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Yaseen MM, Abuharfeil NM, Darmani H. The Role of p53 in HIV Infection. Curr HIV/AIDS Rep 2023; 20:419-427. [PMID: 38010468 DOI: 10.1007/s11904-023-00684-8] [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] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE OF REVIEW This review aims to elucidate the multifaceted role of the tumor suppressor protein p53 in the context of HIV infection. We explore how p53, a pivotal regulator of cellular processes, interacts with various facets of the HIV life cycle. Understanding these interactions could provide valuable insights into potential therapeutic interventions and the broader implications of p53 in viral infections. RECENT FINDINGS Recent research has unveiled a complex interplay between p53 and HIV. Several reports have highlighted the involvement of p53 in restricting the replication of HIV within both immune and nonimmune cells. Various mechanisms have been suggested to unveil how p53 enforces this restriction on HIV replication. However, HIV has developed strategies to manipulate p53, benefiting its replication and evading host defenses. In summary, p53 plays a multifaceted role in HIV infection, impacting viral replication and disease progression. Recent findings underscore the importance of understanding the intricate interactions between p53 and HIV for the development of innovative therapeutic approaches. Manipulating p53 pathways may offer potential avenues to suppress viral replication and ameliorate immune dysfunction, ultimately contributing to the management of HIV/AIDS. Further research is warranted to fully exploit the therapeutic potential of p53 in the context of HIV infection.
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Affiliation(s)
- Mahmoud Mohammad Yaseen
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan.
| | - Nizar Mohammad Abuharfeil
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Homa Darmani
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
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Dwivedi AK, Gornalusse GG, Siegel DA, Barbehenn A, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Reppetti J, Vo PM, Levy CN, Roychoudhury P, Jerome KR, Hladik F, Henrich TJ, Deeks SG, Lee SA. A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size. PLoS Pathog 2023; 19:e1011114. [PMID: 38019897 PMCID: PMC10712869 DOI: 10.1371/journal.ppat.1011114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 12/11/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). There have been few cohort-based studies evaluating host genomic or transcriptomic predictors of the HIV reservoir. We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 ART-suppressed people with HIV (PWH). After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q = 0.006), IL-1/NRLP3 inflammasome (q = 0.008), and IL-10 (q = 0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-α protein associations achieving statistical significance (p<0.05). Plasma IL-10 was also significantly inversely associated with HIV DNA (p = 0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. To our knowledge, this is the largest host transcriptomic study of the HIV reservoir. Our findings suggest that host gene expression may vary in response to the transcriptionally active reservoir and that changes in cellular proliferation genes may influence the size of the HIV reservoir. These findings add important data to the limited host genetic HIV reservoir studies to date.
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Affiliation(s)
- Ashok K. Dwivedi
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Germán G. Gornalusse
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - David A. Siegel
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Alton Barbehenn
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Cassandra Thanh
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Rebecca Hoh
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Kristen S. Hobbs
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Tony Pan
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Erica A. Gibson
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Jeffrey Martin
- Department of Biostatistics & Epidemiology, University of California San Francisco, California, United States of America
| | - Frederick Hecht
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Christopher Pilcher
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Jeffrey Milush
- Department of Medicine, Division of Experimental Medicine, University of California San Francisco, California, United States of America
| | - Michael P. Busch
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Blood Bank, San Francisco, California, United States of America
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Julieta Reppetti
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO- Houssay), Buenos Aires, Argentina
| | - Phuong M. Vo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Claire N. Levy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Florian Hladik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Timothy J. Henrich
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Steven G. Deeks
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
| | - Sulggi A. Lee
- Department of Medicine, Division of HIV, Infectious Diseases & Global Medicine, University of California, San Francisco, California, United States of America
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He MF, Liang JH, Shen YN, Zhang CW, Yang KY, Liu LC, Xie Q, Hu C, Song X, Wang Y. Coptisine Inhibits Influenza Virus Replication by Upregulating p21. Molecules 2023; 28:5398. [PMID: 37513270 PMCID: PMC10386263 DOI: 10.3390/molecules28145398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/09/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The activation of innate antiviral immunity is a promising approach for combatting viral infections. In this study, we screened Chinese herbs that activated human immunity and identified coptisine as a potent inhibitor of the influenza virus with an EC50 of 10.7 μM in MDCK cells. The time of an addition assay revealed that pre-treatment with coptisine was more effective at reducing viral replication than co-treatment or post-treatment. Our bulk RNA-sequencing data showed that coptisine upregulated the p21 signaling pathway in MDCK cells, which was responsible for its antiviral effects. Specifically, coptisine increased the expression of p21 and FOXO1 in a dose-dependent manner while leaving the MELK expression unchanged. Docking analysis revealed that coptisine likely inhibited MELK activity directly by forming hydrogen bonds with ASP-150 and GLU-87 in the catalytic pocket. These findings suggest that coptisine may be a promising antiviral agent that regulates the p21 signaling pathway to inhibit viral replication.
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Affiliation(s)
- Ming-Feng He
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Jian-Hui Liang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yan-Ni Shen
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chao-Wei Zhang
- School of Pharmaceutical Science, Shenzhen University, Shenzhen 518000, China
| | - Kuang-Yang Yang
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Li-Chu Liu
- Foshan Hospital of Traditional Chinese Medicine, Foshan 528000, China
| | - Qian Xie
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xun Song
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Yan Wang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Hokello J, Tyagi P, Dimri S, Sharma AL, Tyagi M. Comparison of the Biological Basis for Non-HIV Transmission to HIV-Exposed Seronegative Individuals, Disease Non-Progression in HIV Long-Term Non-Progressors and Elite Controllers. Viruses 2023; 15:1362. [PMID: 37376660 DOI: 10.3390/v15061362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
HIV-exposed seronegative individuals (HESIs) are a small fraction of persons who are multiply exposed to human immunodeficiency virus (HIV), but do not exhibit serological or clinical evidence of HIV infection. In other words, they are groups of people maintaining an uninfected status for a long time, even after being exposed to HIV several times. The long-term non-progressors (LTNPs), on the other hand, are a group of HIV-infected individuals (approx. 5%) who remain clinically and immunologically stable for an extended number of years without combination antiretroviral therapy (cART). Meanwhile, elite controllers are comprise a much lower number (0.5%) of HIV-infected persons who spontaneously and durably control viremia to below levels of detection for at least 12 months, even when using the most sensitive assays, such as polymerase chain reaction (PCR) in the absence of cART. Despite the fact that there is no universal agreement regarding the mechanisms by which these groups of individuals are able to control HIV infection and/or disease progression, there is a general consensus that the mechanisms of protection are multifaceted and include genetic, immunological as well as viral factors. In this review, we analyze and compare the biological factors responsible for the control of HIV in these unique groups of individuals.
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Affiliation(s)
- Joseph Hokello
- Department of Biology, Faculty of Science and Education, Busitema University, Tororo P.O. Box 236, Uganda
| | - Priya Tyagi
- Cherry Hill East High School, 1750 Kresson Rd, Cherry Hill, NJ 08003, USA
| | - Shelly Dimri
- George C. Marshall High School, Fairfax County Public Schools, 7731 Leesburg Pike, Falls Church, VA 22043, USA
| | | | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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Lin X, Ahmad A, Ivanov AI, Simhadri J, Wang S, Kumari N, Ammosova T, Nekhai S. HIV-1 Transcription Inhibitor 1E7-03 Decreases Nucleophosmin Phosphorylation. Mol Cell Proteomics 2023; 22:100488. [PMID: 36563749 PMCID: PMC9975258 DOI: 10.1016/j.mcpro.2022.100488] [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: 03/11/2022] [Revised: 12/07/2022] [Accepted: 12/18/2022] [Indexed: 12/25/2022] Open
Abstract
Transcription activation of latent human immunodeficiency virus-1 (HIV-1) occurs due to HIV-1 rebound, the interruption of combination antiretroviral therapy, or development of drug resistance. Thus, novel HIV-1 inhibitors, targeting HIV-1 transcription are needed. We previously developed an HIV-1 transcription inhibitor, 1E7-03, that binds to the noncatalytic RVxF-accommodating site of protein phosphatase 1 and inhibits HIV-1 replication in cultured cells and HIV-1-infected humanized mice by impeding protein phosphatase 1 interaction with HIV-1 Tat protein. However, host proteins and regulatory pathways targeted by 1E7-03 that contribute to its overall HIV-1 inhibitory activity remain to be identified. To address this issue, we performed label-free quantitative proteome and phosphoproteome analyses of noninfected and HIV-1-infected CEM T cells that were untreated or treated with 1E7-03. 1E7-03 significantly reprogramed the phosphorylation profile of proteins including PPARα/RXRα, TGF-β, and PKR pathways. Phosphorylation of nucleophosmin (NPM1) at Ser-125 residue in PPARα/RXRα pathway was significantly reduced (>20-fold, p = 1.37 × 10-9), followed by the reduced phosphorylation of transforming growth factor-beta 2 at Ser-46 (TGF-β2, >12-fold, p = 1.37 × 10-3). Downregulation of NPM1's Ser-125 phosphorylation was further confirmed using Western blot. Phosphorylation mimicking NPM1 S125D mutant activated Tat-induced HIV-1 transcription and exhibited enhanced NPM1-Tat interaction compared to NPM1 S125A mutant. Inhibition of Aurora A or Aurora B kinases that phosphorylate NPM1 on Ser-125 residue inhibited HIV-1, further supporting the role of NPM1 in HIV-1 infection. Taken together, 1E7-03 reprogrammed PPARα/RXRα and TGF-β pathways that contribute to the inhibition of HIV-1 transcription. Our findings suggest that NPM1 phosphorylation is a plausible target for HIV-1 transcription inhibition.
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Key Words
- actn4, alpha-actinin-1
- asl, argininosuccinate lyase
- aspm, abnormal spindle-like microcephaly-associated protein
- cart, combination antiretroviral therapy
- cdk2, cell cycle-dependent kinase 2
- ck2, casein kinase 2
- dmso, dimethyl sulfoxide
- egln1, egl-9 family hypoxia inducible factor 1
- erk/p38, extracellular signal-regulated kinase p38
- fa, formic acid
- gadd34, growth arrest and dna damage-inducible protein
- hif-1α, hypoxia-inducible factor 1α
- hiv-1 vif protein, viral infectivity factor, an hiv-1 accessory protein
- hiv-1, human immunodeficiency virus-1
- hsp90, heat shock protein 90
- ipa, ingenuity pathway analysis
- lc-ft/ms, tandem liquid chromatography-fourier transform mass spectrometry
- mapk, mitogen-activated protein kinase
- map3k4, mitogen-activated protein kinase kinase kinase 4
- mita, mediator of interferon response factor 3 activation
- nfat, nuclear factor of activated t cells
- nf-κb, nuclear factor kappa-light-chain-enhancer of activated b cell
- npm1, nucleophosmin
- oa, okadaic acid
- pi3k/akt, phosphoinositide 3-kinase/ ak strain transforming or protein kinase b
- pp, protein phosphatase
- pparα/rxrα, peroxisome proliferator-activated receptor α/ retinoid x receptor α
- ptm, posttranslational modification
- rnr2, ribonucleotide reductase 2
- rt, reverse transcription
- samhd1, sam domain and hd domain-containing protein 1
- smad7, mothers against decapentaplegic homolog 7
- stat5, signal transducer and activator of transcription 5 taf4
- taf4, transcription factor tfiid subunit tata-box-binding protein (tbp)-associated factor 4
- tgf-β2, transforming growth factor-beta
- tp53, tumor protein p53
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Affiliation(s)
- Xionghao Lin
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA; College of Dentistry, Howard University, Washington, District of Columbia, USA
| | - Asrar Ahmad
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Andrey I Ivanov
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Jyothirmai Simhadri
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Songping Wang
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Namita Kumari
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Microbiology, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Medicine, College of Medicine, Howard University, Washington, District of Columbia, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Microbiology, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Medicine, College of Medicine, Howard University, Washington, District of Columbia, USA.
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Martin-Gayo E, Gao C, Calvet-Mirabent M, Ouyang Z, Lichterfeld M, Yu XG. Cooperation between cGAS and RIG-I sensing pathways enables improved innate recognition of HIV-1 by myeloid dendritic cells in elite controllers. Front Immunol 2022; 13:1017164. [PMID: 36569826 PMCID: PMC9768436 DOI: 10.3389/fimmu.2022.1017164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Spontaneous control of HIV-1 replication in the absence of anti-retroviral therapy (ART) naturally occurs in a small proportion of HIV-1-infected individuals known as elite controllers (EC), likely as a result of improved innate and adaptive immune mechanisms. Previous studies suggest that enhanced cytosolic immune recognition of HIV-1 reverse transcripts in conventional dendritic cells (mDC) from EC enables effective induction of antiviral effector T cell responses. However, the specific molecular circuits responsible for such improved innate recognition of HIV-1 in mDC from these individuals remain unknown. Results and methods Here, we identified a subpopulation of EC whose mDC displayed higher baseline abilities to respond to intracellular HIV-1 dsDNA stimulation. A computational analysis of transcriptional signatures from such high responder EC, combined with functional studies, suggested cytosolic recognition of HIV-1 dsDNA by cGAS, combined with sensing of viral mRNA by RIG-I after polymerase III-mediated HIV-1 DNA transcription. Discussion Together, our work identifies collaborative networks of innate sensing pathways that enhance cell-intrinsic abilities of mDC to induce antiviral innate responses against HIV-1; these observations might be useful for the therapeutic induction of effective antiviral immune responses.
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Affiliation(s)
- Enrique Martin-Gayo
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Universidad Autónoma de Madrid, Immunology Unit, Hospital Universitario de la Princesa, Madrid, Spain,*Correspondence: Enrique Martin-Gayo, ; Xu G. Yu,
| | - Ce Gao
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Marta Calvet-Mirabent
- Universidad Autónoma de Madrid, Immunology Unit, Hospital Universitario de la Princesa, Madrid, Spain
| | - Zhengyu Ouyang
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Xu G. Yu
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States,*Correspondence: Enrique Martin-Gayo, ; Xu G. Yu,
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De La Torre-Tarazona E, Ayala-Suárez R, Díez-Fuertes F, Alcamí J. Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes. Front Immunol 2022; 13:926499. [PMID: 35844607 PMCID: PMC9284212 DOI: 10.3389/fimmu.2022.926499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.
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Affiliation(s)
- Erick De La Torre-Tarazona
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rubén Ayala-Suárez
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Francisco Díez-Fuertes
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Francisco Díez-Fuertes,
| | - José Alcamí
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Human Immunodeficiency Virus (HIV) Unit, Hospital Clínic de Barcelona, Barcelona, Spain
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HIV UTR, LTR, and Epigenetic Immunity. Viruses 2022; 14:v14051084. [PMID: 35632825 PMCID: PMC9146425 DOI: 10.3390/v14051084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
The duel between humans and viruses is unending. In this review, we examine the HIV RNA in the form of un-translated terminal region (UTR), the viral DNA in the form of long terminal repeat (LTR), and the immunity of human DNA in a format of epigenetic regulation. We explore the ways in which the human immune responses to invading pathogenic viral nucleic acids can inhibit HIV infection, exemplified by a chromatin vaccine (cVaccine) to elicit the immunity of our genome—epigenetic immunity towards a cure.
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Sugawara S, Reeves RK, Jost S. Learning to Be Elite: Lessons From HIV-1 Controllers and Animal Models on Trained Innate Immunity and Virus Suppression. Front Immunol 2022; 13:858383. [PMID: 35572502 PMCID: PMC9094575 DOI: 10.3389/fimmu.2022.858383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022] Open
Abstract
Although antiretroviral therapy (ART) has drastically changed the lives of people living with human immunodeficiency virus-1 (HIV-1), long-term treatment has been associated with a vast array of comorbidities. Therefore, a cure for HIV-1 remains the best option to globally eradicate HIV-1/acquired immunodeficiency syndrome (AIDS). However, development of strategies to achieve complete eradication of HIV-1 has been extremely challenging. Thus, the control of HIV-1 replication by the host immune system, namely functional cure, has long been studied as an alternative approach for HIV-1 cure. HIV-1 elite controllers (ECs) are rare individuals who naturally maintain undetectable HIV-1 replication levels in the absence of ART and whose immune repertoire might be a desirable blueprint for a functional cure. While the role(s) played by distinct human leukocyte antigen (HLA) expression and CD8+ T cell responses expressing cognate ligands in controlling HIV-1 has been widely characterized in ECs, the innate immune phenotype has been decidedly understudied. Comparably, in animal models such as HIV-1-infected humanized mice and simian Immunodeficiency Virus (SIV)-infected non-human primates (NHP), viremic control is known to be associated with specific major histocompatibility complex (MHC) alleles and CD8+ T cell activity, but the innate immune response remains incompletely characterized. Notably, recent work demonstrating the existence of trained innate immunity may provide new complementary approaches to achieve an HIV-1 cure. Herein, we review the known characteristics of innate immune responses in ECs and available animal models, identify gaps of knowledge regarding responses by adaptive or trained innate immune cells, and speculate on potential strategies to induce EC-like responses in HIV-1 non-controllers.
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Nekhai S, Kumari N. HIV-1 infection in sickle cell disease and sickle cell trait: role of iron and innate response. Expert Rev Hematol 2022; 15:253-263. [PMID: 35322747 PMCID: PMC9041812 DOI: 10.1080/17474086.2022.2054799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Sickle cell disease (SCD), an inherited hemoglobinopathy, affects primarily African Americans in the U.S.A. In addition, about 15% African Americans carry sickle cell trait (SCT). Despite the risk associated with blood transfusions, SCD patients have lower risk of acquiring HIV-1 infection. SCT individuals might also have some protection from HIV-1 infection. AREAS COVERED Here, we will review recent and previous studies with the focus on molecular mechanisms that might underlie and contribute to the protection of individuals with SCD and SCT from HIV-1 infection. As both of these conditions predispose to hemolysis, we will focus our discussion on the effects of systemic and intracellular iron on HIV-1 infection and progression. We will also review changes in iron metabolism and activation of innate antiviral responses in SCD and SCT and their effects on HIV-1 infection. EXPERT OPINION Previous studies, including ours, showed that SCD might protect from HIV-1 infection. This protection is likely due to the upregulation of complex protein network in response to hemolysis, hypoxia and interferon signaling. These findings are important not only for HIV-1 field but also for SCD cure efforts as antiviral state of SCD patients may adversely affect lentivirus-based gene therapy efforts.
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Affiliation(s)
- Sergei Nekhai
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington DC, USA
- Department of Medicine, Howard University, Washington DC, USA
- Corresponding Author: Sergei Nekhai, , Center for Sickle Cell Disease, Howard University, HUIRB, Suite 321D, 2201 Georgia Avenue, NW, Washington DC 20059, USA, Phone: (202) 806-3378
| | - Namita Kumari
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington DC, USA
- Department of Medicine, Howard University, Washington DC, USA
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Differential Expression of CREM/ICER Isoforms Is Associated with the Spontaneous Control of HIV Infection. mBio 2022; 13:e0197921. [PMID: 35041523 PMCID: PMC8725591 DOI: 10.1128/mbio.01979-21] [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] [Indexed: 11/20/2022] Open
Abstract
A rare subset of HIV-infected individuals, termed elite controllers (ECs), can maintain long-term control over HIV replication in the absence of antiretroviral therapy (ART). To elucidate the biological mechanism of resistance to HIV replication at the molecular and cellular levels, we performed RNA sequencing and identified alternative splicing variants from ECs, HIV-infected individuals undergoing ART, ART-naive HIV-infected individuals, and healthy controls. We identified differential gene expression patterns that are specific to ECs and may influence HIV resistance, including alternative RNA splicing and exon usage variants of the CREM/ICER gene (cyclic AMP [cAMP]-responsive element modulator/inducible cAMP early repressors). The knockout and knockdown of specific ICER exons that were found to be upregulated in ECs resulted in significantly increased HIV infection in a CD4+ T cell line and primary CD4+ T cells. Overexpression of ICER isoforms decreased HIV infection in primary CD4+ T cells. Furthermore, ICER regulated HIV long terminal repeat (LTR) promoter activity in a Tat-dependent manner. Together, these results suggest that ICER is an HIV host factor that may contribute to the HIV resistance of ECs. These findings will help elucidate the mechanisms of HIV control by ECs and may yield a new approach for treatment of HIV. IMPORTANCE A small group of HIV-infected individuals, termed elite controllers (ECs), display control of HIV replication in the absence of antiretroviral therapy (ART). However, the mechanism of ECs' resistance to HIV replication is not clear. In our work, we found an increased expression of specific, small isoforms of ICER in ECs. Further experiments proved that ICER is a robust host factor to regulate viral replication. Furthermore, we found that ICER regulates HIV LTR promoter activity in a Tat-dependent manner. These findings suggest that ICER is related to spontaneous control of HIV infection in ECs. This study may help elucidate a novel target for treatment of HIV.
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p21 restricts influenza A virus by perturbing the viral polymerase complex and upregulating type I interferon signaling. PLoS Pathog 2022; 18:e1010295. [PMID: 35180274 PMCID: PMC8920271 DOI: 10.1371/journal.ppat.1010295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/14/2022] [Accepted: 01/20/2022] [Indexed: 11/19/2022] Open
Abstract
Many cellular genes and networks induced in human lung epithelial cells infected with the influenza virus remain uncharacterized. Here, we find that p21 levels are elevated in response to influenza A virus (IAV) infection, which is independent of p53. Silencing, pharmacological inhibition or deletion of p21 promotes virus replication in vitro and in vivo, indicating that p21 is an influenza restriction factor. Mechanistically, p21 binds to the C-terminus of IAV polymerase subunit PA and competes with PB1 to limit IAV polymerase activity. Besides, p21 promotes IRF3 activation by blocking K48-linked ubiquitination degradation of HO-1 to enhance type I interferons expression. Furthermore, a synthetic p21 peptide (amino acids 36 to 43) significantly inhibits IAV replication in vitro and in vivo. Collectively, our findings reveal that p21 restricts IAV by perturbing the viral polymerase complex and activating the host innate immune response, which may aid the design of desperately needed new antiviral therapeutics. Influenza A virus (IAV) poses a continuous threat to public health and economic stability. The ribonucleoprotein (RNP) of IAV is responsible for the transcription and replication of the viral RNA. These processes require interplay between host factors and RNP components. Here, we report that p21 can be activated by IAV infection and is controlled by a p53-independent pathway. We demonstrate that p21 directly binds to the viral polymerase acidic protein and limits IAV polymerase activity through disrupting the formation of the ribonucleoprotein complex. Additionally, p21 activation promotes IRF3 activation by blocking K48-linked polyubiquitination degradation of HO-1, thereby activating the type I interferon pathway. We further identify an 8-amino-acid peptide of p21 as the minimum motif that effectively inhibits IAV replication and presents therapeutic efficacy both in vitro and in vivo. Thus, our studies not only identify p21 as an antiviral protein, but also provide mechanistic insight to facilitate drug development.
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13
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MicroRNA let-7 and viral infections: focus on mechanisms of action. Cell Mol Biol Lett 2022; 27:14. [PMID: 35164678 PMCID: PMC8853298 DOI: 10.1186/s11658-022-00317-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are fundamental post-transcriptional modulators of several critical cellular processes, a number of which are involved in host defense mechanisms. In particular, miRNA let-7 functions as an essential regulator of the function and differentiation of both innate and adaptive immune cells. Let-7 is involved in several human diseases, including cancer and viral infections. Several viral infections have found ways to dysregulate the expression of miRNAs. Extracellular vesicles (EV) are membrane-bound lipid structures released from many types of human cells that can transport proteins, lipids, mRNAs, and miRNAs, including let-7. After their release, EVs are taken up by the recipient cells and their contents released into the cytoplasm. Let-7-loaded EVs have been suggested to affect cellular pathways and biological targets in the recipient cells, and can modulate viral replication, the host antiviral response, and the action of cancer-related viruses. In the present review, we summarize the available knowledge concerning the expression of let-7 family members, functions, target genes, and mechanistic involvement in viral pathogenesis and host defense. This may provide insight into the development of new therapeutic strategies to manage viral infections.
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14
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Nwagha TU, Ugwu AO, Nweke M. Does Sickle Cell Disease Protect against HIV Infection: A Systematic Review. Med Princ Pract 2022; 31:516-523. [PMID: 36096094 PMCID: PMC9841758 DOI: 10.1159/000526993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/22/2022] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE The aim of this systematic review was to investigate whether sickle cell disease (SCD) protects against human immunodeficiency virus (HIV) infection by determining the association between SCD and the incidence and virulence of HIV infection. METHODS This is a systematic review that used MEDLINE, PubMed, CINAHL, and Academic Search Complete as data sources. Articles describing the relationship of SCD with HIV infection were included in this review. The effect measures were converted to correlation coefficients and synthesized accordingly to examine the putative protective role of SCD against HIV infection. Independent full-text screening and data extraction were conducted on all eligible studies. The risk of bias was assessed using the mixed methods appraisal tool. We employed a random-effects model of meta-analysis to estimate the pooled prevalence. We computed Cochrane's Q statistics, I2, and prediction interval to quantify effect size heterogeneity. RESULTS SCD reduces the risk of HIV infection by 75% (odds ratio [OR] = 0.25; r = -0.36, p < 0.001; I2 = 71.65). There was no publication bias (Egger's t value = 0.411; p = 0.721). Similarly, risk of HIV virulence was reduced by 77% (OR = 0.23; r = -0.38; p < 0.001; I2 = 63.07). The mechanisms implicated in the protective influence of SCD include autosplenectomy, reduced CCR5 expression, and increased expression of heme and iron-regulated genes. CONCLUSIONS SCD appears to protect against HIV infection and slows HIV progression.
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Affiliation(s)
- Theresa Ukamaka Nwagha
- Department of Haematology and Immunology, Faculty of Medicine, University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| | - Angela Ogechukwu Ugwu
- Department of Haematology and Immunology, Faculty of Medicine, University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
- *Angela Ogechukwu Ugwu,
| | - Martins Nweke
- Fledgelight Evidence Consult, Enugu, Nigeria
- Physiotherapy Department, Evangel University Akaeze, Ebonyi State, Nigeria
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15
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Identification and characterization of Stathmin 1 as a host factor involved in HIV-1 latency. Biochem Biophys Res Commun 2021; 567:106-111. [PMID: 34146904 DOI: 10.1016/j.bbrc.2021.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022]
Abstract
Latency remains a barrier to achieving a sterilizing cure to HIV infection. It is thus important to find new host factor(s) to better understand maintenance of HIV latency and be exploited to develop new and more efficient latency reversing agents (LRAs). Here we employed RNA interference screening with a latently HIV-1-infected cell-line to identify Stathmin 1 (STMN1) as a host factor required for maintaining HIV-1 latency. Depletion of STMN1 significantly enhanced HIV-1 expression in a STMN1 depletion-dependent manner and forced expression of exogenous STMN1 suppressed it. We further showed that STMN1 depletion increases HIV-1 proviral transcriptional elongation. Moreover, chromatin immunoprecipitation (ChIP)-qPCR assays revealed STMN1 accumulation on/near the HIV-1 5' LTR region compared to other regions on the HIV-1 provirus, suggesting the possible contribution of STMN1 to HIV-1 transcription. These results suggest that STMN1 is required for the maintenance of HIV-1 latency and implicates STMN1 as a novel therapeutic target to eradicate HIV-1.
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Svensson JP. Targeting Epigenetics to Cure HIV-1: Lessons From (and for) Cancer Treatment. Front Cell Infect Microbiol 2021; 11:668637. [PMID: 34026665 PMCID: PMC8137950 DOI: 10.3389/fcimb.2021.668637] [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: 02/16/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) integrates in the host genome as a provirus resulting in a long-lived reservoir of infected CD4 cells. As a provirus, HIV-1 has several aspects in common with an oncogene. Both the HIV-1 provirus and oncogenes only cause disease when expressed. A successful cure of both cancer and HIV-1 includes elimination of all cells with potential to regenerate the disease. For over two decades, epigenetic drugs developed against cancer have been used in the HIV-1 field to modulate the state of the proviral chromatin. Cells with an intact HIV-1 provirus exist in three states of infection: productive, inducible latent, and non-inducible latent. Here focus is on HIV-1, transcription control and chromatin structure; how the inducible proviruses are maintained in a chromatin structure that allows reactivation of transcription; and how transcription switches between different stages to allow for an abundance of different transcripts from a single promoter. Recently it was shown that a functional cure of HIV can be achieved by encapsulating all intact HIV-1 proviruses in heterochromatin, giving hope that epigenetic interventions may be used to end the HIV-1 epidemic.
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Affiliation(s)
- J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet (KI), Huddinge, Sweden
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17
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Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies. Cell Rep 2020; 30:984-996.e4. [PMID: 31995767 PMCID: PMC6990401 DOI: 10.1016/j.celrep.2019.12.087] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 10/27/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
The induction of broadly neutralizing antibodies (bnAbs) is highly desired for an effective vaccine against HIV-1. Typically, bnAbs develop in patients with high viremia, but they can also evolve in some untreated HIV-1 controllers with low viral loads. Here, we identify a subgroup of neutralizer-controllers characterized by myeloid DCs (mDCs) with a distinct inflammatory signature and a superior ability to prime T follicular helper (Tfh)-like cells in an STAT4-dependent fashion. This distinct immune profile is associated with a higher frequency of Tfh-like cells in peripheral blood (pTfh) and an enrichment for Tfh-defining genes in circulating CD4+ T cells. Correspondingly, monocytes from this neutralizer controller subgroup upregulate genes encoding for chemotaxis and inflammation, and they secrete high levels of IL-12 in response to TLR stimulation. Our results suggest the existence of multi-compartment immune networks between mDCs, Tfh, and monocytes that may facilitate the development of bnAbs in a subgroup of HIV-1 controllers. HIV-1 controllers with neutralizing Abs are subdivided in two subgroups (Nt1 and Nt2) HIV-1-specific antibodies from Nt2 individuals display superior neutralization potency Nt2 exhibit distinct transcriptional signatures in DC, monocytes, and CD4 T cells Transcriptional and functional data suggest improved DC-pTFH interactions in Nt2
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18
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Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, Chen SMY, Hua S, Rhee B, Chang K, Blackmer JE, Osborn M, Peluso MJ, Hoh R, Somsouk M, Milush J, Bertagnolli LN, Sweet SE, Varriale JA, Burbelo PD, Chun TW, Laird GM, Serrao E, Engelman AN, Carrington M, Siliciano RF, Siliciano JM, Deeks SG, Walker BD, Lichterfeld M, Yu XG. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 2020; 585:261-267. [PMID: 32848246 PMCID: PMC7837306 DOI: 10.1038/s41586-020-2651-8] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/15/2020] [Indexed: 02/01/2023]
Abstract
Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected individuals (here termed 'elite controllers'), despite the presence of a replication-competent viral reservoir1. Inducing such an ability to spontaneously maintain undetectable plasma viraemia is a major objective of HIV-1 cure research, but the characteristics of proviral reservoirs in elite controllers remain to be determined. Here, using next-generation sequencing of near-full-length single HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. In contrast to individuals treated with long-term antiretroviral therapy, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in Krüppel-associated box domain-containing zinc finger genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, the integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. These data suggest that a distinct configuration of the proviral reservoir represents a structural correlate of natural viral control, and that the quality, rather than the quantity, of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, in one elite controller, we were unable to detect intact proviral sequences despite analysing more than 1.5 billion peripheral blood mononuclear cells, which raises the possibility that a sterilizing cure of HIV-1 infection, which has previously been observed only following allogeneic haematopoietic stem cell transplantation2,3, may be feasible in rare instances.
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Affiliation(s)
- Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Joshua M Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ben Rhee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Kaylee Chang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael J Peluso
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Jeffrey Milush
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Lynn N Bertagnolli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E Sweet
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph A Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | | | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Steven G Deeks
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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Abstract
Antiretroviral therapies efficiently block HIV-1 replication but need to be maintained for life. Moreover, chronic inflammation is a hallmark of HIV-1 infection that persists despite treatment. There is, therefore, an urgent need to better understand the mechanisms driving HIV-1 pathogenesis and to identify new targets for therapeutic intervention. In the past few years, the decisive role of cellular metabolism in the fate and activity of immune cells has been uncovered, as well as its impact on the outcome of infectious diseases. Emerging evidence suggests that immunometabolism has a key role in HIV-1 pathogenesis. The metabolic pathways of CD4+ T cells and macrophages determine their susceptibility to infection, the persistence of infected cells and the establishment of latency. Immunometabolism also shapes immune responses against HIV-1, and cell metabolic products are key drivers of inflammation during infection. In this Review, we summarize current knowledge of the links between HIV-1 infection and immunometabolism, and we discuss the potential opportunities and challenges for therapeutic interventions.
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Budiarti R, Khairunisa SQ, Nasronudin, Kuntaman, Guritno. Hyperbaric hyperoxia exposure in suppressing human immunodeficiency virus replication: An experimental in vitro in peripheral mononuclear blood cells culture. Infect Dis Rep 2020; 12:8743. [PMID: 32874469 PMCID: PMC7447945 DOI: 10.4081/idr.2020.8743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular immune has an important role in response HIV infection, which is attack the infected cells to activate signaling molecule. Hyperbaric Oxygen (HBO) worked as complementary treatment for HIV infection. The production of ROS and RNS molecules during hyperbaric exposure can affect gene expression which contributes to cellular adaptative response. This study was conducted to explore the mechanisms of cellular adaptive response to HIV infection during hyperbaric exposure. This study was carried on in vitro using healthy volunteers’ PBMCs (Peripheral Blood Mononuclear Cells) cultures infected with HIV-1. The study was conducted as a posttest only group design. The experimental unit was PBMC from venous blood of healthy volunteers which were cultured in vitro and infected by co-culturing with HIV- 1 in MT4 cell line. The experimental unit consist of treatment and control group. Each group examined the expression of transcription factor NFκB, Interferon α, reverse transcriptase inhibitors (p21), and the amount of HIV-1 p24 antigen. There were increasingly significant differences in the expression of the trancription factor of NFκB, p21, andHIV-1 p24 antigen,as well as mRNA transcription of interferon α2 between treatment and controlgroup. By decreasing p24 antigen showed that HBO exposure was able to suppress HIV-1 replication. The exposure to hyperbaric oxygen at the pressure of 2.4 ATAand 98% oxygen wasable to produce ROS and RNS molecules, which play a role in cellular adaptive responses through increasing the expression of nfĸb, p21 and mRNA of interferon α2 plays a role in inhibition mechanism of HIV-1 replication in cells.
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Affiliation(s)
- Retno Budiarti
- Department of Microbiology, Faculty of Medicine, Hang Tuah University
| | | | | | - Kuntaman
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga
| | - Guritno
- Faculty of Medicine, Universitas Pembangunan Nasional Veteran, Jakarta, Indonesia
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21
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Increased expression of CDKN1A/p21 in HIV-1 controllers is correlated with upregulation of ZC3H12A/MCPIP1. Retrovirology 2020; 17:18. [PMID: 32615986 PMCID: PMC7333275 DOI: 10.1186/s12977-020-00522-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background Some multifunctional cellular proteins, as the monocyte chemotactic protein-induced protein 1 (ZC3H12A/MCPIP1) and the cyclin-dependent kinase inhibitor CDKN1A/p21, are able to modulate the cellular susceptibility to the human immunodeficiency virus type 1 (HIV-1). Several studies showed that CDKN1A/p21 is expressed at high levels ex vivo in cells from individuals who naturally control HIV-1 replication (HIC) and a recent study supports a coordinate regulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in a model of renal carcinoma cells. Here, we explored the potential associations between mRNA expression of ZC3H12A/MCPIP1 and CDKN1A/p21 in HIC sustaining undetectable (elite controllers–EC) or low (viremic controllers–VC) viral loads. Results We found a selective upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in PBMC from HIC compared with both ART–suppressed and HIV–negative control groups (P≤ 0.02) and higher MCPIP1 and p21 proteins levels in HIC than in HIV-1 negative subjects. There was a moderate positive correlation (r ≥ 0.57; P ≤ 0.014) between expressions of both transcripts in HIC and in HIC combined with control groups. We found positive correlations between the mRNA level of CDKN1A/p21 with activated CD4+ T cells levels in HIC (r ≥ 0.53; P ≤ 0.017) and between the mRNA levels of both CDKN1A/p21 (r = 0.74; P = 0.005) and ZC3H12A/MCPIP1 (r = 0.58; P = 0.040) with plasmatic levels of sCD14 in EC. Reanalysis of published transcriptomic data confirmed the positive association between ZC3H12A/MCPIP1 and CDKN1A/p21 mRNA levels in CD4+ T cells and monocytes from disparate cohorts of HIC and other HIV-positive control groups. Conclusions These data show for the first time the simultaneous upregulation of ZC3H12A/MCPIP1 and CDKN1A/p21 transcripts in the setting of natural suppression of HIV-1 replication in vivo and the positive correlation of the expression of these cellular factors in disparate cohorts of HIV-positive individuals. The existence of a common regulatory pathway connecting ZC3H12A/MCPIP1 and CDKN1A/p21 could have a synergistic effect on HIV-1 replication control and pharmacological manipulation of these multifunctional host factors may open novel therapeutic perspectives to prevent HIV-1 replication and disease progression.
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22
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García M, López-Fernández L, Mínguez P, Morón-López S, Restrepo C, Navarrete-Muñoz MA, López-Bernaldo JC, Benguría A, García MI, Cabello A, Fernández-Guerrero M, De la Hera FJ, Estrada V, Barros C, Martínez-Picado J, Górgolas M, Benito JM, Rallón N. Transcriptional signature of resting-memory CD4 T cells differentiates spontaneous from treatment-induced HIV control. J Mol Med (Berl) 2020; 98:1093-1105. [PMID: 32556382 DOI: 10.1007/s00109-020-01930-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 01/29/2023]
Abstract
The HIV reservoir is the main barrier to eradicating HIV infection, and resting memory CD4 T (Trm) cells are one of the most relevant cellular component harboring latent proviruses. This is the first study analyzing the transcriptional profile of Trm cells, in two well-characterized groups of HIV patients with distinct mechanisms of viral replication control (spontaneous versus treatment-induced). We use a systems biology approach to unravel subtle but important differences in the molecular mechanisms operating at the cellular level that could be associated with the host's ability to control virus replication and persistence. Despite the absence of significant differences in the transcriptome of Trm cells between Elite Controllers (ECs) and cART-treated (TX) patients at the single gene level, we found 353 gene ontology (GO) categories upregulated in EC compared with TX. Our results suggest the existence of mechanisms at two different levels: first boosting both adaptive and innate immune responses, and second promoting active viral replication and halting HIV latency in the Trm cell compartment of ECs as compared with TX patients. These differences in the transcriptional profile of Trm cells could be involved in the lower HIV reservoir observed in ECs compared with TX individuals, although mechanistic studies are needed to confirm this hypothesis. Combining transcriptome analysis and systems biology methods is likely to provide important findings to help us in the design of therapeutic strategies aimed at purging the HIV reservoir. KEY MESSAGES: HIV-elite controllers have the lowest HIV-DNA content in resting memory CD4 T cells. HIV-ECs show a particular transcriptional profile in resting memory CD4 T cells. Molecular mechanisms of enhanced adaptative and innate immune response in HIV-ECs. High viral replication and low viral latency establishment associate to the EC status.
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Affiliation(s)
- Marcial García
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Luis López-Fernández
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pablo Mínguez
- Bioinformatics Unit, Genetics Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | | | - Clara Restrepo
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - María A Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | | | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Isabel García
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alfonso Cabello
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | | | | | | | | | - Javier Martínez-Picado
- irsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Miguel Górgolas
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
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23
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Preclinical Development and Clinical-Scale Manufacturing of HIV Gag-Specific, LentivirusModified CD4 T Cells for HIV Functional Cure. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:1048-1060. [PMID: 32462053 PMCID: PMC7240062 DOI: 10.1016/j.omtm.2020.04.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Activation, infection, and eventual depletion of human immunodeficiency virus (HIV)-specific cluster of differentiation 4 (CD4) T cells are the crucial pathogenetic events in acquired immunodeficiency syndrome (AIDS). We developed a cell and gene therapy to reconstitute HIV-specific CD4 T cells and prevent their destruction by HIV. Antigen-specific CD4 T cells will provide helper functions to support antiviral cytotoxic T lymphocyte (CTL) function and the production of virus-specific antibodies. However, ex vivo expansion of HIV-specific CD4 T cells is poor and previous gene therapies focused on bulk CD4 T cells without enriching for an antigen-specific subset. We developed a method for manufacturing autologous CD4+ T cell products highly enriched with Gag-specific T cells. Rare Gag-specific CD4 T cells in peripheral blood mononuclear cells (PBMCs) were increased nearly 1,000-fold by stimulating PBMC with Gag peptides, followed by depleting nontarget cells and transducing with lentivirus vector AGT103 to protect against HIV-mediated depletion and inhibit HIV release from latently infected cells. The average percentage of HIV-specific CD4 cells in the final products was 15.13%, and the average yield was 7 × 108 cells. The protocol for clinical-scale manufacturing of HIV-specific and HIV-resistant CD4 T cells is an important step toward effective immunotherapy for HIV disease.
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24
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Khan N, Chen X, Geiger JD. Role of Divalent Cations in HIV-1 Replication and Pathogenicity. Viruses 2020; 12:E471. [PMID: 32326317 PMCID: PMC7232465 DOI: 10.3390/v12040471] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/09/2020] [Accepted: 04/18/2020] [Indexed: 12/22/2022] Open
Abstract
Divalent cations are essential for life and are fundamentally important coordinators of cellular metabolism, cell growth, host-pathogen interactions, and cell death. Specifically, for human immunodeficiency virus type-1 (HIV-1), divalent cations are required for interactions between viral and host factors that govern HIV-1 replication and pathogenicity. Homeostatic regulation of divalent cations' levels and actions appear to change as HIV-1 infection progresses and as changes occur between HIV-1 and the host. In people living with HIV-1, dietary supplementation with divalent cations may increase HIV-1 replication, whereas cation chelation may suppress HIV-1 replication and decrease disease progression. Here, we review literature on the roles of zinc (Zn2+), iron (Fe2+), manganese (Mn2+), magnesium (Mg2+), selenium (Se2+), and copper (Cu2+) in HIV-1 replication and pathogenicity, as well as evidence that divalent cation levels and actions may be targeted therapeutically in people living with HIV-1.
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Affiliation(s)
| | | | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA; (N.K.); (X.C.)
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25
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Trypsteen W, White CH, Mukim A, Spina CA, De Spiegelaere W, Lefever S, Planelles V, Bosque A, Woelk CH, Vandekerckhove L, Beliakova-Bethell N. Long non-coding RNAs and latent HIV - A search for novel targets for latency reversal. PLoS One 2019; 14:e0224879. [PMID: 31710657 PMCID: PMC6844474 DOI: 10.1371/journal.pone.0224879] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/23/2019] [Indexed: 12/23/2022] Open
Abstract
The latent cellular reservoir of HIV is recognized as the major barrier to cure from HIV infection. Long non-coding RNAs (lncRNAs) are more tissue and cell type-specific than protein coding genes, and may represent targets of choice for HIV latency reversal. Using two in vitro primary T-cell models, we identified lncRNAs dysregulated in latency. PVT1 and RP11-347C18.3 were up-regulated in common between the two models, and RP11-539L10.2 was down-regulated. The major component of the latent HIV reservoir, memory CD4+ T-cells, had higher expression of these lncRNAs, compared to naïve T-cells. Guilt-by-association analysis demonstrated that lncRNAs dysregulated in latency were associated with several cellular pathways implicated in HIV latency establishment and maintenance: proteasome, spliceosome, p53 signaling, and mammalian target of rapamycin (MTOR). PVT1, RP11-347C18.3, and RP11-539L10.2 were down-regulated by latency reversing agents, suberoylanilide hydroxamic acid and Romidepsin, suggesting that modulation of lncRNAs is a possible secondary mechanism of action of these compounds. These results will facilitate prioritization of lncRNAs for evaluation as targets for HIV latency reversal. Importantly, our study provides insights into regulatory function of lncRNA during latent HIV infection.
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Affiliation(s)
- Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Cory H. White
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
| | - Amey Mukim
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States of America
| | - Celsa A. Spina
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States of America
- Department of Pathology, University of California San Diego, La Jolla, CA, United States of America
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Sciences, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States of America
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, United States of America
| | - Christopher H. Woelk
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nadejda Beliakova-Bethell
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States of America
- Department of Medicine, University of California San Diego, La Jolla, CA, United States of America
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26
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Díez-Fuertes F, De La Torre-Tarazona HE, Calonge E, Pernas M, Alonso-Socas MDM, Capa L, García-Pérez J, Sakuntabhai A, Alcamí J. Transcriptome Sequencing of Peripheral Blood Mononuclear Cells from Elite Controller-Long Term Non Progressors. Sci Rep 2019; 9:14265. [PMID: 31582776 PMCID: PMC6776652 DOI: 10.1038/s41598-019-50642-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/12/2019] [Indexed: 11/24/2022] Open
Abstract
The elite controller (EC)-long term non-progressor (LTNP) phenotype represent a spontaneous and advantageous model of HIV-1 control in the absence of therapy. The transcriptome of peripheral blood mononuclear cells (PBMCs) collected from EC-LTNPs was sequenced by RNA-Seq and compared with the transcriptomes from other phenotypes of disease progression. The transcript abundance estimation combined with the use of supervised classification algorithms allowed the selection of 20 genes and pseudogenes, mainly involved in interferon-regulated antiviral mechanisms and cell machineries of transcription and translation, as the best predictive genes of disease progression. Differential expression analyses between phenotypes showed an altered calcium homeostasis in EC-LTNPs evidenced by the upregulation of several membrane receptors implicated in calcium-signaling cascades and intracellular calcium-mobilization and by the overrepresentation of NFAT1/Elk-1-binding sites in the promoters of the genes differentially expressed in these individuals. A coordinated upregulation of host genes associated with HIV-1 reverse transcription and viral transcription was also observed in EC-LTNPs –i.e. p21/CDKN1A, TNF, IER3 and GADD45B. We also found an upregulation of ANKRD54 in EC-LTNPs and viremic LTNPs in comparison with typical progressors and a clear alteration of type-I interferon signaling as a consequence of viremia in typical progressors before and after receiving antiretroviral therapy.
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Affiliation(s)
- Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain. .,Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.
| | - Humberto Erick De La Torre-Tarazona
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain
| | - Esther Calonge
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain
| | - Maria Pernas
- Molecular Virology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain
| | | | - Laura Capa
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain
| | - Javier García-Pérez
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases, Pasteur Institute, 75015, Paris, France
| | - José Alcamí
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220, Majadahonda, Madrid, Spain. .,Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.
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27
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Gebara NY, El Kamari V, Rizk N. HIV-1 elite controllers: an immunovirological review and clinical perspectives. J Virus Erad 2019; 5:163-166. [PMID: 31700663 PMCID: PMC6816117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
HIV type 1 (HIV-1) elite controllers (ECs) represent a rare group of individuals with an ability to maintain an undetectable HIV-1 viral load overtime in the absence of previous antiretroviral therapy. The mechanisms associated with this paradigm remain not clearly defined. However, loss of virological control, morbidity and mortality persist in these individuals, such as progress to AIDS-defining conditions together with persistent high rate of immune activation. Further insight into potential therapeutic options is therefore warranted. In this review, we discuss recent data on the type of immune responses understood to be associated with chronic virological control, the potential for disease progression and therapeutic options in ECs.
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Affiliation(s)
- Nour Y Gebara
- Faculty of Medicine,
American University of Beirut,
Medical Center,
Lebanon
| | - Vanessa El Kamari
- Division Reserve University,
University Hospitals Cleveland Medical Center and Case Western University,
OH,
USA
| | - Nesrine Rizk
- Faculty of Medicine,
American University of Beirut,
Medical Center,
Lebanon,Department of Internal Medicine,
Division of Infectious Diseases,
American University of Beirut Medical Center,
Lebanon,Corresponding author: Nesrine Rizk
Department of Internal Medicine,
Division of Infectious Diseases,
American University of Beirut Medical Center,
PO Box 11-0236, Riad El Solh 1107 2020,
Beirut,
Lebanon
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28
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Abstract
HIV-1 has evolved many strategies to circumvent the host’s antiviral innate immune responses and establishes disseminated infection; the molecular mechanisms of these strategies are not entirely clear. We showed previously that USP18 contributes to HIV-1 replication by abrogating p21 antiviral function. Here, we demonstrate a mechanism by which USP18 mediates p21 downregulation in myeloid cells. USP18, by its protease activity, accumulates misfolded p53, which requires ISG15 for clearance. Depletion of ISG15 causes accumulation of misfolded dominant negative p53, which supports HIV-1 replication. This work clarifies the function and consequences of p53 modification by ISG15 and implicates USP18 in HIV-1 infection and potentially in carcinogenesis. Macrophages and dendritic cells dominate early immune responses to lentiviruses. HIV-1 sensing by pathogen recognition receptors induces signaling cascades that culminate in type I alpha/beta interferon (IFN-α/β) induction. IFN-α/β signals back via the IFN-α/β receptors, inducing a plethora of IFN-stimulated gene (ISGs), including ISG15, p53, and p21Cip1. p21 inhibits HIV-1 replication by inactivating the deoxynucleoside triphosphate (dNTP) biosynthesis pathway and activating the restriction factor SAMHD1. p21 is induced by functional p53. ISG15-specific isopeptidase USP18 negatively regulates IFN signaling. We showed previously that USP18 contributes to HIV-1 replication by abrogating p21 antiviral function. Here, we demonstrate a mechanism by which USP18 mediates p21 downregulation in myeloid cells. USP18, by its protease activity, accumulates misfolded p53, which requires ISG15 for its degradation. Depletion of ISG15 causes accumulation of misfolded dominant negative p53, which enhances HIV-1 replication. This work clarifies the function and consequences of p53 modification by ISG15 and implicates USP18 in HIV-1 infection and potentially in carcinogenesis.
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29
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Kulkarni S, Lied A, Kulkarni V, Rucevic M, Martin MP, Walker-Sperling V, Anderson SK, Ewy R, Singh S, Nguyen H, McLaren PJ, Viard M, Naranbhai V, Zou C, Lin Z, Gatanaga H, Oka S, Takiguchi M, Thio CL, Margolick J, Kirk GD, Goedert JJ, Hoots WK, Deeks SG, Haas DW, Michael N, Walker B, Le Gall S, Chowdhury FZ, Yu XG, Carrington M. CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome. Nat Immunol 2019; 20:824-834. [PMID: 31209403 PMCID: PMC6584055 DOI: 10.1038/s41590-019-0406-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/25/2019] [Indexed: 12/16/2022]
Abstract
Multiple genome-wide studies have identified associations between outcome of human immunodeficiency virus (HIV) infection and polymorphisms in and around the gene encoding the HIV co-receptor CCR5, but the functional basis for the strongest of these associations, rs1015164A/G, is unknown. We found that rs1015164 marks variation in an activating transcription factor 1 binding site that controls expression of the antisense long noncoding RNA (lncRNA) CCR5AS. Knockdown or enhancement of CCR5AS expression resulted in a corresponding change in CCR5 expression on CD4+ T cells. CCR5AS interfered with interactions between the RNA-binding protein Raly and the CCR5 3' untranslated region, protecting CCR5 messenger RNA from Raly-mediated degradation. Reduction in CCR5 expression through inhibition of CCR5AS diminished infection of CD4+ T cells with CCR5-tropic HIV in vitro. These data represent a rare determination of the functional importance of a genome-wide disease association where expression of a lncRNA affects HIV infection and disease progression.
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Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
| | - Alexandra Lied
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Viraj Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Marijana Rucevic
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Olink Proteomic, Watertown, MA, USA
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Victoria Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rodger Ewy
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Hoang Nguyen
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Paul J McLaren
- J.C. Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vivek Naranbhai
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Chengcheng Zou
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Zhansong Lin
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Chloe L Thio
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Margolick
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - W Keith Hoots
- Division of Blood Diseases and Resources, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven G Deeks
- San Francisco General Hospital Medical Center, San Francisco, CA, USA
| | - David W Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Fatema Z Chowdhury
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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31
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Garcia-Vidal E, Badia R, Pujantell M, Castellví M, Felip E, Clotet B, Riveira-Muñoz E, Ballana E, Esté JA. Dual effect of the broad spectrum kinase inhibitor midostaurin in acute and latent HIV-1 infection. Antiviral Res 2019; 168:18-27. [PMID: 31077767 DOI: 10.1016/j.antiviral.2019.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/03/2019] [Accepted: 05/07/2019] [Indexed: 01/26/2023]
Abstract
Midostaurin is a multi-kinase inhibitor with antineoplastic activity. We assessed the capacity of midostaurin to affect early and late steps of HIV-1 infection and to reactivate HIV-1 latently infected cells, alone or in combination with histone deacetylase inhibitors (HDACi) known to act as latency-reversing agents (LRA). Acute HIV-1 infection was assessed by flow cytometry in three cell types treated with midostaurin in the presence or absence of SAMHD1. Non-infected cells were treated with midostaurin and harvested for Western blot analysis. Macrophage infections were also measured by quantitative RT-PCR. HIV-1 latency reactivation was assessed in several latency models. Midostaurin induced G2/M arrest and inhibited CDK2, preventing the phosphorylation of SAMHD1 associated to inhibition of its dNTPase activity. In the presence of SAMHD1, midostaurin blocked HIV-1 DNA formation and viral replication. However, following Vpx-mediated SAMHD1 degradation, midostaurin increased viral transcripts and virus replication. In three out of four HIV-1 latency models, including primary CD4+ T cells, midostaurin effectively reversed HIV-1 latency and was synergistic in combination with LRA vorinostat and panobinostat. Our study describes a dual effect for midostaurin in HIV-1 infection, antiviral or proviral depending on SAMHD1 activation, and highlights a role for active SAMHD1 in regulating the activity of potential HIV-1 latency reversal agents.
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Affiliation(s)
- Edurne Garcia-Vidal
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Roger Badia
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Maria Pujantell
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Marc Castellví
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eudald Felip
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eva Riveira-Muñoz
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ester Ballana
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
| | - José A Esté
- AIDS Research Institute - IrsiCaixa, AIDS Unit and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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Gonzalo-Gil E, Rapuano PB, Ikediobi U, Leibowitz R, Mehta S, Coskun AK, Porterfield JZ, Lampkin TD, Marconi VC, Rimland D, Walker BD, Deeks S, Sutton RE. Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members. eLife 2019; 8:e44360. [PMID: 30964004 PMCID: PMC6456299 DOI: 10.7554/elife.44360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
HIV +Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4 +T cells with resistance specific to R5-tropic HIV, reversed after introduction of ccr5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4 +T cells of these EC/VCs had lower ccr2 and ccr5 RNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of ccr2 and ccr5, despite having more accessible chromatin by ATAC-seq. Other nearby genes were also down-regulated, over a region of ~500 kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with ccr2/ccr5 down-regulation, suggesting that the phenotype is heritable.
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Affiliation(s)
- Elena Gonzalo-Gil
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Patrick B Rapuano
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Uchenna Ikediobi
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Rebecca Leibowitz
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Sameet Mehta
- Yale Center for Genome Analysis Bioinformatics groupYale University School of MedicineNew HavenUnited States
| | - Ayse K Coskun
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - J Zachary Porterfield
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
| | - Teagan D Lampkin
- Infectious Diseases SectionDallas VA Medical CenterDallasUnited States
| | - Vincent C Marconi
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - David Rimland
- Atlanta VA Medical Center, Emory University School of MedicineAtlantaUnited States
| | - Bruce D Walker
- Ragon Institute of MGHMIT and Harvard UniversityCambridgeUnited States
| | - Steven Deeks
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Department of Epidemiology and BiostatisticsUniversity of California San FranciscoSan FranciscoUnited States
| | - Richard E Sutton
- Section of Infectious Diseases, Department of Internal MedicineYale University School of MedicineNew HavenUnited States
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Beliakova-Bethell N, Mukim A, White CH, Deshmukh S, Abewe H, Richman DD, Spina CA. Histone deacetylase inhibitors induce complex host responses that contribute to differential potencies of these compounds in HIV reactivation. J Biol Chem 2019; 294:5576-5589. [PMID: 30745362 PMCID: PMC6462528 DOI: 10.1074/jbc.ra118.005185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/07/2019] [Indexed: 12/23/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors (HDACis) have been widely tested in clinical trials for their ability to reverse HIV latency but have yielded only limited success. One HDACi, suberoylanilide hydroxamic acid (SAHA), exhibits off-target effects on host gene expression predicted to interfere with induction of HIV transcription. Romidepsin (RMD) has higher potency and specificity for class I HDACs implicated in maintaining HIV provirus in the latent state. More robust HIV reactivation has indeed been achieved with RMD use ex vivo than with SAHA; however, reduction of viral reservoir size has not been observed in clinical trials. Therefore, using RNA-Seq, we sought to compare the effects of SAHA and RMD on gene expression in primary CD4+ T cells. Among the genes whose expression was modulated by both HDACi agents, we identified genes previously implicated in HIV latency. Two genes, SMARCB1 and PARP1, whose modulation by SAHA and RMD is predicted to inhibit HIV reactivation, were evaluated in the major maturation subsets of CD4+ T cells and were consistently either up- or down-regulated by both HDACi compounds. Our results indicate that despite having different potencies and HDAC specificities, SAHA and RMD modulate an overlapping set of genes, implicated in HIV latency regulation. Some of these genes merit exploration as additional targets to improve the therapeutic outcomes of "shock and kill" strategies. The overall complexity of HDACi-induced responses among host genes with predicted stimulatory or inhibitory effects on HIV expression likely contributes to differential HDACi potencies and dictates the outcome of HIV reactivation.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Amey Mukim
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Cory H White
- the University of California San Diego, La Jolla, California 92093
| | - Savitha Deshmukh
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
| | - Hosiana Abewe
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Douglas D Richman
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
| | - Celsa A Spina
- From the Veterans Affairs San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California 92161 and
- the University of California San Diego, La Jolla, California 92093
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Jansons J, Sominskaya I, Petrakova N, Starodubova ES, Smirnova OA, Alekseeva E, Bruvere R, Eliseeva O, Skrastina D, Kashuba E, Mihailova M, Kochetkov SN, Ivanov AV, Isaguliants MG. The Immunogenicity in Mice of HCV Core Delivered as DNA Is Modulated by Its Capacity to Induce Oxidative Stress and Oxidative Stress Response. Cells 2019; 8:cells8030208. [PMID: 30823485 PMCID: PMC6468923 DOI: 10.3390/cells8030208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/06/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022] Open
Abstract
HCV core is an attractive HCV vaccine target, however, clinical or preclinical trials of core-based vaccines showed little success. We aimed to delineate what restricts its immunogenicity and improve immunogenic performance in mice. We designed plasmids encoding full-length HCV 1b core and its variants truncated after amino acids (aa) 60, 98, 152, 173, or up to aa 36 using virus-derived or synthetic polynucleotides (core191/60/98/152/173/36_191v or core152s DNA, respectively). We assessed their level of expression, route of degradation, ability to trigger the production of reactive oxygen species/ROS, and to activate the components of the Nrf2/ARE antioxidant defense pathway heme oxygenase 1/HO-1 and NAD(P)H: quinone oxidoreductase/Nqo-1. All core variants with the intact N-terminus induced production of ROS, and up-regulated expression of HO-1 and Nqo-1. The capacity of core variants to induce ROS and up-regulate HO-1 and Nqo-1 expression predetermined their immunogenicity in DNA-immunized BALB/c and C57BL/6 mice. The most immunogenic was core 152s, expressed at a modest level and inducing moderate oxidative stress and oxidative stress response. Thus, immunogenicity of HCV core is shaped by its ability to induce ROS and oxidative stress response. These considerations are important in understanding the mechanisms of viral suppression of cellular immune response and in HCV vaccine design.
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Affiliation(s)
- Juris Jansons
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| | - Irina Sominskaya
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Natalia Petrakova
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Elizaveta S Starodubova
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Olga A Smirnova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Ekaterina Alekseeva
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Ruta Bruvere
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Olesja Eliseeva
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Dace Skrastina
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Elena Kashuba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
- RE Kavetsky Institite of Experimental Pathology, Oncology and Radiobiology, The National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine.
| | - Marija Mihailova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Alexander V Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Maria G Isaguliants
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
- N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- MP Chumakov Center for Research and Development of Immune and Biological Preparations of RAS, 108819 Moscow, Russia.
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Couturier J, Orozco AF, Liu H, Budhiraja S, Siwak EB, Nehete PN, Sastry KJ, Rice AP, Lewis DE. Regulation of cyclin T1 during HIV replication and latency establishment in human memory CD4 T cells. Virol J 2019; 16:22. [PMID: 30786885 PMCID: PMC6381639 DOI: 10.1186/s12985-019-1128-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/12/2019] [Indexed: 01/30/2023] Open
Abstract
Background The regulatory cyclin, Cyclin T1 (CycT1), is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. The importance of CycT1 and the Positive Transcription Elongation Factor b (P-TEFb) complex for HIV replication is well-established, but regulation of CycT1 expression and protein levels during HIV replication and latency establishment in CD4 T cells is less characterized. Methods To better define the regulation of CycT1 levels during HIV replication in CD4 T cells, multiparameter flow cytometry was utilized to study the interaction between HIV replication (intracellular p24) and CycT1 of human peripheral blood memory CD4 T cells infected with HIV in vitro. CycT1 was further examined in CD4 T cells of human lymph nodes. Results In activated (CD3+CD28 costimulation) uninfected blood memory CD4 T cells, CycT1 was most significantly upregulated in maximally activated (CD69+CD25+ and HLA.DR+CD38+) cells. In memory CD4 T cells infected with HIV in vitro, two distinct infected populations of p24+CycT1+ and p24+CycT1- cells were observed during 7 days infection, suggestive of different phases of productive HIV replication and subsequent latency establishment. Intriguingly, p24+CycT1- cells were the predominant infected population in activated CD4 T cells, raising the possibility that productively infected cells may transition into latency subsequent to CycT1 downregulation. Additionally, when comparing infected p24+ cells to bystander uninfected p24- cells (after bulk HIV infections), HIV replication significantly increased T cell activation (CD69, CD25, HLA.DR, CD38, and Ki67) without concomitantly increasing CycT1 protein levels, possibly due to hijacking of P-TEFb by the viral Tat protein. Lastly, CycT1 was constitutively expressed at higher levels in lymph node CD4 T cells compared to blood T cells, potentially enhancing latency generation in lymphoid tissues. Conclusions CycT1 is most highly upregulated in maximally activated memory CD4 T cells as expected, but may become less associated with T cell activation during HIV replication. The progression into latency may further be predicated by substantial generation of p24+CycT1- cells during HIV replication. Electronic supplementary material The online version of this article (10.1186/s12985-019-1128-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacob Couturier
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Aaron F Orozco
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hongbing Liu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sona Budhiraja
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Edward B Siwak
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pramod N Nehete
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
| | - K Jagannadha Sastry
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew P Rice
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dorothy E Lewis
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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Cellular Determinants of HIV Persistence on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1075:213-239. [PMID: 30030795 DOI: 10.1007/978-981-13-0484-2_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The era of antiretroviral therapy has made HIV-1 infection a manageable chronic disease for those with access to treatment. Despite treatment, virus persists in tissue reservoirs seeded with long-lived infected cells that are resistant to cell death and immune recognition. Which cells contribute to this reservoir and which factors determine their persistence are central questions that need to be answered to achieve viral eradication. In this chapter, we describe how cell susceptibility to infection, resistance to cell death, and immune-mediated killing as well as natural cell life span and turnover potential are central components that allow persistence of different lymphoid and myeloid cell subsets that were recently identified as key players in harboring latent and actively replicating virus. The relative contribution of these subsets to persistence of viral reservoir is described, and the open questions are highlighted.
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Van Hecke C, Trypsteen W, Malatinkova E, De Spiegelaere W, Vervisch K, Rutsaert S, Kinloch-de Loes S, Sips M, Vandekerckhove L. Early treated HIV-1 positive individuals demonstrate similar restriction factor expression profile as long-term non-progressors. EBioMedicine 2019; 41:443-454. [PMID: 30770230 PMCID: PMC6442000 DOI: 10.1016/j.ebiom.2019.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- Clarissa Van Hecke
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Karen Vervisch
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Sabine Kinloch-de Loes
- Division of Infection and Immunitys, Royal Free Hospital and Royal Free Campus, University College London, Pont St, Hampstead, London NW3 2QG, United Kingdom
| | - Magdalena Sips
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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Lee SY, Park YK, Yoon CH, Kim K, Kim KC. Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. BMC Med Genomics 2019; 12:3. [PMID: 30626383 PMCID: PMC6325803 DOI: 10.1186/s12920-018-0443-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background In the absence of antiretroviral treatments (ARTs), a small group of individuals infected with HIV, including long-term non-progressors (LTNPs) who maintain high levels of CD4+ T cells for more than 7–10 years in the absence of ART and in particular a subgroup of LTNPs, elite controllers (ECs), who have low levels of viremia, remain clinically and/or immunologically stable for years. However, the mechanism of stable disease progression in LTNPs and ECs needs to be elucidated to help those infected with HIV-1 remain healthy. In this study, to identify the characteristics of gene expression profiles and biomarkers in LTNPs, we performed a meta-analysis using multiple gene expression profiles among LTNPs, individuals infected with HIV-1 without ART, individuals infected with HIV-1 with ART, and healthy controls. Methods The gene expression profiles obtained from the Gene Expression Omnibus (GEO) microarray data repositories were classified into three groups: LTNPs versus healthy controls (first group, 3 studies), LTNPs versus patients infected with HIV-1 without ART (second group, 3 studies), and LTNPs versus patients infected with HIV-1 with ART (third group, 3 studies). In addition, we considered a fourth group, patients infected with HIV-1 without ART versus healthy controls (3 studies), to exclude genes associated with HIV-1 infection in the three groups. For each group, we performed a meta-analysis using the RankProd method to identify and compare the differentially expressed genes (DEGs) in the three groups. Results We identified the 14 common DEGs in the three groups when comparing them with each other. Most belonged to immune responses, antigen processing and presentation, the interferon-gamma-mediated signaling pathway, and T cell co-stimulation. Of these DEGs, PHLDA1 was up-regulated and ACTB and ACTG1 were down-regulated in all three groups. However, the rest of the up- or down-regulated genes were discordant in the three groups. Additionally, ACTB and ACTG1 are known to inhibit viral assembly and production, and THBS1 is known to inhibit HIV-1 infection. Conclusions These results suggest that significant genes identified in a meta-analysis provide clues to the cause of delayed disease progression and give a deeper understanding of HIV pathogenesis in LTNPs. Electronic supplementary material The online version of this article (10.1186/s12920-018-0443-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sun Young Lee
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Yong Kwang Park
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Kisoon Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Kyung-Chang Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju, Chungbuk, 28159, Republic of Korea.
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Chen L, Keppler OT, Schölz C. Post-translational Modification-Based Regulation of HIV Replication. Front Microbiol 2018; 9:2131. [PMID: 30254620 PMCID: PMC6141784 DOI: 10.3389/fmicb.2018.02131] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.
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Affiliation(s)
- Lin Chen
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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Weydert C, van Heertum B, Dirix L, De Houwer S, De Wit F, Mast J, Husson SJ, Busschots K, König R, Gijsbers R, De Rijck J, Debyser Z. Y-box-binding protein 1 supports the early and late steps of HIV replication. PLoS One 2018; 13:e0200080. [PMID: 29995936 PMCID: PMC6040738 DOI: 10.1371/journal.pone.0200080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 06/19/2018] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) depends on cellular proteins, so-called cofactors, to complete its replication cycle. In search for new therapeutic targets we identified the DNA and RNA binding protein Y-box-binding Protein 1 (YB-1) as a cofactor supporting early and late steps of HIV replication. YB-1 depletion resulted in a 10-fold decrease in HIV-1 replication in different cell lines. Dissection of the replication defects revealed that knockdown of YB-1 is associated with a 2- to 5-fold decrease in virion production due to interference with the viral RNA metabolism. Using single-round virus infection experiments we demonstrated that early HIV-1 replication also depends on the cellular YB-1 levels. More precisely, using quantitative PCR and an in vivo nuclear import assay with fluorescently labeled viral particles, we showed that YB-1 knockdown leads to a block between reverse transcription and nuclear import of HIV-1. Interaction studies revealed that YB-1 associates with integrase, although a direct interaction with HIV integrase could not be unambiguously proven. In conclusion, our results indicate that YB-1 affects multiple stages of HIV replication. Future research on the interaction between YB-1 and the virus will reveal whether this protein qualifies as a new antiviral target.
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Affiliation(s)
- Caroline Weydert
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Bart van Heertum
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Lieve Dirix
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, KU Leuven, Belgium
| | - Stéphanie De Houwer
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Flore De Wit
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan Mast
- Veterinary and Agrochemical Research Centre, VAR-CODA-CERVA, Brussels, Belgium
| | - Steven J. Husson
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, 3000 Leuven, Belgium
- Systemic Physiological & Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, 2000 Antwerp, Belgium
| | - Katrien Busschots
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Rik Gijsbers
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jan De Rijck
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Zeger Debyser
- Division of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- * E-mail:
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Madlala P, Van de Velde P, Van Remoortel B, Vets S, Van Wijngaerden E, Van Laethem K, Gijsbers R, Schrijvers R, Debyser Z. Analysis of ex vivo HIV-1 infection in a controller-discordant couple. J Virus Erad 2018. [DOI: 10.1016/s2055-6640(20)30268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Madlala P, Van de Velde P, Van Remoortel B, Vets S, Van Wijngaerden E, Van Laethem K, Gijsbers R, Schrijvers R, Debyser Z. Analysis of ex vivo HIV-1 infection in a controller-discordant couple. J Virus Erad 2018; 4:170-173. [PMID: 30050679 PMCID: PMC6038135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Elite controllers (EC) are a rare group of individuals living with HIV-1 who naturally control HIV-1 replication to levels below the limit of detection without antiretroviral therapy (ART) and rarely progress to AIDS. The mechanisms contributing to this control remain incompletely elucidated. In the present study, we have assessed whether cellular host factors could modulate HIV-1 replication post-entry in a controller-discordant couple living with HIV-1. METHODS CD4 T cells from a controller-discordant couple, one partner being an EC and the other an HIV-1 progressor (PR), and healthy controls (HC) were isolated, activated and infected with VSV-G pseudotyped yellow fluorescent protein-encoding single-round HIV-1 virus (HIV-YFP). Viral reverse transcripts, 2-LTR circles and integrated proviral HIV-1 DNA were monitored by quantitative PCR (qPCR) and integration sites were analysed. We further measured LEDGF/p75 and p21 mRNA expression levels by qPCR. RESULTS Infection of activated CD4 T cells with HIV-YFP was reduced in EC compared with the PR partner, and HC. Evaluation of viral DNA forms suggested a block after entry and during the early steps of HIV-1 reverse transcription in EC. The integration site distribution pattern in EC, PR and HC was similar. The p21 expression in CD4 T cells of EC was elevated compared with the PR or HC, in line with previous work. CONCLUSIONS Our study suggests a reduced permissiveness to HIV-1 infection of CD4 T cells from EC due to a block of HIV-1 replication after entry and before integration that might contribute to the EC phenotype in our patient.
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Affiliation(s)
| | | | - Barbara Van Remoortel
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences,
KU Leuven,
Belgium
| | - Sofie Vets
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences,
KU Leuven,
Belgium
| | - Eric Van Wijngaerden
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology,
KU Leuven,
Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology,
KU Leuven,
Belgium
| | - Rik Gijsbers
- Laboratory of Clinical Immunology, Department of Microbiology and Immunology,
KU Leuven,
Belgium
| | - Rik Schrijvers
- Laboratory of Clinical Immunology, Department of Microbiology and Immunology,
KU Leuven,
Belgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences,
KU Leuven,
Belgium,Corresponding author: Zeger Debyser,
Kapucijnenvoer 33 VCTB+5, B-3000 Leuven,
Flanders,
Belgium
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43
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Kuo HH, Ahmad R, Lee GQ, Gao C, Chen HR, Ouyang Z, Szucs MJ, Kim D, Tsibris A, Chun TW, Battivelli E, Verdin E, Rosenberg ES, Carr SA, Yu XG, Lichterfeld M. Anti-apoptotic Protein BIRC5 Maintains Survival of HIV-1-Infected CD4 + T Cells. Immunity 2018; 48:1183-1194.e5. [PMID: 29802019 DOI: 10.1016/j.immuni.2018.04.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/17/2018] [Accepted: 04/02/2018] [Indexed: 01/16/2023]
Abstract
HIV-1 infection of CD4+ T cells leads to cytopathic effects and cell demise, which is counter to the observation that certain HIV-1-infected cells possess a remarkable long-term stability and can persist lifelong in infected individuals treated with suppressive antiretroviral therapy (ART). Using quantitative mass spectrometry-based proteomics, we showed that HIV-1 infection activated cellular survival programs that were governed by BIRC5, a molecular inhibitor of cell apoptosis that is frequently overexpressed in malignant cells. BIRC5 and its upstream regulator OX40 were upregulated in productively and latently infected CD4+ T cells and were functionally involved in maintaining their viability. Moreover, OX40-expressing CD4+ T cells from ART-treated patients were enriched for clonally expanded HIV-1 sequences, and pharmacological inhibition of BIRC5 resulted in a selective decrease of HIV-1-infected cells in vitro. Together, these findings suggest that BIRC5 supports long-term survival of HIV-1-infected cells and may lead to clinical strategies to reduce persisting viral reservoirs.
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Affiliation(s)
- Hsiao-Hsuan Kuo
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Rushdy Ahmad
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Guinevere Q Lee
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hsiao-Rong Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew J Szucs
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Dhohyung Kim
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD 20892, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
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44
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Shi B, Sharifi HJ, DiGrigoli S, Kinnetz M, Mellon K, Hu W, de Noronha CMC. Inhibition of HIV early replication by the p53 and its downstream gene p21. Virol J 2018; 15:53. [PMID: 29587790 PMCID: PMC5870690 DOI: 10.1186/s12985-018-0959-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 03/07/2018] [Indexed: 11/10/2022] Open
Abstract
Background The tumor suppressor gene p53 has been found to suppress HIV infection by various mechanisms, but the inhibition of HIV at an early stage of replication by host cell p53 and its downstream gene p21 has not been well studied. Method VSV-G pseudotyped HIV-1 or HIV-2 viruses with GFP or luciferase reporter gene were used to infect HCT116 p53+/+ cells, HCT116 p53−/− cells and hMDMs. The infections were detected by flow cytometry or measured by luciferase assay. Reverse transcription products were quantified by a TaqMan real time PCR. siRNA knockdown experiments were applied to study potential roles of p53 and p21 genes in their restriction to HIV infection. Western blot experiments were used to analyze changes in gene expression. Results The infection of HIV-1 was inhibited in HCT116 p53+/+ cells in comparison to HCT116 p53−/− cells. The fold of inhibition was largely increased when cell cycle switched from cycling to non-cycling status. Further analysis showed that both p53 and p21 expressions were upregulated in non-cycling HCT116 p53+/+ cells and HIV-1 reverse transcription was subsequently inhibited. siRNA knockdown of either p53 or p21 rescued HIV-1 reverse transcription from the inhibition in non-cycling HCT116 p53+/+ cells. It was identified that the observed restrictions by p53 and p21 were associated with the suppression of RNR2 expression and phosphorylation of SAMHD1. These observations were confirmed by using siRNA knockdown experiments. In addition, p53 also inhibited HIV-2 infection in HCT116 p53+/+ cells and siRNA knockdown of p21 increased HIV-2 infection in hMDMs. Finally the expressions of p53 and p21 were found to be induced in hMDMs shortly after HIV-1 infection. Conclusions The p53 and its downstream gene p21 interfere with HIV early stage of replication in non-cycling cells and hMDMs.
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Affiliation(s)
- Binshan Shi
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Ave, Albany, NY, 12208, USA.
| | - Hamayun J Sharifi
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Ave, Albany, NY, 12208, USA
| | - Sara DiGrigoli
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Ave, Albany, NY, 12208, USA
| | - Michaela Kinnetz
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Ave, Albany, NY, 12208, USA
| | - Katie Mellon
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Ave, Albany, NY, 12208, USA
| | - Wenwei Hu
- Rutgers Cancer Institute of New Jersey, Rutgers the State University of New Jersey, New Brunswick, NJ, 08903, USA
| | - Carlos M C de Noronha
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, Albany, NY, 12208, USA
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45
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Are microRNAs Important Players in HIV-1 Infection? An Update. Viruses 2018; 10:v10030110. [PMID: 29510515 PMCID: PMC5869503 DOI: 10.3390/v10030110] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 has already claimed over 35 million human lives globally. No curative treatments are currently available, and the only treatment option for over 36 million people currently living with HIV/AIDS are antiretroviral drugs that disrupt the function of virus-encoded proteins. However, such virus-targeted therapeutic strategies are constrained by the ability of the virus to develop drug-resistance. Despite major advances in HIV/AIDS research over the years, substantial knowledge gaps exist in many aspects of HIV-1 replication, especially its interaction with the host. Hence, understanding the mechanistic details of virus–host interactions may lead to novel therapeutic strategies for the prevention and/or management of HIV/AIDS. Notably, unprecedented progress in deciphering host gene silencing processes mediated by several classes of cellular small non-coding RNAs (sncRNA) presents a promising and timely opportunity for developing non-traditional antiviral therapeutic strategies. Cellular microRNAs (miRNA) belong to one such important class of sncRNAs that regulate protein synthesis. Evidence is mounting that cellular miRNAs play important roles in viral replication, either usurped by the virus to promote its replication or employed by the host to control viral infection by directly targeting the viral genome or by targeting cellular proteins required for productive virus replication. In this review, we summarize the findings to date on the role of miRNAs in HIV-1 biology.
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46
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Barrett AJ, Prockop S, Bollard CM. Reprint of: Virus-Specific T Cells: Broadening Applicability. Biol Blood Marrow Transplant 2018; 24:S1-S6. [PMID: 29425515 DOI: 10.1016/j.bbmt.2017.12.787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 01/03/2023]
Abstract
Virus infection remains an appreciable cause of morbidity and mortality after hematopoietic stem cell transplantation (HSCT). Although pharmacotherapy and/or antibody therapy may help prevent or treat viral disease, these drugs are expensive, toxic, and often ineffective due to primary or secondary resistance. Further, effective treatments are limited for many infections (eg, adenovirus, BK virus), which are increasingly detected after alternative donor transplants. These deficiencies in conventional therapeutics have increased interest in an immunotherapeutic approach to viral disorders, leading to adoptive transfer of virus-specific cytotoxic T lymphocytes (VSTs), which can rapidly reconstitute antiviral immunity post-transplantation without causing graft-versus-host disease. This review will explore how the VST field has improved outcomes for many patients with life-threatening viral infections after HSCT, and how to broaden applicability beyond the "patient-specific" products, as well as extending to other viral diseases even outside the context of HSCT.
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Affiliation(s)
- A John Barrett
- Stem Cell Allotransplantation Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Susan Prockop
- Pediatric BMT Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Departments of Pediatrics and Microbiology, Immunology and Tropical Medicine, Children's National Medical Center and The George Washington University, Washington, District of Columbia.
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47
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T cells with low CD2 levels express reduced restriction factors and are preferentially infected in therapy naïve chronic HIV-1 patients. J Int AIDS Soc 2018; 20:21865. [PMID: 28953327 PMCID: PMC5964667 DOI: 10.7448/ias.20.1.21865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Restriction factors (RFs) suppress HIV-1 in cell lines and primary cell models. Hence, RFs might be attractive targets for novel antiviral strategies, but their importance for virus control in vivo is controversial. METHODS We profiled the expression of RFs in primary blood-derived mononuclear cells (PBMC) from therapy-naïve HIV-1 patients and quantified infection. RESULTS Overall, there was no correlation between individual RF expression and HIV-1 status in total PBMC. However, we identified a T cell population with low levels of intracellular CD2 and reduced expression of SAMHD1, p21 and SerinC5. CD2low T cells with reduced RF expression were markedly positive for HIV-1 p24. In contrast, CD2+ T cells were less infected and expressed higher levels of RFs. CD2low T cell infection correlated with viral loads and was associated with HIV-1 disease progression. CONCLUSIONS In untreated therapy naïve chronic HIV-1 patients, RF expression in T cells is associated with CD2 expression and seems to influence viral loads. Our study suggests that RFs help to control HIV-1 infection in certain T cells in vivo and supports the potential for RFs as promising targets for therapeutic intervention.
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48
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Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Genome Biol 2018; 19:10. [PMID: 29378643 PMCID: PMC5789701 DOI: 10.1186/s13059-017-1385-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 12/23/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. RESULTS To overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification. Applying it, we discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. By integrating information from existing genomic databases into our reproducibility-based analysis, we identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells from healthy individuals in vitro. CONCLUSIONS Overall, our results demonstrate how single-cell approaches can reveal previously unappreciated, yet important, immune behaviors and empower rational frameworks for modulating systems-level immune responses that may prove therapeutically and prophylactically useful.
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Affiliation(s)
| | - Michael B Cole
- Department of Physics, University of California, Berkeley, CA, USA
| | - Kellie E Kolb
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhengyu Ouyang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Samuel W Kazer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Electrical Engineering & Computer Sciences, UC Berkeley, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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Abstract
Retroviruses are genome invaders that have shared a long history of coevolution with vertebrates and their immune system. Found endogenously in genomes as traces of past invasions, retroviruses are also considerable threats to human health when they exist as exogenous viruses such as HIV. The immune response to retroviruses is engaged by germline-encoded sensors of innate immunity that recognize viral components and damage induced by the infection. This response develops with the induction of antiviral effectors and launching of the clonal adaptive immune response, which can contribute to protective immunity. However, retroviruses efficiently evade the immune response, owing to their rapid evolution. The failure of specialized immune cells to respond, a form of neglect, may also contribute to inadequate antiretroviral immune responses. Here, we discuss the mechanisms by which immune responses to retroviruses are mounted at the molecular, cellular, and organismal levels. We also discuss how intrinsic, innate, and adaptive immunity may cooperate or conflict during the generation of immune responses.
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Affiliation(s)
- Asier Sáez-Cirión
- HIV Inflammation and Persistence, Institut Pasteur, 75015 Paris, France;
| | - Nicolas Manel
- Immunity and Cancer Department, INSERM U932, Institut Curie, PSL Research University, 75005 Paris, France;
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50
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p21 Restricts HIV-1 in Monocyte-Derived Dendritic Cells through the Reduction of Deoxynucleoside Triphosphate Biosynthesis and Regulation of SAMHD1 Antiviral Activity. J Virol 2017; 91:JVI.01324-17. [PMID: 28931685 DOI: 10.1128/jvi.01324-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023] Open
Abstract
HIV-1 infection of noncycling cells, such as dendritic cells (DCs), is impaired due to limited availability of deoxynucleoside triphosphates (dNTPs), which are needed for HIV-1 reverse transcription. The levels of dNTPs are tightly regulated during the cell cycle and depend on the balance between dNTP biosynthesis and degradation. SAMHD1 potently blocks HIV-1 replication in DCs, although the underlying mechanism is still unclear. SAMHD1 has been reported to be able to degrade dNTPs and viral nucleic acids, which may both hamper HIV-1 reverse transcription. The relative contribution of these activities may differ in cycling and noncycling cells. Here, we show that inhibition of HIV-1 replication in monocyte-derived DCs (MDDCs) is associated with an increased expression of p21cip1/waf, a cell cycle regulator that is involved in the differentiation and maturation of DCs. Induction of p21 in MDDCs decreases the pool of dNTPs and increases the antiviral active isoform of SAMHD1. Although both processes are complementary in inhibiting HIV-1 replication, the antiviral activity of SAMHD1 in our primary cell model appears to be, at least partially, independent of its dNTPase activity. The reduction in the pool of dNTPs in MDDCs appears rather mostly due to a p21-mediated suppression of several enzymes involved in dNTP synthesis (i.e., RNR2, TYMS, and TK-1). These results are important to better understand the interplay between HIV-1 and DCs and may inform the design of new therapeutic approaches to decrease viral dissemination and improve immune responses against HIV-1.IMPORTANCE DCs play a key role in the induction of immune responses against HIV. However, HIV has evolved ways to exploit these cells, facilitating immune evasion and virus dissemination. We have found that the expression of p21, a cyclin-dependent kinase inhibitor involved in cell cycle regulation and monocyte differentiation and maturation, potentially can contribute to the inhibition of HIV-1 replication in monocyte-derived DCs through multiple mechanisms. p21 decreased the size of the intracellular dNTP pool. In parallel, p21 prevented SAMHD1 phosphorylation and promoted SAMHD1 dNTPase-independent antiviral activity. Thus, induction of p21 resulted in conditions that allowed the effective inhibition of HIV-1 replication through complementary mechanisms. Overall, p21 appears to be a key regulator of HIV infection in myeloid cells.
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