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Symons J, Chopra A, Malatinkova E, De Spiegelaere W, Leary S, Cooper D, Abana CO, Rhodes A, Rezaei SD, Vandekerckhove L, Mallal S, Lewin SR, Cameron PU. Erratum to: HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology 2017; 14:23. [PMID: 28347330 PMCID: PMC5366998 DOI: 10.1186/s12977-017-0340-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shay Leary
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Don Cooper
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Chike O Abana
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Simin D Rezaei
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia. .,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
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Symons J, Chopra A, Malatinkova E, De Spiegelaere W, Leary S, Cooper D, Abana CO, Rhodes A, Rezaei SD, Vandekerckhove L, Mallal S, Lewin SR, Cameron PU. HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology 2017; 14:2. [PMID: 28086908 PMCID: PMC5237276 DOI: 10.1186/s12977-016-0325-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position. RESULTS We modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines. Latently infected cell lines infected with intact virus demonstrated multiple distinct HIV integration sites (28 different sites in U1, 110 in ACH-2 and 117 in J1.1 per 150,000 cells). In contrast, cell lines infected with replication-incompetent viruses (J-Lat cells) demonstrated single integration sites. Following in vitro passaging of the ACH-2 cell line, we observed a significant increase in the frequency of unique HIV integration sites and there were multiple mutations and large deletions in the proviral DNA. When the ACH-2 cell line was cultured with the integrase inhibitor raltegravir, there was a significant decrease in the number of unique HIV integration sites and a transient increase in the frequency of 2-LTR circles consistent with virus replication in these cells. CONCLUSION Cell lines latently infected with intact HIV demonstrated multiple unique HIV integration sites indicating that these cell lines are not clonal and in the ACH-2 cell line there was evidence of low level virus replication. These findings have implications for the use of latently infected cell lines as models of HIV latency and for the use of these cells as standards.
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Affiliation(s)
- Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Eva Malatinkova
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Ward De Spiegelaere
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shay Leary
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Don Cooper
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia
| | - Chike O Abana
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Simin D Rezaei
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Murdoch, WA, Australia.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, 792 Elizabeth St, Melbourne, VIC, 3000, Australia. .,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia.
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Anderson JL, Mota TM, Evans VA, Kumar N, Rezaei SD, Cheong K, Solomon A, Wightman F, Cameron PU, Lewin SR. Understanding Factors That Modulate the Establishment of HIV Latency in Resting CD4+ T-Cells In Vitro. PLoS One 2016; 11:e0158778. [PMID: 27383184 PMCID: PMC4934909 DOI: 10.1371/journal.pone.0158778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/21/2016] [Indexed: 11/18/2022] Open
Abstract
Developing robust in vitro models of HIV latency is needed to better understand how latency is established, maintained and reversed. In this study, we examined the effects of donor variability, HIV titre and co-receptor usage on establishing HIV latency in vitro using two models of HIV latency. Using the CCL19 model of HIV latency, we found that in up to 50% of donors, CCL19 enhanced latent infection of resting CD4+ T-cells by CXCR4-tropic HIV in the presence of low dose IL-2. Increasing the infectious titre of CXCR4-tropic HIV increased both productive and latent infection of resting CD4+ T-cells. In a different model where myeloid dendritic cells (mDC) were co-cultured with resting CD4+ T-cells, we observed a higher frequency of latently infected cells in vitro than CCL19-treated or unstimulated CD4+ T-cells in the presence of low dose IL-2. In the DC-T-cell model, latency was established with both CCR5- and CXCR4-tropic virus but higher titres of CCR5-tropic virus was required in most donors. The establishment of latency in vitro through direct infection of resting CD4+ T-cells is significantly enhanced by CCL19 and mDC, but the efficiency is dependent on virus titre, co-receptor usage and there is significant donor variability.
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Affiliation(s)
- Jenny L Anderson
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Talia M Mota
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Vanessa A Evans
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nitasha Kumar
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Simin D Rezaei
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Karey Cheong
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ajantha Solomon
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fiona Wightman
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul U Cameron
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Victoria, Australia
| | - Sharon R Lewin
- Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Monash University and Alfred Hospital, Melbourne, Victoria, Australia
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Abstract
The persistence of human immunodeficiency virus type 1 (HIV-1) in latent reservoirs is a major barrier to HIV cure. Reservoir establishment depends on low viral expression that may be related to provirus integration sites (IS). In vitro, in cell lines and primary T cells, latency is associated with specific IS through reduced viral expression mediated by transcriptional interference by host cellular promoters, reverse orientation, and the presence of specific epigenetic modifiers. In primary T cell models of latency, specific IS are associated with intracellular viral antigen expression that is not directly related to cell activation. In contrast, in patient CD4+ T cells, there is enrichment for IS in genes controlling cell cycle and survival and in some clonally expanded T cell subpopulations. Multiple insertion sites within some specific genes may suggest that integrated HIV can increase the host’s T cell survival.
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Affiliation(s)
- Simin D. Rezaei
- Faculty of Medicine, Dentistry and Health Sciences, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, The University of Melbourne, 4th Floor, 786-798 Elizabeth St, Melbourne, 3010 Australia
| | - Paul U. Cameron
- Faculty of Medicine, Dentistry and Health Sciences, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, The University of Melbourne, 4th Floor, 786-798 Elizabeth St, Melbourne, 3010 Australia
- Infectious Diseases Unit, Department of Infectious Diseases, Alfred Hospital, 85 Commercial Rd, Melbourne, Victoria 3004 Australia
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Rezaei SD, Hearps AC, Mills J, Pedersen J, Tachedjian G. No association between XMRV or related gammaretroviruses in Australian prostate cancer patients. Virol J 2013; 10:20. [PMID: 23305518 PMCID: PMC3560155 DOI: 10.1186/1743-422x-10-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/03/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus reported to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS). While the association of XMRV with CFS and PC has recently been discredited, no studies have been performed in Australian patients to investigate the association between PC and XMRV or related murine leukemia virus (MLV) in matched PC and normal tissue. METHODS Genomic DNA (gDNA) was purified from matched normal and cancer formalin-fixed paraffin-embedded (FFPE) prostate tissue from 35 Australian PC patients with Gleason scores ranging from 7 - 10. The presence of the ribonuclease L (RNase L) polymorphism R462Q was determined by allele specific PCR. Samples were screened for XMRV and related murine leukemia virus (MLV) variants by qPCR. Contaminating mouse DNA was detected using qPCR targeting mouse intracisternal A particle long terminal repeat DNA. RESULTS gDNA was successfully purified from 94% (66/70) of normal and cancer FFPE prostate tissues. RNase L typing revealed 8% were homozygous (QQ), 60% were heterozygous (RQ) and 32% were wild-type (RR) for the RNase L mutation. None of the 66 samples tested were positive for XMRV or related MLV sequences using broad MLV or XMRV specific primers with detection sensitivities of 1 viral copy of MLV/XMRV and XMRV DNA, respectively. CONCLUSIONS Using highly sensitive qPCR we found no evidence of XMRV or related gammaretroviruses in prostate tissues from 35 Australian PC patients. Our findings are consistent with other studies demonstrating that XMRV is a laboratory contaminant that has no role in the aetiology of PC.
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Affiliation(s)
- Simin D Rezaei
- Retroviral Biology and Antivirals Laboratory, Centre for Virology, Burnet Institute, 85 Commercial Road, Melbourne, Victoria 3004, Australia
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