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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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2
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Suryawanshi GW, Arokium H, Kim S, Khamaikawin W, Lin S, Shimizu S, Chupradit K, Lee Y, Xie Y, Guan X, Suryawanshi V, Presson AP, An DS, Chen ISY. Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias. Stem Cell Res Ther 2021; 12:528. [PMID: 34620229 PMCID: PMC8499514 DOI: 10.1186/s13287-021-02601-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Current understanding of hematopoiesis is largely derived from mouse models that are physiologically distant from humans. Humanized mice provide the most physiologically relevant small animal model to study human diseases, most notably preclinical gene therapy studies. However, the clonal repopulation dynamics of human hematopoietic stem and progenitor cells (HSPC) in these animal models is only partially understood. Using a new clonal tracking methodology designed for small sample volumes, we aim to reveal the underlying clonal dynamics of human cell repopulation in a mouse environment. METHODS Humanized bone marrow-liver-thymus (hu-BLT) mice were generated by transplanting lentiviral vector-transduced human fetal liver HSPC (FL-HSPC) in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice implanted with a piece of human fetal thymus. We developed a methodology to track vector integration sites (VIS) in a mere 25 µl of mouse blood for longitudinal and quantitative clonal analysis of human HSPC repopulation in mouse environment. We explored transcriptional and epigenetic features of human HSPC for possible VIS bias. RESULTS A total of 897 HSPC clones were longitudinally tracked in hu-BLT mice-providing a first-ever demonstration of clonal dynamics and coordinated expansion of therapeutic and control vector-modified human cell populations simultaneously repopulating in the same humanized mice. The polyclonal repopulation stabilized at 19 weeks post-transplant and the contribution of the largest clone doubled within 4 weeks. Moreover, 550 (~ 60%) clones persisted over 6 weeks and were highly shared between different organs. The normal clonal profiles confirmed the safety of our gene therapy vectors. Multi-omics analysis of human FL-HSPC revealed that 54% of vector integrations in repopulating clones occurred within ± 1 kb of H3K36me3-enriched regions. CONCLUSIONS Human repopulation in mice is polyclonal and stabilizes more rapidly than that previously observed in humans. VIS preference for H3K36me3 has no apparent negative effects on HSPC repopulation. Our study provides a methodology to longitudinally track clonal repopulation in small animal models extensively used for stem cell and gene therapy research and with lentiviral vectors designed for clinical applications. Results of this study provide a framework for understanding the clonal behavior of human HPSC repopulating in a mouse environment, critical for translating results from humanized mice models to the human settings.
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Affiliation(s)
- Gajendra W Suryawanshi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Hubert Arokium
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Sanggu Kim
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Wannisa Khamaikawin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Samantha Lin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Saki Shimizu
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | | | - YooJin Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Yiming Xie
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Xin Guan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Vasantika Suryawanshi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Angela P Presson
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, 84108, USA
- Department of Biostatistics, University of California, Los Angeles, 90095, USA
| | - Dong-Sung An
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Irvin S Y Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA.
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA.
- Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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3
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Yeh YHJ, Yang K, Razmi A, Ho YC. The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence. Viruses 2021; 13:1858. [PMID: 34578439 PMCID: PMC8473165 DOI: 10.3390/v13091858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
More than 50% of the HIV-1 latent reservoir is maintained by clonal expansion. The clonally expanded HIV-1-infected cells can contribute to persistent nonsuppressible low-level viremia and viral rebound. HIV-1 integration site and proviral genome landscape profiling reveals the clonal expansion dynamics of HIV-1-infected cells. In individuals under long-term suppressive antiretroviral therapy (ART), HIV-1 integration sites are enriched in specific locations in certain cancer-related genes in the same orientation as the host transcription unit. Single-cell transcriptome analysis revealed that HIV-1 drives aberrant cancer-related gene expression through HIV-1-to-host RNA splicing. Furthermore, the HIV-1 promoter dominates over the host gene promoter and drives high levels of cancer-related gene expression. When HIV-1 integrates into cancer-related genes and causes gain of function of oncogenes or loss of function of tumor suppressor genes, HIV-1 insertional mutagenesis drives the proliferation of HIV-1-infected cells and may cause cancer in rare cases. HIV-1-driven aberrant cancer-related gene expression at the integration site can be suppressed by CRISPR-mediated inhibition of the HIV-1 promoter or by HIV-1 suppressing agents. Given that ART does not suppress HIV-1 promoter activity, therapeutic agents that suppress HIV-1 transcription and halt the clonal expansion of HIV-1-infected cells should be explored to block the clonal expansion of the HIV-1 latent reservoir.
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Affiliation(s)
| | | | | | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA; (Y.-H.J.Y.); (K.Y.); (A.R.)
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Xue W, Zheng X, Hu X, Zhang Y. Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma. Am J Mens Health 2021; 15:15579883211011380. [PMID: 33906487 PMCID: PMC8108076 DOI: 10.1177/15579883211011380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
To study the differential gene expression and clinical significance in human immunodeficiency virus-infected individuals (HIVIIs) with penile squamous cell carcinoma. At our hospital from 2019 to 2020, we selected six samples of HIV-related penile squamous cell carcinoma for the experimental group and six samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential Gene Ontology (GO) enrichment analysis and differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out, and the reads per kilobase per million reads (RPKM) value was used as a measure of gene expression. A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1 and p value <.05). On the basis of the significance of the GO enrichment analysis, we found that the tumor protein p63 (TP63) gene was significantly upregulated and that the LIM domain only 4 (LMO4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and cell adhesion molecule (CAM) metabolism was the most significant pathway associated with the downregulated genes. The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of non-AIDS-defining cancers (NADCs). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.
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Affiliation(s)
- Wenrui Xue
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
| | - Xin Zheng
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
| | - Xiaopeng Hu
- Beijing Chaoyang Hospital of Capital Medical University, Chaoyang District, Beijing China
| | - Yu Zhang
- Beijing Youan Hospital of Capital Medical University, Fengtai District, Beijing China
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Ferreira RC, Prodger JL, Redd AD, Poon AFY. Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir. Virus Evol 2021; 7:veaa104. [PMID: 33505711 PMCID: PMC7816690 DOI: 10.1093/ve/veaa104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Among people living with human immunodeficiency virus type 1 (HIV-1), the long-term persistence of a population of cells carrying transcriptionally silent integrated viral DNA (provirus) remains the primary barrier to developing an effective cure. Ongoing cell division via proliferation is generally considered to be the driving force behind the persistence of this latent HIV-1 reservoir. The contribution of this mechanism (clonal expansion) is supported by the observation that proviral sequences sampled from the reservoir are often identical. This outcome is quantified as the ‘clonality’ of the sample population, e.g. the fraction of provirus sequences observed more than once. However, clonality as a quantitative measure is inconsistently defined and its statistical properties are not well understood. In this Reflections article, we use mathematical and phylogenetic frameworks to formally examine the inherent problems of using clonality to characterize the dynamics and proviral composition of the reservoir. We describe how clonality is not adequate for this task due to the inherent complexity of how infected cells are ‘labeled’ by proviral sequences—the outcome of a sampling process from the evolutionary history of active viral replication before treatment—as well as variation in cell birth and death rates among lineages and over time. Lastly, we outline potential directions in statistical and phylogenetic research to address these issues.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, 1151 Richmond Street London, ON, Canada
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5640 Fishers Lane Rockville, MD 20852, USA.,Department of Medicine, Johns Hopkins School of Medicine, 600 N. Wolfe Street Baltimore, MD 21205-2196, USA
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street London, ON, Canada
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Wu VH, Nobles CL, Kuri-Cervantes L, McCormick K, Everett JK, Nguyen S, Del Rio Estrada PM, González-Navarro M, Torres-Ruiz F, Ávila-Ríos S, Reyes-Terán G, Bushman FD, Betts MR. Assessment of HIV-1 integration in tissues and subsets across infection stages. JCI Insight 2020; 5:139783. [PMID: 32970634 PMCID: PMC7605534 DOI: 10.1172/jci.insight.139783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/17/2020] [Indexed: 12/19/2022] Open
Abstract
The integration of HIV DNA into the host genome contributes to lifelong infection in most individuals. Few studies have examined integration in lymphoid tissue, where HIV predominantly persists before and after antiretroviral treatment (ART). Of particular interest is whether integration site distributions differ between infection stages with paired blood and tissue comparisons. Here, we profiled HIV integration site distributions in sorted memory, tissue-resident, and/or follicular helper CD4+ T cell subsets from paired blood and lymphoid tissue samples from acute, chronic, and ART-treated individuals. We observed minor differences in the frequency of nonintronic and nondistal intergenic sites, varying with tissue and residency phenotypes during ART. Genomic and epigenetic annotations were generally similar. Clonal expansion of cells marked by identical integration sites was detected, with increased detection in chronic and ART-treated individuals. However, overlap between or within CD4+ T cell subsets or tissue compartments was only observed in 8 unique sites of the 3540 sites studied. Together, these findings suggest that shared integration sites between blood and tissue may, depending on the tissue site, be the exception rather than the rule and indicate that additional studies are necessary to fully understand the heterogeneity of tissue-sequestered HIV reservoirs.
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Affiliation(s)
- Vincent H Wu
- Department of Microbiology and.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Leticia Kuri-Cervantes
- Department of Microbiology and.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Son Nguyen
- Department of Microbiology and.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Perla M Del Rio Estrada
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio González-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | | | - Michael R Betts
- Department of Microbiology and.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Hughes K, Akturk G, Gnjatic S, Chen B, Klotman M, Blasi M. Proliferation of HIV-infected renal epithelial cells following virus acquisition from infected macrophages. AIDS 2020; 34:1581-1591. [PMID: 32701578 PMCID: PMC7579771 DOI: 10.1097/qad.0000000000002589] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVES HIV-1 can infect and persist in different organs and tissues, resulting in the generation of multiple viral compartments and reservoirs. Increasing evidence supports the kidney as such a reservoir. Previous work demonstrated that HIV-1 infected CD4 T-cells transfer virus to renal tubule epithelial (RTE) cells through cell-to-cell contact. In addition to CD4 T cells, macrophages represent the other major target of HIV-1. Renal macrophages induce and regulate inflammatory responses and are critical to homeostatic regulation of the kidney environment. Combined with their ability to harbour virus, macrophages may also play an important role in the spread of HIV-1 infection in the kidney. DESIGN AND METHODS Multiparametric histochemistry analysis was performed on kidney biopsies from individuals with HIV-1 associated nephropathy (HIVAN). Primary monocyte-derived macrophages were infected with a GFP-expressing replication competent HIV-1. HIV-1 transfer from macrophages to RTE cells was carried out in a coculture system and evaluated by fluorescence-microscopy and flow-cytometry. Live imaging was performed to assess the fate of HIV-1 infected RTE cells over time. RESULTS We show that macrophages are abundantly present in the renal inflammatory infiltrate of individuals with HIVAN. We observed contact-dependent HIV-1 transfer from infected macrophages to both primary and immortalized renal cells. Live imaging of HIV-1 infected RTE cells revealed four different fates: proliferation, hypertrophy, latency and cell death. CONCLUSION Our study suggests that macrophages may play a role in the dissemination of HIV-1 in the kidney and that proliferation of infected renal cells may contribute to HIV-1 persistence in this compartment.
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Affiliation(s)
- Kelly Hughes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Guray Akturk
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Chen
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary Klotman
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Maria Blasi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
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Puronen CE, Ford ES, Uldrick TS. Immunotherapy in People With HIV and Cancer. Front Immunol 2019; 10:2060. [PMID: 31555284 PMCID: PMC6722204 DOI: 10.3389/fimmu.2019.02060] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
HIV infection alters the natural history of several cancers, in large part due to its effect on the immune system. Immune function in people living with HIV may vary from normal to highly dysfunctional and is largely dependent on the timing of initiation (and continuation) of effective antiretroviral therapy (ART). An individual's level of immune function in turn affects their cancer risk, management, and outcomes. HIV-associated lymphocytopenia and immune dysregulation permit immune evasion of oncogenic viruses and premalignant lesions and are associated with inferior outcomes in people with established cancers. Various types of immunotherapy, including monoclonal antibodies, interferon, cytokines, immunomodulatory drugs, allogeneic hematopoietic stem cell transplant, and most importantly ART have shown efficacy in HIV-related cancer. Emerging data suggest that checkpoint inhibitors targeting the PD-1/PD-L1 pathway can be safe and effective in people with HIV and cancer. Furthermore, some cancer immunotherapies may also affect HIV persistence by influencing HIV latency and HIV-specific immunity. Studying immunotherapy in people with HIV and cancer will advance clinical care of all people living with HIV and presents a unique opportunity to gain insight into mechanisms for HIV eradication.
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Affiliation(s)
- Camille E Puronen
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Emily S Ford
- Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Thomas S Uldrick
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Division of Global Oncology, Department of Medicine, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Ferris AL, Wells DW, Guo S, Del Prete GQ, Swanstrom AE, Coffin JM, Wu X, Lifson JD, Hughes SH. Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans. PLoS Pathog 2019; 15:e1007869. [PMID: 31291371 PMCID: PMC6619828 DOI: 10.1371/journal.ppat.1007869] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Clonal expansion of HIV infected cells plays an important role in the formation and persistence of the reservoir that allows the virus to persist, in DNA form, despite effective antiretroviral therapy. We used integration site analysis to ask if there is a similar clonal expansion of SIV infected cells in macaques. We show that the distribution of HIV and SIV integration sites in vitro is similar and that both viruses preferentially integrate in many of the same genes. We obtained approximately 8000 integration sites from blood samples taken from SIV-infected macaques prior to the initiation of ART, and from blood, spleen, and lymph node samples taken at necropsy. Seven clones were identified in the pre-ART samples; one persisted for a year on ART. An additional 100 clones were found only in on-ART samples; a number of these clones were found in more than one tissue. The timing and extent of clonal expansion of SIV-infected cells in macaques and HIV-infected cells in humans is quite similar. This suggests that SIV-infected macaques represent a useful model of the clonal expansion of HIV infected cells in humans that can be used to evaluate strategies intended to control or eradicate the viral reservoir.
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Affiliation(s)
- Andrea L. Ferris
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, United States of America
| | - David W. Wells
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Adrienne E. Swanstrom
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston MA, United States of America
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, United States of America
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10
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Gene therapy targeting haematopoietic stem cells for inherited diseases: progress and challenges. Nat Rev Drug Discov 2019; 18:447-462. [DOI: 10.1038/s41573-019-0020-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Carrillo J, Clotet B, Blanco J. Antibodies and Antibody Derivatives: New Partners in HIV Eradication Strategies. Front Immunol 2018; 9:2429. [PMID: 30405624 PMCID: PMC6205993 DOI: 10.3389/fimmu.2018.02429] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/02/2018] [Indexed: 12/25/2022] Open
Abstract
Promptly after primoinfection, HIV generates a pool of infected cells carrying transcriptionally silent integrated proviral DNA, the HIV-1 reservoir. These cells are not cleared by combined antiretroviral therapy (cART), and persist lifelong in treated HIV-infected individuals. Defining clinical strategies to eradicate the HIV reservoir and cure HIV-infected individuals is a major research field that requires a deep understanding of the mechanisms of seeding, maintenance and destruction of latently infected cells. Although CTL responses have been classically associated with the control of HIV replication, and hence with the size of HIV reservoir, broadly neutralizing antibodies (bNAbs) have emerged as new players in HIV cure strategies. Several reasons support this potential role: (i) over the last years a number of bNAbs with high potency and ability to cope with the extreme variability of HIV have been identified; (ii) antibodies not only block HIV replication but mediate effector functions that may contribute to the removal of infected cells and to boost immune responses against HIV; (iii) a series of new technologies have allowed for the in vitro design of improved antibodies with increased antiviral and effector functions. Recent studies in non-human primate models and in HIV-infected individuals have shown that treatment with recombinant bNAbs isolated from HIV-infected individuals is safe and may have a beneficial effect both on the seeding of the HIV reservoir and on the inhibition of HIV replication. These promising data and the development of antibody technology have paved the way for treating HIV infection with engineered monoclonal antibodies with high potency of neutralization, wide coverage of HIV diversity, extended plasma half-life in vivo and improved effector functions. The exciting effects of these newly designed antibodies in vivo, either alone or in combination with other cure strategies (latency reversing agents or therapeutic vaccines), open a new hope in HIV eradication.
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Affiliation(s)
- Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Institut de Recerca Germans Trias i Pujol, Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Institut de Recerca Germans Trias i Pujol, Badalona, Spain.,Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CEES), Faculty of Medicine, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Institut de Recerca Germans Trias i Pujol, Badalona, Spain.,Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CEES), Faculty of Medicine, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
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