390/v14061321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) accessory protein, Vpr, arrests the cell cycle of the G2 phase, and this Vpr-mediated G2 arrest is implicated in an efficient HIV-1 spread in monocyte-derived macrophages. Here, we screened new candidates for Vpr-targeting HIV-1 inhibitors by using fission yeast- and mammalian cell-based high-throughput screening. First, fission yeast strains expressing the HIV-1 Vpr protein were generated and then treated for 48 h with 20 μM of a synthetic library, including 140,000 chemical compounds. We identified 268 compounds that recovered the growth of Vpr-overexpressing yeast. The selected compounds were then tested in mammalian cells, and those displaying high cytotoxicity were excluded from further cell cycle analysis and imaging-based screening. A flow cytometry analysis confirmed that seven compounds recovered from the Vpr-induced G2 arrest. The cell toxicity and inhibitory effect of HIV-1 replication in human monocyte-derived macrophages (MDM) were examined, and three independent structural compounds, VTD227, VTD232, and VTD263, were able to inhibit HIV-1 replication in MDM. Furthermore, we showed that VTD227, but not VTD232 and VTD263, can directly bind to Vpr. Our results indicate that three new compounds and their derivatives represent new drugs targeting HIV-1 replication and can be potentially used in clinics to improve the current antiretroviral therapy.
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Affiliation(s)
- Hirotaka Sato
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Department of Microbiology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Shimotsuga, Tochigi 321-0293, Japan
| | - Tomoyuki Murakami
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Ryosuke Matsuura
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masako Abe
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
| | - Seiji Matsuoka
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
| | - Yoko Yashiroda
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (M.A.); (S.M.); (M.Y.)
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
| | - Hirofumi Akari
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan;
| | - Yosuke Nagasawa
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (H.S.); (T.M.); (R.M.)
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamichou, Itabashi-ku, Tokyo 173-8610, Japan; (Y.N.); (M.T.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence:
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18
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Galvão-Lima LJ, Zambuzi FA, Soares LS, Fontanari C, Meireles AFG, Brauer VS, Faccioli LH, Gama L, Figueiredo LTM, Bou-Habib DC, Frantz FG. HIV-1 Gag and Vpr impair the inflammasome activation and contribute to the establishment of chronic infection in human primary macrophages. Mol Immunol 2022; 148:68-80. [PMID: 35659727 DOI: 10.1016/j.molimm.2022.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 02/07/2023]
Abstract
The successful establishment of HIV-1 infection is related to inflammasome blocking or inactivation, which can result in the viral evasion of the immune responses and formation of reservoirs in several tissues. In this sense, we aimed to evaluate the viral and cellular mechanisms activated during HIV-1 infection in human primary macrophages that allow an effective viral replication in these cells. We found that resting HIV-1-infected macrophages, but not those activated in classical or alternative patterns, released IL-1β and other pro-inflammatory cytokines, and showed increased CXCL10 expression, without changes in the NLRP3, AIM2 or RIG-I inflammasome pathways. Also, similar levels of Casp-1, phosphorylated NF-κB (p65) and NLRP3 proteins were found in uninfected and HIV-1-infected macrophages. Likewise, no alterations were detected in ASC specks released in the culture supernatant after HIV-1 infection, suggesting that macrophages remain viable after infection. Using in silico prediction studies, we found that the HIV-1 proteins Gag and Vpr interact with several host proteins. Comparable levels of trans-LTB4 were found in the supernatants of uninfected and HIV-1-infected macrophages, whereas ROS production was impaired in infected cells, which was not reversed after the PMA stimulus. Immunofluorescence analysis showed structural alterations in the mitochondrial architecture and an increase of BIM in the cytoplasm of infected cells. Our data suggest that HIV-1 proteins Gag and Vpr, through interacting with cellular proteins in the early steps of infection, preclude the inflammasome activation and the development of effective immune responses, thus allowing the establishment of the infection.
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Affiliation(s)
- Leonardo J Galvão-Lima
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil; Laboratory of Technological Innovation in Health (LAIS), Hospital Universitário Onofre Lopes, Federal University of Rio Grande do Norte (UFRN), Natal, Brazil
| | - Fabiana A Zambuzi
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Luana S Soares
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Caroline Fontanari
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Aline F Galvão Meireles
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Verônica S Brauer
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Lúcia H Faccioli
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Lúcio Gama
- Retrovirus Lab, Johns Hopkins University - School of Medicine, Baltimore, MD, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Luiz T M Figueiredo
- Virology Research Center, Medical School of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Dumith Chequer Bou-Habib
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Fabiani G Frantz
- School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Brazil.
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Atindaana E, Kissi-Twum A, Emery S, Burnett C, Pitcher J, Visser M, Kidd JM, Telesnitsky A. Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells. mBio 2022; 13:e0374821. [PMID: 35384697 PMCID: PMC9040753 DOI: 10.1128/mbio.03748-21] [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: 12/15/2021] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Integration site landscapes, clonal dynamics, and latency reversal with or without vpr were compared in HIV-1-infected Jurkat cell populations, and the properties of individual clones were defined. Clones differed in fractions of long terminal repeat (LTR)-active daughter cells, with some clones containing few to no LTR-active cells, while almost all cells were LTR active for others. Clones varied over 4 orders of magnitude in virus release per active cell. Proviruses in largely LTR-active clones were closer to preexisting enhancers and promoters than low-LTR-active clones. Unsurprisingly, major vpr+ clones contained fewer LTR-active cells than vpr- clones, and predominant vpr+ proviruses were farther from enhancers and promoters than those in vpr- pools. Distances to these marks among intact proviruses previously reported for antiretroviral therapy (ART)-suppressed patients revealed that patient integration sites were more similar to those in the vpr+ pool than to vpr- integrants. Complementing vpr-defective proviruses with vpr led to the rapid loss of highly LTR-active clones, indicating that the effect of Vpr on proviral populations occurred after integration. However, major clones in the complemented pool and its vpr- parent population did not differ in burst sizes. When the latency reactivation agents prostratin and JQ1 were applied separately or in combination, vpr+ and vpr- population-wide trends were similar, with dual-treatment enhancement being due in part to reactivated clones that did not respond to either drug applied separately. However, the expression signatures of individual clones differed between populations. These observations highlight how Vpr, exerting selective pressure on proviral epigenetic variation, can shape integration site landscapes, proviral expression patterns, and reactivation properties. IMPORTANCE A bedrock assumption in HIV-1 population modeling is that all active cells release the same amount of virus. However, the findings here revealed that when HIV-infected cells expand into clones, each clone differs in virus production. Reasoning that this variation in expression patterns constituted a population of clones from which differing subsets would prevail under differing environmental conditions, the cytotoxic HIV-1 protein Vpr was introduced, and population dynamics and expression properties were compared in the presence and absence of Vpr. The results showed that whereas most clones produced fairly continuous levels of virus in the absence of Vpr, its presence selected for a distinct subset of clones with properties reminiscent of persistent populations in patients, suggesting the possibility that the interclonal variation in expression patterns observed in culture may contribute to proviral persistence in vivo.
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Affiliation(s)
- Edmond Atindaana
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Abena Kissi-Twum
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Greater Accra Region, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Greater Accra Region, Ghana
| | - Sarah Emery
- Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jake Pitcher
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Myra Visser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jeffrey M. Kidd
- Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Martins LJ, Szaniawski MA, Williams ESCP, Coiras M, Hanley TM, Planelles V. HIV-1 Accessory Proteins Impart a Modest Interferon Response and Upregulate Cell Cycle-Related Genes in Macrophages. Pathogens 2022; 11:pathogens11020163. [PMID: 35215107 PMCID: PMC8878269 DOI: 10.3390/pathogens11020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 01/23/2022] [Indexed: 12/10/2022] Open
Abstract
HIV-1 infection of myeloid cells is associated with the induction of an IFN response. How HIV-1 manipulates and subverts the IFN response is of key interest for the design of therapeutics to improve immune function and mitigate immune dysregulation in people living with HIV. HIV-1 accessory genes function to improve viral fitness by altering host pathways in ways that enable transmission to occur without interference from the immune response. We previously described changes in transcriptomes from HIV-1 infected and from IFN-stimulated macrophages and noted that transcription of IFN-regulated genes and genes related to cell cycle processes were upregulated during HIV-1 infection. In the present study, we sought to define the roles of individual viral accessory genes in upregulation of IFN-regulated and cell cycle-related genes using RNA sequencing. We observed that Vif induces a set of genes involved in mitotic processes and that these genes are potently downregulated upon stimulation with type-I and -II IFNs. Vpr also upregulated cell cycle-related genes and was largely responsible for inducing an attenuated IFN response. We note that the induced IFN response most closely resembled a type-III IFN response. Vpu and Nef-regulated smaller sets of genes whose transcriptomic signatures upon infection related to cytokine and chemokine processes. This work provides more insight regarding processes that are manipulated by HIV-1 accessory proteins at the transcriptional level.
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Affiliation(s)
- Laura J. Martins
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
| | - Matthew A. Szaniawski
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA;
| | - Elizabeth S. C. P. Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology (CNM) Instituto de Salud Carlos III (ISDIII), 28222 Madrid, Spain;
| | - Timothy M. Hanley
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
- Division of Hematopathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Correspondence: (T.M.H.); (V.P.)
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
- Correspondence: (T.M.H.); (V.P.)
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21
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Huang P, Zhang B, Zhao J, Li MD. Integrating the Epigenome and Transcriptome of Hepatocellular Carcinoma to Identify Systematic Enhancer Aberrations and Establish an Aberrant Enhancer-Related Prognostic Signature. Front Cell Dev Biol 2022; 10:827657. [PMID: 35300417 PMCID: PMC8921559 DOI: 10.3389/fcell.2022.827657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Recently, emerging evidence has indicated that aberrant enhancers, especially super-enhancers, play pivotal roles in the transcriptional reprogramming of multiple cancers, including hepatocellular carcinoma (HCC). In this study, we performed integrative analyses of ChIP-seq, RNA-seq, and whole-genome bisulfite sequencing (WGBS) data to identify intergenic differentially expressed enhancers (DEEs) and genic differentially methylated enhancers (DMEs), along with their associated differentially expressed genes (DEE/DME-DEGs), both of which were also identified in independent cohorts and further confirmed by HiC data. Functional enrichment and prognostic model construction were conducted to explore the functions and clinical significance of the identified enhancer aberrations. We identified a total of 2,051 aberrant enhancer-associated DEGs (AE-DEGs), which were highly concurrent in multiple HCC datasets. The enrichment results indicated the significant overrepresentations of crucial biological processes and pathways implicated in cancer among these AE-DEGs. A six AE-DEG-based prognostic signature, whose ability to predict the overall survival of HCC was superior to that of both clinical phenotypes and previously published similar prognostic signatures, was established and validated in TCGA-LIHC and ICGC-LIRI cohorts, respectively. In summary, our integrative analysis depicted a landscape of aberrant enhancers and associated transcriptional dysregulation in HCC and established an aberrant enhancer-derived prognostic signature with excellent predictive accuracy, which might be beneficial for the future development of epigenetic therapy for HCC.
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Affiliation(s)
- Peng Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junsheng Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
- *Correspondence: Ming D. Li,
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22
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Thippeshappa R, Polacino P, Chandrasekar SS, Truong K, Misra A, Aulicino PC, Hu SL, Kaushal D, Kimata JT. In vivo Serial Passaging of Human-Simian Immunodeficiency Virus Clones Identifies Characteristics for Persistent Viral Replication. Front Microbiol 2021; 12:779460. [PMID: 34867922 PMCID: PMC8636705 DOI: 10.3389/fmicb.2021.779460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
We previously reported that a human immunodeficiency virus type 1 with a simian immunodeficiency virus vif substitution (HSIV-vifNL4-3) could replicate in pigtailed macaques (PTMs), demonstrating that Vif is a species-specific tropism factor of primate lentiviruses. However, infections did not result in high-peak viremia or setpoint plasma viral loads, as observed during simian immunodeficiency virus (SIV) infection of PTMs. Here, we characterized variants isolated from one of the original infected animals with CD4 depletion after nearly 4years of infection to identify determinants of increased replication fitness. In our studies, we found that the HSIV-vif clones did not express the HIV-1 Vpr protein due to interference from the vpx open reading frame (ORF) in singly spliced vpr mRNA. To examine whether these viral genes contribute to persistent viral replication, we generated infectious HSIV-vif clones expressing either the HIV-1 Vpr or SIV Vpx protein. And then to determine viral fitness determinants of HSIV-vif, we conducted three rounds of serial in vivo passaging in PTMs, starting with an initial inoculum containing a mixture of CXCR4-tropic [Vpr-HSIV-vifNL4-3 isolated at 196 (C/196) and 200 (C/200) weeks post-infection from a PTM with depressed CD4 counts] and CCR5-tropic HSIV (Vpr+ HSIV-vif derivatives based NL-AD8 and Bru-Yu2 and a Vpx expressing HSIV-vifYu2). Interestingly, all infected PTMs showed peak plasma viremia close to or above 105 copies/ml and persistent viral replication for more than 20weeks. Infectious molecular clones (IMCs) recovered from the passage 3 PTM (HSIV-P3 IMCs) included mutations required for HIV-1 Vpr expression and those mutations encoded by the CXCR4-tropic HSIV-vifNL4-3 isolate C/196. The data indicate that the viruses selected during long-term infection acquired HIV-1 Vpr expression, suggesting the importance of Vpr for in vivo pathogenesis. Further passaging of HSIV-P3 IMCs in vivo may generate pathogenic variants with higher replication capacity, which will be a valuable resource as challenge virus in vaccine and cure studies.
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Affiliation(s)
- Rajesh Thippeshappa
- Disease Intervention and Prevention Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Patricia Polacino
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States
| | - Shaswath S Chandrasekar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Khanghy Truong
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Anisha Misra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Shiu-Lok Hu
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States.,Department of Pharmaceutics, University of Washington, Seattle, WA, United States
| | - Deepak Kaushal
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Jason T Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
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23
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Murakami T, Matsuura R, Chutiwitoonchai N, Takei M, Aida Y. Huntingtin-Interacting Protein 1 Promotes Vpr-Induced G2 Arrest and HIV-1 Infection in Macrophages. Viruses 2021; 13:v13112308. [PMID: 34835114 PMCID: PMC8624357 DOI: 10.3390/v13112308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) modulates the host cell cycle. The HIV-1 accessory protein Vpr arrests the cell cycle at the G2 phase in dividing cells, and the ability of Vpr to induce G2 arrest is well conserved among primate lentiviruses. Additionally, Vpr-mediated G2 arrest likely correlates with enhanced HIV-1 infection in monocyte-derived macrophages. Here, we screened small-interfering RNA to reveal candidates that suppress Vpr-induced G2 arrest and identified Huntingtin-interacting protein 1 (HIP1) required for efficient G2 arrest. Interestingly, HIP1 was not essential for Vpr-induced DNA double-strand breaks, which are required for activation of the DNA-damage checkpoint and G2 arrest. Furthermore, HIP1 knockdown suppressed HIV-1 infection in monocyte-derived macrophages. This study identifies HIP1 as a factor promoting Vpr-induced G2 arrest and HIV-1 infection in macrophages.
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Affiliation(s)
- Tomoyuki Murakami
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (T.M.); (R.M.); (N.C.)
| | - Ryosuke Matsuura
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (T.M.); (R.M.); (N.C.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nopporn Chutiwitoonchai
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (T.M.); (R.M.); (N.C.)
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi, Tokyo 173-8610, Japan;
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (T.M.); (R.M.); (N.C.)
- Laboratory of Global Infectious Diseases Control Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence:
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24
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Martin MM, Matkovic R, Larrous P, Morel M, Lasserre A, Vauthier V, Margottin-Goguet F. Binding to DCAF1 distinguishes TASOR and SAMHD1 degradation by HIV-2 Vpx. PLoS Pathog 2021; 17:e1009609. [PMID: 34699574 PMCID: PMC8570500 DOI: 10.1371/journal.ppat.1009609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/05/2021] [Accepted: 10/15/2021] [Indexed: 01/18/2023] Open
Abstract
Human Immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) succeed to evade host immune defenses by using their viral auxiliary proteins to antagonize host restriction factors. HIV-2/SIVsmm Vpx is known for degrading SAMHD1, a factor impeding the reverse transcription. More recently, Vpx was also shown to counteract HUSH, a complex constituted of TASOR, MPP8 and periphilin, which blocks viral expression from the integrated viral DNA. In a classical ubiquitin ligase hijacking model, Vpx bridges the DCAF1 ubiquitin ligase substrate adaptor to SAMHD1, for subsequent ubiquitination and degradation. Here, we investigated whether the same mechanism is at stake for Vpx-mediated HUSH degradation. While we confirm that Vpx bridges SAMHD1 to DCAF1, we show that TASOR can interact with DCAF1 in the absence of Vpx. Nonetheless, this association was stabilized in the presence of Vpx, suggesting the existence of a ternary complex. The N-terminal PARP-like domain of TASOR is involved in DCAF1 binding, but not in Vpx binding. We also characterized a series of HIV-2 Vpx point mutants impaired in TASOR degradation, while still degrading SAMHD1. Vpx mutants ability to degrade TASOR correlated with their capacity to enhance HIV-1 minigenome expression as expected. Strikingly, several Vpx mutants impaired for TASOR degradation, but not for SAMHD1 degradation, had a reduced binding affinity for DCAF1, but not for TASOR. In macrophages, Vpx R34A-R42A and Vpx R42A-Q47A-V48A, strongly impaired in DCAF1, but not in TASOR binding, could not degrade TASOR, while being efficient in degrading SAMHD1. Altogether, our results highlight the central role of a robust Vpx-DCAF1 association to trigger TASOR degradation. We then propose a model in which Vpx interacts with both TASOR and DCAF1 to stabilize a TASOR-DCAF1 complex. Furthermore, our work identifies Vpx mutants enabling the study of HUSH restriction independently from SAMHD1 restriction in primary myeloid cells. Human Immunodeficiency Virus (HIV) is still a major public health issue. The understanding of the molecular battle occurring during viral infection, between HIV components and cellular antiviral factors, the so-called restriction factors, is a key determinant for new treatment development. Namely, HIV auxiliary proteins are powerful to induce the downregulation of cellular restriction factors by hijacking the Ubiquitin/proteasome pathway, in order to facilitate the completion of a well-processed HIV replication cycle. For instance, HIV-2 Vpx eases reverse transcription in myeloid cells by counteracting the SAMDH1 restriction factor. More recently, we discovered the ability of Vpx to induce the degradation of the HUSH epigenetic repressor complex to favor in turn, the expression of the provirus. In this study, we uncovered the mechanisms by which Vpx antagonizes TASOR, the core subunit of the HUSH complex. We highlighted key differences between Vpx-induced TASOR and SAMHD1 degradation. These findings will help to propose strategies to study or to target either HUSH or SAMHD1, especially in myeloid cells where SAMHD1 restriction operates.
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Affiliation(s)
| | - Roy Matkovic
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
| | - Pauline Larrous
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
| | - Marina Morel
- Institut Cochin, Université de Paris, INSERM U1016, Paris, France
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Coronavirus Porcine Epidemic Diarrhea Virus Nucleocapsid Protein Interacts with p53 To Induce Cell Cycle Arrest in S-Phase and Promotes Viral Replication. J Virol 2021; 95:e0018721. [PMID: 34037422 DOI: 10.1128/jvi.00187-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Subversion of the host cell cycle to facilitate viral replication is a common feature of coronavirus infections. Coronavirus nucleocapsid (N) protein can modulate the host cell cycle, but the mechanistic details remain largely unknown. Here, we investigated the effects of manipulation of porcine epidemic diarrhea virus (PEDV) N protein on the cell cycle and the influence on viral replication. Results indicated that PEDV N induced Vero E6 cell cycle arrest at S-phase, which promoted viral replication (P < 0.05). S-phase arrest was dependent on the N protein nuclear localization signal S71NWHFYYLGTGPHADLRYRT90 and the interaction between N protein and p53. In the nucleus, the binding of N protein to p53 maintained consistently high-level expression of p53, which activated the p53-DREAM pathway. The key domain of the N protein interacting with p53 was revealed to be S171RGNSQNRGNNQGRGASQNRGGNN194 (NS171-N194), in which G183RG185 are core residues. NS171-N194 and G183RG185 were essential for N-induced S-phase arrest. Moreover, small molecular drugs targeting the NS171-N194 domain of the PEDV N protein were screened through molecular docking. Hyperoside could antagonize N protein-induced S-phase arrest by interfering with interaction between N protein and p53 and inhibit viral replication (P < 0.05). The above-described experiments were also validated in porcine intestinal cells, and data were in line with results in Vero E6 cells. Therefore, these results reveal the PEDV N protein interacts with p53 to activate the p53-DREAM pathway, and subsequently induces S-phase arrest to create a favorable environment for virus replication. These findings provide new insight into the PEDV-host interaction and the design of novel antiviral strategies against PEDV. IMPORTANCE Many viruses subvert the host cell cycle to create a cellular environment that promotes viral growth. PEDV, an emerging and reemerging coronavirus, has led to substantial economic loss in the global swine industry. Our study is the first to demonstrate that PEDV N-induced cell cycle arrest during the S-phase promotes viral replication. We identified a novel mechanism of PEDV N-induced S-phase arrest, where the binding of PEDV N protein to p53 maintains consistently high levels of p53 expression in the nucleus to mediate S-phase arrest by activating the p53-DREAM pathway. Furthermore, a small molecular compound, hyperoside, targeted the PEDV N protein, interfering with the interaction between the N protein and p53 and, importantly, inhibited PEDV replication by antagonizing cell cycle arrest. This study reveals a new mechanism of PEDV-host interaction and also provides a novel antiviral strategy for PEDV. These data provide a foundation for further research into coronavirus-host interactions.
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Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. J Virol 2021; 95:e0097120. [PMID: 34011540 DOI: 10.1128/jvi.00971-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 encodes several accessory proteins-Nef, Vif, Vpr, and Vpu-whose functions are to modulate the cellular environment to favor immune evasion and viral replication. While Vpr was shown to mediate a G2/M cell cycle arrest and provide a replicative advantage during infection of myeloid cells, the mechanisms underlying these functions remain unclear. In this study, we defined HIV-1 Vpr proximity interaction network using the BioID proximity labeling approach and identified 352 potential Vpr partners/targets, including several complexes, such as the cell cycle-regulatory anaphase-promoting complex/cyclosome (APC/C). Herein, we demonstrate that both the wild type and cell cycle-defective mutants of Vpr induce the degradation of APC1, an essential APC/C scaffolding protein, and show that this activity relies on the recruitment of DCAF1 by Vpr and the presence of a functional proteasome. Vpr forms a complex with APC1, and the APC/C coactivators Cdh1 and Cdc20 are associated with these complexes. Interestingly, we found that Vpr encoded by the prototypic HIV-1 NL4.3 does not interact efficiently with APC1 and is unable to mediate its degradation as a result of a N28S-G41N amino acid substitution. In contrast, we show that APC1 degradation is a conserved feature of several primary Vpr variants from transmitted/founder virus. Functionally, Vpr-mediated APC1 degradation did not impact the ability of the protein to induce a G2 cell cycle arrest during infection of CD4+ T cells or enhance HIV-1 replication in macrophages, suggesting that this conserved activity may be important for other aspects of HIV-1 pathogenesis. IMPORTANCE The function of the Vpr accessory protein during HIV-1 infection remains poorly defined. Several cellular targets of Vpr were previously identified, but their individual degradation does not fully explain the ability of Vpr to impair the cell cycle or promote HIV-1 replication in macrophages. Here, we used the unbiased proximity labeling approach, called BioID, to further define the Vpr proximity interaction network and identified several potentially new Vpr partners/targets. We validated our approach by focusing on a cell cycle master regulator, the APC/C complex, and demonstrated that Vpr mediated the degradation of a critical scaffolding component of APC/C called APC1. Furthermore, we showed that targeting of APC/C by Vpr did not impact the known activity of Vpr. Since degradation of APC1 is a conserved feature of several primary variants of Vpr, it is likely that the interplay between Vpr and APC/C governs other aspects of HIV-1 pathogenesis.
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Priyanka PP, Yenugu S. Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology. Reprod Sci 2021; 28:2725-2734. [PMID: 33942254 DOI: 10.1007/s43032-021-00595-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/22/2021] [Indexed: 01/10/2023]
Abstract
The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.
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Affiliation(s)
| | - Suresh Yenugu
- Department of Animal Biology, University of Hyderabad, Hyderabad, 500046, India.
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Salamango DJ, Harris RS. Demystifying Cell Cycle Arrest by HIV-1 Vif. Trends Microbiol 2021; 29:381-384. [PMID: 33478820 DOI: 10.1016/j.tim.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Although APOBEC3 degradation is the canonical function of HIV-1 Vif, this viral protein also induces potent cell cycle arrest through a newly defined mechanism. Here, we review recent advances in this area and propose that the scope of this activity may go beyond subversion of the host cell cycle.
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Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.
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Salamango DJ, Harris RS. Dual Functionality of HIV-1 Vif in APOBEC3 Counteraction and Cell Cycle Arrest. Front Microbiol 2021; 11:622012. [PMID: 33510734 PMCID: PMC7835321 DOI: 10.3389/fmicb.2020.622012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 01/02/2023] Open
Abstract
Accessory proteins are a key feature that distinguishes primate immunodeficiency viruses such as human immunodeficiency virus type I (HIV-1) from other retroviruses. A prime example is the virion infectivity factor, Vif, which hijacks a cellular co-transcription factor (CBF-β) to recruit a ubiquitin ligase complex (CRL5) to bind and degrade antiviral APOBEC3 enzymes including APOBEC3D (A3D), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H). Although APOBEC3 antagonism is essential for viral pathogenesis, and a more than sufficient functional justification for Vif’s evolution, most viral proteins have evolved multiple functions. Indeed, Vif has long been known to trigger cell cycle arrest and recent studies have shed light on the underlying molecular mechanism. Vif accomplishes this function using the same CBF-β/CRL5 ubiquitin ligase complex to degrade a family of PPP2R5 phospho-regulatory proteins. These advances have helped usher in a new era of accessory protein research and fresh opportunities for drug development.
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Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States
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Khan H, Sumner RP, Rasaiyaah J, Tan CP, Rodriguez-Plata MT, Van Tulleken C, Fink D, Zuliani-Alvarez L, Thorne L, Stirling D, Milne RSB, Towers GJ. HIV-1 Vpr antagonizes innate immune activation by targeting karyopherin-mediated NF-κB/IRF3 nuclear transport. eLife 2020; 9:e60821. [PMID: 33300875 PMCID: PMC7759385 DOI: 10.7554/elife.60821] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 must replicate in cells that are equipped to defend themselves from infection through intracellular innate immune systems. HIV-1 evades innate immune sensing through encapsidated DNA synthesis and encodes accessory genes that antagonize specific antiviral effectors. Here, we show that both particle associated, and expressed HIV-1 Vpr, antagonize the stimulatory effect of a variety of pathogen associated molecular patterns by inhibiting IRF3 and NF-κB nuclear transport. Phosphorylation of IRF3 at S396, but not S386, was also inhibited. We propose that, rather than promoting HIV-1 nuclear import, Vpr interacts with karyopherins to disturb their import of IRF3 and NF-κB to promote replication in macrophages. Concordantly, we demonstrate Vpr-dependent rescue of HIV-1 replication in human macrophages from inhibition by cGAMP, the product of activated cGAS. We propose a model that unifies Vpr manipulation of nuclear import and inhibition of innate immune activation to promote HIV-1 replication and transmission.
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Affiliation(s)
- Hataf Khan
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rebecca P Sumner
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Jane Rasaiyaah
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Choon Ping Tan
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Chris Van Tulleken
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Douglas Fink
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Lucy Thorne
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - David Stirling
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Richard SB Milne
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
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Lubow J, Collins KL. Vpr Is a VIP: HIV Vpr and Infected Macrophages Promote Viral Pathogenesis. Viruses 2020; 12:E809. [PMID: 32726944 PMCID: PMC7472745 DOI: 10.3390/v12080809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
HIV infects several cell types in the body, including CD4+ T cells and macrophages. Here we review the role of macrophages in HIV infection and describe complex interactions between viral proteins and host defenses in these cells. Macrophages exist in many forms throughout the body, where they play numerous roles in healthy and diseased states. They express pattern-recognition receptors (PRRs) that bind viral, bacterial, fungal, and parasitic pathogens, making them both a key player in innate immunity and a potential target of infection by pathogens, including HIV. Among these PRRs is mannose receptor, a macrophage-specific protein that binds oligosaccharides, restricts HIV replication, and is downregulated by the HIV accessory protein Vpr. Vpr significantly enhances infection in vivo, but the mechanism by which this occurs is controversial. It is well established that Vpr alters the expression of numerous host proteins by using its co-factor DCAF1, a component of the DCAF1-DDB1-CUL4 ubiquitin ligase complex. The host proteins targeted by Vpr and their role in viral replication are described in detail. We also discuss the structure and function of the viral protein Env, which is stabilized by Vpr in macrophages. Overall, this literature review provides an updated understanding of the contributions of macrophages and Vpr to HIV pathogenesis.
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Affiliation(s)
- Jay Lubow
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Kathleen L. Collins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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