1
|
Gianella S, Anderson C, Chaillon A, Wells A, Porrachia M, Caballero G, Vargas M, Lonergan J, Woodworth B, Gaitan N, Rawlings SA, Muttera L, Harkness L, Little SJ, May S, Smith D. Impact of influenza and pneumococcal vaccines on HIV persistence and immune dynamics during suppressive antiretroviral therapy. AIDS 2024; 38:1131-1140. [PMID: 38526550 PMCID: PMC11141237 DOI: 10.1097/qad.0000000000003882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
OBJECTIVE We sought to determine if standard influenza and pneumococcal vaccines can be used to stimulate HIV reservoirs during antiretroviral therapy (ART). DESIGN A prospective, randomized, double-blinded, placebo-controlled, crossover trial of two clinically recommended vaccines (influenza and pneumococcal). METHODS Persons with HIV on ART ( N = 54) were enrolled in the clinical trial. Blood was collected at baseline and days 2,4,7,14, and 30 postimmunizations. Levels of cellular HIV RNA and HIV DNA were measured by ddPCR. Expression of immunological markers on T cell subsets was measured by flow cytometry. Changes in unspliced cellular HIV RNA from baseline to day 7 postinjection between each vaccine and placebo was the primary outcome. RESULTS Forty-seven participants completed at least one cycle and there were no serious adverse events related to the intervention. We observed no significant differences in the change in cellular HIV RNA after either vaccine compared with placebo at any timepoint. In secondary analyses, we observed a transient increase in total HIV DNA levels after influenza vaccine, as well as increased T cell activation and exhaustion on CD4 + T cells after pneumococcal vaccine. CONCLUSION Clinically recommended vaccines were well tolerated but did not appear to stimulate the immune system strongly enough to elicit significantly noticeable HIV RNA transcription during ART.Clinicaltrials.gov identifier: NCT02707692.
Collapse
Affiliation(s)
- Sara Gianella
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Christy Anderson
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Antoine Chaillon
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Alan Wells
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Magali Porrachia
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Gemma Caballero
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Milenka Vargas
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Joseph Lonergan
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Brendon Woodworth
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Noah Gaitan
- Department of Medicine, University of California San Diego, La Jolla, CA
| | | | - Leticia Muttera
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Liliana Harkness
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Susan J. Little
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Susanne May
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Davey Smith
- Department of Medicine, University of California San Diego, La Jolla, CA
| |
Collapse
|
2
|
Kisaka JK, Rauch D, Griffith M, Kyei GB. A macrophage-cell model of HIV latency reveals the unusual importance of the bromodomain axis. Virol J 2024; 21:80. [PMID: 38581045 PMCID: PMC10996205 DOI: 10.1186/s12985-024-02343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Although macrophages are now recognized as an essential part of the HIV latent reservoir, whether and how viral latency is established and reactivated in these cell types is poorly understood. To understand the fundamental mechanisms of viral latency in macrophages, there is an urgent need to develop latency models amenable to genetic manipulations and screening for appropriate latency-reversing agents (LRAs). Given that differentiated THP-1 cells resemble monocyte-derived macrophages in HIV replication mechanisms, we set out to establish a macrophage cell model for HIV latency using THP-1 cells. METHODS We created single-cell clones of THP-1 cells infected with a single copy of the dual-labeled HIVGKO in which a codon switched eGFP (csGFP) is under the control of the HIV-1 5' LTR promoter, and a monomeric Kusabira orange 2 (mKO2) under the control of cellular elongation factor one alpha promoter (EF1α). Latently infected cells are csGFP-, mKO2+, while cells with actively replicating HIV (or reactivated virus) are csGFP+,mKO2+. After sorting for latently infected cells, each of the THP-1 clones with unique integration sites for HIV was differentiated into macrophage-like cells with phorbol 12-myristate 13-acetate (PMA) and treated with established LRAs to stimulate HIV reactivation. Monocyte-derived macrophages (MDMs) harboring single copies of HIVGKO were used to confirm our findings. RESULTS We obtained clones of THP-1 cells with latently infected HIV with unique integration sites. When the differentiated THP-1 or primary MDMs cells were treated with various LRAs, the bromodomain inhibitors JQ1 and I-BET151 were the most potent compounds. Knockdown of BRD4, the target of JQ1, resulted in increased reactivation, thus confirming the pharmacological effect. The DYRK1A inhibitor Harmine and lipopolysaccharide (LPS) also showed significant reactivation across all three MDM donors. Remarkably, LRAs like PMA/ionomycin, bryostatin-1, and histone deacetylase inhibitors known to potently reactivate latent HIV in CD4 + T cells showed little activity in macrophages. CONCLUSIONS Our results indicate that this model could be used to screen for appropriate LRAs for macrophages and show that HIV latency and reactivation mechanisms in macrophages may be distinct from those of CD4 + T cells.
Collapse
Affiliation(s)
- Javan K Kisaka
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Daniel Rauch
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO, 63108, USA
| | - George B Kyei
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Virology, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
- Medical and Scientific Research Center, University of Ghana Medical Center, Accra, Ghana.
| |
Collapse
|
3
|
Xu B, Powell K. Quality Control of an Isogenic H/N/KRAS-Less Mouse Embryonic Fibroblast Cell Line Panel. Methods Mol Biol 2024; 2797:337-350. [PMID: 38570471 DOI: 10.1007/978-1-0716-3822-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Isogenic H/N/KRAS-less mouse embryonic fibroblast (MEF) cell lines have been developed to assist in cell-based assays of RAS inhibitors. The quality control assessment of a panel of these isogenic MEFs is described here, with a focus on ensuring the proper insertion of the desired mutant RAS transgene, a determination of gene copy number, and an investigation of potential off-target mutations which could lead to phenotypes which are undesired in downstream experiments. Using this suite of quality control tools, a MEF cell line can be readily validated, and researchers can be assured of the rationale for an observed phenotype.
Collapse
Affiliation(s)
- Bingfang Xu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
4
|
Kim J, Park M, Baek G, Kim JI, Kwon E, Kang BC, Kim JI, Kang HJ. Tagmentation-based analysis reveals the clonal behavior of CAR-T cells in association with lentivector integration sites. Mol Ther Oncolytics 2023; 30:1-13. [PMID: 37360944 PMCID: PMC10285042 DOI: 10.1016/j.omto.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Integration site (IS) analysis is essential in ensuring safety and efficacy of gene therapies when integrating vectors are used. Although clinical trials of gene therapy are rapidly increasing, current methods have limited use in clinical settings because of their lengthy protocols. Here, we describe a novel genome-wide IS analysis method, "detection of the integration sites in a time-efficient manner, quantifying clonal size using tagmentation sequencing" (DIStinct-seq). In DIStinct-seq, a bead-linked Tn5 transposome is used, allowing the sequencing library to be prepared within a single day. We validated the quantification performance of DIStinct-seq for measuring clonal size with clones of known IS. Using ex vivo chimeric antigen receptor (CAR)-T cells, we revealed the characteristics of lentiviral IS. We then applied it to CAR-T cells collected at various times from tumor-engrafted mice, detecting 1,034-6,233 IS. Notably, we observed that the highly expanded clones had a higher integration frequency in the transcription units and vice versa in genomic safe harbors (GSH). Also, in GSH, persistent clones had more frequent IS. Together with these findings, the new IS analysis method will help to improve the safety and efficacy of gene therapies.
Collapse
Affiliation(s)
- Jaeryuk Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Miyoung Park
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Gyungwon Baek
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Joo-Il Kim
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Euna Kwon
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byeong-Cheol Kang
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Biomedical Center for Animal Resource and Development; Seoul National University College of Medicine, Seoul, Republic of Korea
- Designed Animal Resource Center, Institute of GreenBio Science Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Hyoung Jin Kang
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
- Wide River Institute of Immunology, Hongcheon, Republic of Korea
| |
Collapse
|
5
|
Botha JC, Demirov D, Gordijn C, Katusiime MG, Bale MJ, Wu X, Wells D, Hughes SH, Cotton MF, Mellors JW, Kearney MF, van Zyl GU. The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs. mBio 2023; 14:e0111623. [PMID: 37530525 PMCID: PMC10470503 DOI: 10.1128/mbio.01116-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Combination antiretroviral therapy (cART) suppresses viral replication but does not cure HIV infection because a reservoir of infectious (intact) HIV proviruses persists in long-lived CD4+T cells. However, a large majority (>95%) of HIV-infected cells that persist on effective cART carry defective (non-infectious) proviruses. Defective proviruses consisting of only a single LTR (solo long terminal repeat) are commonly found as endogenous retroviruses in many animal species, but the frequency of solo-LTR HIV proviruses has not been well defined. Here we show that, in five pediatric donors whose viremia was suppressed on cART for at least 5 years, the proviruses in the nine largest clones of HIV-infected cells were solo LTRs. The sizes of five of these clones were assayed longitudinally by integration site-specific quantitative PCR. Minor waxing and waning of the clones was observed, suggesting that these clones are generally stable over time. Our findings show that solo LTRs comprise a large fraction of the proviruses in infected cell clones that persist in children on long-term cART. IMPORTANCE This work highlights that severely deleted HIV-1 proviruses comprise a significant proportion of the proviral landscape and are often overlooked.
Collapse
Affiliation(s)
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Mary Grace Katusiime
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J. Bale
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Xiaolin Wu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Daria Wells
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | |
Collapse
|
6
|
Mohamed H, Berman R, Connors J, Haddad EK, Miller V, Nonnemacher MR, Dampier W, Wigdahl B, Krebs FC. Immunomodulatory Effects of Non-Thermal Plasma in a Model for Latent HIV-1 Infection: Implications for an HIV-1-Specific Immunotherapy. Biomedicines 2023; 11:122. [PMID: 36672628 PMCID: PMC9856147 DOI: 10.3390/biomedicines11010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
In people living with HIV-1 (PLWH), antiretroviral therapy (ART) eventually becomes necessary to suppress the emergence of human immunodeficiency virus type 1 (HIV-1) replication from latent reservoirs because HIV-1-specific immune responses in PLWH are suboptimal. Immunotherapies that enhance anti-HIV-1 immune responses for better control of virus reemergence from latent reservoirs are postulated to offer ART-free control of HIV-1. Toward the goal of developing an HIV-1-specific immunotherapy based on non-thermal plasma (NTP), the early immunological responses to NTP-exposed latently infected T lymphocytes were examined. Application of NTP to the J-Lat T-lymphocyte cell line (clones 10.6 and 15.4) stimulated monocyte recruitment and macrophage maturation, which are key steps in initiation of an immune response. In contrast, CD8+ T lymphocytes in a mixed lymphocyte reaction assay were not stimulated by the presence of NTP-exposed J-Lat cells. Furthermore, co-culture of NTP-exposed J-Lat cells with mature phagocytes did not modulate their antigen presentation to primary CD8+ T lymphocytes (cross-presentation). However, reactivation from latency was stimulated in a clone-specific manner by NTP. Overall, these studies, which demonstrated that ex vivo application of NTP to latently infected lymphocytes can stimulate key immune cell responses, advance the development of an NTP-based immunotherapy that will provide ART-free control of HIV-1 reactivation in PLWH.
Collapse
Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Jennifer Connors
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Elias K. Haddad
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Vandana Miller
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Fred C. Krebs
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| |
Collapse
|
7
|
Zhang W, Zhou M, Chen C, Wu S, Wang L, Xia B, Liu J, Ma X, Pan T, Zhang H, Li L, Liu B. Identification of CD98 as a Novel Biomarker for HIV-1 Permissiveness and Latent Infection. mBio 2022; 13:e0249622. [PMID: 36214569 PMCID: PMC9765422 DOI: 10.1128/mbio.02496-22] [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: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) can integrate viral DNA into host cell chromosomes to establish a long-term stable latent reservoir, which is a major obstacle to cure HIV-1 infection. The characteristics of the HIV-1 latent reservoir have not been fully understood. Here, we identified 126 upregulated plasma membrane proteins in HIV-1 latently infected cells by a label-free liquid chromatography-tandem mass spectrometry analysis. The higher levels of CD98 expression in multiple HIV-1 latently infected cell lines and primary CD4+ T cells compared to uninfected cells were further confirmed by quantitative reverse transcription PCR (RT-qPCR) and flow cytometry analyses. In addition, CD98high CD4+ T cells displayed hyper-permissiveness to HIV-1 infection and possessed distinct immune phenotypic profiles associated with Th17 and peripheral follicular T helper (pTFH) characteristics. Notably, the CD98high resting memory CD4+ T cells harbored significantly higher cell-associated viral RNA and intact provirus than CD98low counterparts in HIV-1-infected individuals receiving combined antiretroviral therapy. Furthermore, CD98high CD4+ T cells exhibited a robust proliferative capacity and significantly contributed to the clonal expansion of the HIV-1 latent reservoir. Our study demonstrates that CD98 can be used as a novel biomarker of HIV-1 latently infected cells to indicate the effect of various strategies to reduce the viral reservoir. IMPORTANCE Identification of cellular biomarkers is the crucial challenge to eradicate the HIV-1 latent reservoir. In our study, we identified CD98 as a novel plasma membrane biomarker for HIV-1 permissiveness and latent infection. Importantly, CD98high CD4+ T cells exhibited a hyper-permissiveness to HIV-1 infection and significantly contributed to the clonal expansion of the HIV-1 latent reservoir. CD98 could be targeted to develop therapeutic strategies to reduce the HIV-1 latent reservoir in further research.
Collapse
Affiliation(s)
- Wanying Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Infectious Diseases Center, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Mo Zhou
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cancan Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shiyu Wu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lilin Wang
- Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Baijin Xia
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Liu
- Qianyang Biomedical Research Institute, Guangzhou, Guangdong, China
| | - Xiancai Ma
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Pan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Linghua Li
- Infectious Diseases Center, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bingfeng Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
8
|
Shao L, Shi R, Zhao Y, Liu H, Lu A, Ma J, Cai Y, Fuksenko T, Pelayo A, Shah NN, Kochenderfer JN, Norberg SM, Hinrichs C, Highfill SL, Somerville RP, Panch SR, Jin P, Stroncek DF. Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products. J Transl Med 2022; 20:514. [DOI: 10.1186/s12967-022-03729-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Clinical CAR T-cell therapy using integrating vector systems represents a promising approach for the treatment of hematological malignancies. Lentiviral and γ-retroviral vectors are the most commonly used vectors in the manufacturing process. However, the integration pattern of these viral vectors and subsequent effect on CAR T-cell products is still unclear.
Methods
We used a modified viral integration sites analysis (VISA) pipeline to evaluate viral integration events around the whole genome in pre-infusion CAR T-cell products. We compared the differences of integration pattern between lentiviral and γ-retroviral products. We also explored whether the integration sites correlated with clinical outcomes.
Results
We found that γ-retroviral vectors were more likely to insert than lentiviral vectors into promoter, untranslated, and exon regions, while lentiviral vector integration sites were more likely to occur in intron and intergenic regions. Some integration events affected gene expression at the transcriptional and post-transcriptional level. Moreover, γ-retroviral vectors showed a stronger impact on the host transcriptome. Analysis of individuals with different clinical outcomes revealed genes with differential enrichment of integration events. These genes may affect biological functions by interrupting amino acid sequences and generating abnormal proteins, instead of by affecting mRNA expression. These results suggest that vector integration is associated with CAR T-cell efficacy and clinical responses.
Conclusion
We found differences in integration patterns, insertion hotspots and effects on gene expression vary between lentiviral and γ-retroviral vectors used in CAR T-cell products and established a foundation upon which we can conduct further analyses.
Collapse
|
9
|
Guo S, Luke BT, Henry AR, Darko S, Brandt LD, Su L, Sun D, Wells D, Joseph KW, Demirov D, Halvas EK, Douek DC, Wu X, Mellors JW, Hughes SH. HIV infected CD4+ T cell clones are more stable than uninfected clones during long-term antiretroviral therapy. PLoS Pathog 2022; 18:e1010726. [PMID: 36044447 PMCID: PMC9432747 DOI: 10.1371/journal.ppat.1010726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
Although combination antiretroviral therapy (ART) blocks HIV replication, it is not curative because infected CD4+ T cells that carry intact, infectious proviruses persist. Understanding the behavior of clones of infected T cells is important for understanding the stability of the reservoir; however, the stabilities of clones of infected T cells in persons on long-term ART are not well defined. We determined the relative stabilities of clones of infected and uninfected CD4+ T cells over time intervals of one to four years in three individuals who had been on ART for 9–19 years. The largest clones of uninfected T cells were larger than the largest clones of infected T cells. Clones of infected CD4+ T cells were more stable than clones of uninfected CD4+ T cells of a similar size. Individual clones of CD4+ T cells carrying intact, infectious proviruses can expand, contract, or remain stable over time. In HIV infected individuals, infected T cells can clonally expand and persist for many years, which is one of the primary reasons current anti-retroviral therapy (ART), which blocks viral replication, does not cure HIV infections. We compared the relative stabilities of clones of infected and uninfected T cells in three donors who had been on successful long-term ART for more than 9 years. The clones of infected T cells were much more stable than similar-sized clones of uninfected T cells. We were initially surprised by this result but, because ART blocks viral replication, we realized that all of the infected clones must be “old” and must have originated before ART was initiated. In contrast, the clones of uninfected cells would have included both old and new clones. In addition, we looked at the behavior of three clones (one in each donor) each of which carries an intact, replication-competent, provirus. The data show that even after more than 9 years, clones that carry replication-competent proviruses can either increase or decrease in size.
Collapse
Affiliation(s)
- Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Brian T. Luke
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda Maryland, United States of America
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda Maryland, United States of America
| | - Leah D. Brandt
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ling Su
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David Sun
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Daria Wells
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kevin W. Joseph
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dimiter Demirov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Elias K. Halvas
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda Maryland, United States of America
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail:
| |
Collapse
|
10
|
Ha T, DiPrima M, Koparde V, Jailwala P, Ohnuki H, Feng JX, Palangat M, Larson D, Tosato G. Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:877-891. [PMID: 35694213 PMCID: PMC9163427 DOI: 10.1016/j.omtn.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022]
Abstract
Advances in gene therapy research have resulted in the successful development of new therapies for clinical use. Here, we explored a gene targeting approach to deplete ephrinB2 from colorectal cancer cells using an inducible lentiviral vector. EphrinB2, a transmembrane ephrin ligand, promotes colorectal cancer cell growth and viability and predicts poor patient survival when expressed at high levels in colorectal cancer tissues. We discovered that lentiviral vector integration and expression in the host DNA frequently drive divergent host gene transcription, generating antisense reads coupled with splicing events and generation of chimeric vector/host transcripts. Antisense transcription of host DNA was linked to development of an integrated stress response and cell death. Despite recent successes, off-target effects remain a concern in genetic medicine. Our results provide evidence that divergent gene transcription is a previously unrecognized off-target effect of lentiviral vector integration with built-in properties for regulation of gene expression.
Collapse
|
11
|
Malatinkova E, Thomas J, De Spiegelaere W, Rutsaert S, Geretti AM, Pollakis G, Paxton WA, Vandekerckhove L, Ruggiero A. Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences. Life (Basel) 2021; 11:life11121410. [PMID: 34947941 PMCID: PMC8706387 DOI: 10.3390/life11121410] [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] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2–5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. Alu-5LTR assay sensitivity was also determined using an “integrated standard”; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Faculty of Veterinary Sciences, Ghent University, B-9820 Ghent, Belgium;
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Anna Maria Geretti
- Fondazione PTV and Faculty of Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
- Department Neurosciences, Biomedicine and Movement Sciences, School of Medicine-University of Verona, 37129 Verona, Italy
- Correspondence: ; Tel.: +39-045-802-7190
| |
Collapse
|
12
|
Coffin JM, Hughes SH. Clonal Expansion of Infected CD4+ T Cells in People Living with HIV. Viruses 2021; 13:v13102078. [PMID: 34696507 PMCID: PMC8537114 DOI: 10.3390/v13102078] [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: 09/02/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 01/16/2023] Open
Abstract
HIV infection is not curable with current antiretroviral therapy (ART) because a small fraction of CD4+ T cells infected prior to ART initiation persists. Understanding the nature of this latent reservoir and how it is created is essential to development of potentially curative strategies. The discovery that a large fraction of the persistently infected cells in individuals on suppressive ART are members of large clones greatly changed our view of the reservoir and how it arises. Rather than being the products of infection of resting cells, as was once thought, HIV persistence is largely or entirely a consequence of infection of cells that are either expanding or are destined to expand, primarily due to antigen-driven activation. Although most of the clones carry defective proviruses, some carry intact infectious proviruses; these clones comprise the majority of the reservoir. A large majority of both the defective and the intact infectious proviruses in clones of infected cells are transcriptionally silent; however, a small fraction expresses a few copies of unspliced HIV RNA. A much smaller fraction is responsible for production of low levels of infectious virus, which can rekindle infection when ART is stopped. Further understanding of the reservoir will be needed to clarify the mechanism(s) by which provirus expression is controlled in the clones of cells that constitute the reservoir.
Collapse
Affiliation(s)
- John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute in Frederick, Frederick, MD 21702, USA
- Correspondence:
| |
Collapse
|
13
|
Mellors JW, Guo S, Naqvi A, Brandt LD, Su L, Sun Z, Joseph KW, Demirov D, Halvas EK, Butcher D, Scott B, Hamilton A, Heil M, Karim B, Wu X, Hughes SH. Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas. SCIENCE ADVANCES 2021; 7:eabi8795. [PMID: 34644108 PMCID: PMC8514100 DOI: 10.1126/sciadv.abi8795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Retroviruses cause cancers in animals by integrating in or near oncogenes. Although HIV-1 infection increases the risk of cancer, most of the risk is associated with immunodeficiency and coinfection by oncogenic virus (Epstein-Barr virus, Kaposi sarcoma herpesvirus, and human papillomavirus). HIV-1 proviruses integrated in some oncogenes cause clonal expansion of infected T cells in vivo; however, the infected cells are not transformed, and it is generally believed that HIV-1 does not cause cancer directly. We show that HIV-1 proviruses integrated in the first introns of signal transducer and activator of transcription 3 (STAT3) and lymphocyte-specific protein tyrosine kinase (LCK) can play an important role in the development of T cell lymphomas. The development of these cancers appears to be a multistep process involving additional nonviral mutations, which could help explain why T cell lymphomas are rare in persons with HIV-1 infection.
Collapse
Affiliation(s)
- John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Asma Naqvi
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah D. Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ling Su
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhonghe Sun
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kevin W. Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter Demirov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donna Butcher
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Beth Scott
- Roche Molecular Diagnostics, Pleasanton, CA, USA
| | | | | | - Baktiar Karim
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD, USA
| |
Collapse
|
14
|
Brandt LD, Guo S, Joseph KW, Jacobs JL, Naqvi A, Coffin JM, Kearney MF, Halvas EK, Wu X, Hughes SH, Mellors JW. Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR. Viruses 2021; 13:1235. [PMID: 34202310 PMCID: PMC8310066 DOI: 10.3390/v13071235] [Citation(s) in RCA: 7] [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: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022] Open
Abstract
Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them.
Collapse
Affiliation(s)
- Leah D. Brandt
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., 8560 Progress Drive, ATRF, Room C3004, Frederick, MD 21701, USA; (S.G.); (X.W.)
| | - Kevin W. Joseph
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Jana L. Jacobs
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Asma Naqvi
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, 145 Harrison Avenue, Jaharis 409, Boston, MA 02111, USA;
| | - Mary F. Kearney
- HIV-Dynamics and Replication Program, National Cancer Institute, 1050 Boyles Street, Building 535, Room 308, Frederick, MD 21702, USA; (M.F.K.); (S.H.H.)
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., 8560 Progress Drive, ATRF, Room C3004, Frederick, MD 21701, USA; (S.G.); (X.W.)
| | - Stephen H. Hughes
- HIV-Dynamics and Replication Program, National Cancer Institute, 1050 Boyles Street, Building 535, Room 308, Frederick, MD 21702, USA; (M.F.K.); (S.H.H.)
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, 3550 Terrace Street, Scaife Hall-818, Pittsburgh, PA 15261, USA; (L.D.B.); (K.W.J.); (J.L.J.); (A.N.); (E.K.H.)
| |
Collapse
|
15
|
Retrieval of vector integration sites from cell-free DNA. Nat Med 2021; 27:1458-1470. [PMID: 34140705 DOI: 10.1038/s41591-021-01389-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/07/2021] [Indexed: 12/23/2022]
Abstract
Gene therapy (GT) has rapidly attracted renewed interest as a treatment for otherwise incurable diseases, with several GT products already on the market and many more entering clinical testing for selected indications. Clonal tracking techniques based on vector integration enable monitoring of the fate of engineered cells in the blood of patients receiving GT and allow assessment of the safety and efficacy of these procedures. However, owing to the limited number of cells that can be tested and the impracticality of studying cells residing in peripheral organs without performing invasive biopsies, this approach provides only a partial snapshot of the clonal repertoire and dynamics of genetically modified cells and reduces the predictive power as a safety readout. In this study, we developed liquid biopsy integration site sequencing, or LiBIS-seq, a polymerase chain reaction technique optimized to quantitatively retrieve vector integration sites from cell-free DNA released into the bloodstream by dying cells residing in several tissues. This approach enabled longitudinal monitoring of in vivo liver-directed GT and clonal tracking in patients receiving hematopoietic stem cell GT, improving our understanding of the clonal composition and turnover of genetically modified cells in solid tissues and, in contrast to conventional analyses based only on circulating blood cells, enabling earlier detection of vector-marked clones that are aberrantly expanding in peripheral tissues.
Collapse
|
16
|
Abstract
HIV-1 integrates its genome into the DNA of host cells. Consequently, HIV-1 genomes are copied with the host cell DNA during cellular division. Little is known about the emergence and persistence of human immunodeficiency virus (HIV)-infected T-cell clones in perinatally infected children. We analyzed peripheral blood mononuclear cells (PBMCs) for clonal expansion in 11 children who initiated antiretroviral therapy (ART) between 1.8 and 17.4 months of age and with viremia suppressed for 6 to 9 years. We obtained 8,662 HIV type 1 (HIV-1) integration sites from pre-ART samples and 1,861 sites from on-ART samples. Expanded clones of infected cells were detected pre-ART in 10/11 children. In 8 children, infected cell clones detected pre-ART persisted for 6 to 9 years on ART. A comparison of integration sites in the samples obtained on ART with healthy donor PBMCs infected ex vivo showed selection for cells with proviruses integrated in BACH2 and STAT5B. Our analyses indicate that, despite marked differences in T-cell composition and dynamics between children and adults, HIV-infected cell clones are established early in children, persist for up to 9 years on ART, and can be driven by proviral integration in proto-oncogenes.
Collapse
|
17
|
Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy. PLoS Pathog 2021; 17:e1009141. [PMID: 33826675 PMCID: PMC8055010 DOI: 10.1371/journal.ppat.1009141] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 15,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 395,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, but modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 7 specific genes, and by clonal expansion. Clones in which a provirus integrated in an oncogene contributed to cell survival comprised only a small fraction of the clones persisting in on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist. In HIV-infected individuals, a small fraction of the infected cells persist and divide. This reservoir persists during fully suppressive ART and can rekindle the infection if ART is discontinued. Because the number of possible sites of HIV DNA integration is very large, each infected cell, and all of its descendants, can be identified by the site where the provirus is integrated (IS). To understand the selective forces that determine the fates of infected cells in vivo, we compared the distribution of HIV IS in freshly-infected cells to cells from HIV-infected donors sampled both before and during ART. We found that, as previously reported, integration favors highly-expressed genes. However, over time, the fraction of cells with proviruses integrated in highly-expressed genes decreases, implying that they grow less well. There are exceptions to this broad negative selection. When a provirus is integrated in a specific region in one of seven genes, the proviruses affect the expression of the target gene, promoting growth and/or survival of the cell. Although this effect is striking, it is only a minor component of the forces that promote the growth and survival of the population of infected cells during ART.
Collapse
|
18
|
Abstract
In vivo clonal expansion of HIV-infected T cells is an important mechanism of viral persistence. In some cases, clonal expansion is driven by HIV proviral DNA integrated into one of a handful of genes. To investigate this phenomenon in vitro, we infected primary CD4+ T cells with an HIV construct expressing GFP and, after nearly 2 mo of culture and multiple rounds of activation, analyzed the resulting integration site distribution. In each of three replicates from each of two donors, we detected large clusters of integration sites with multiple breakpoints, implying clonal selection. These clusters all mapped to a narrow region within the STAT3 gene. The presence of hybrid transcripts splicing HIV to STAT3 sequences supports a model of LTR-driven STAT3 overexpression as a driver of preferential growth. Thus, HIV integration patterns linked to selective T cell outgrowth can be reproduced in cell culture. The single report of an HIV provirus in a case of AIDS-associated B-cell lymphoma with an HIV provirus in the same part of STAT3 also has implications for HIV-induced malignancy.
Collapse
|
19
|
Wells DW, Guo S, Shao W, Bale MJ, Coffin JM, Hughes SH, Wu X. Correction to: An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses. BMC Genomics 2020; 21:517. [PMID: 32727364 PMCID: PMC7388206 DOI: 10.1186/s12864-020-06924-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Daria W Wells
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA
| | - Wei Shao
- Advanced Biomedical Computational Science, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA.
| |
Collapse
|