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Ranga U, Panchapakesan A, Saini C. HIV-1 subtypes and latent reservoirs. Curr Opin HIV AIDS 2024; 19:87-92. [PMID: 38169308 DOI: 10.1097/coh.0000000000000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW We explore the current status of research on HIV-1 subtype-specific variations and their impact on HIV-1 latency. We also briefly address the controversy surrounding the decision-making process governing the ON/OFF states of HIV-1 transcription, specifically focusing on the regulatory elements, the long terminal repeat (LTR), and Tat. Understanding the decision-making process is crucial for developing effective intervention strategies, such as the 'shock-and-kill' approach, to reactivate latent HIV-1. RECENT FINDINGS Attention has been drawn to subtype-specific transcription factor binding site (TFBS) variations and the possible impact of these variations on viral latency. Further, diverse subtype-specific assays have been developed to quantify the latent viral reservoirs. One interesting observation is the relatively larger latent reservoirs in HIV-1B infection than those of other viral subtypes, which needs rigorous validation. The emergence of LTR-variant viral strains in HIV-1C demonstrating significantly higher levels of latency reversal has been reported. SUMMARY Despite persistent and substantial efforts, latent HIV-1 remains a formidable challenge to a functional cure. Determined and continued commitment is needed to understand the ON/OFF decision-making process of HIV-1 latency, develop rigorous assays for accurately quantifying the latent reservoirs, and identify potent latency-reversing agents and cocktails targeting multiple latency stages. The review emphasizes the importance of including diverse viral subtypes in future latency research.
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Affiliation(s)
- Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
| | - Arun Panchapakesan
- Molecular Biology Laboratory, Y R Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, Tamil Nadu, India
| | - Chhavi Saini
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
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Madlala P, Mkhize Z, Naicker S, Khathi SP, Maikoo S, Gopee K, Dong KL, Ndung'u T. Genetic variation of the HIV-1 subtype C transmitted/founder viruses long terminal repeat elements and the impact on transcription activation potential and clinical disease outcomes. PLoS Pathog 2023; 19:e1011194. [PMID: 37307292 DOI: 10.1371/journal.ppat.1011194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023] Open
Abstract
A genetic bottleneck is a hallmark of HIV-1 transmission such that only very few viral strains, termed transmitted/founder (T/F) variants establish infection in a newly infected host. Phenotypic characteristics of these variants may determine the subsequent course of disease. The HIV-1 5' long terminal repeat (LTR) promoter drives viral gene transcription and is genetically identical to the 3' LTR. We hypothesized that HIV-1 subtype C (HIV-1C) T/F virus LTR genetic variation is a determinant of transcriptional activation potential and clinical disease outcome. The 3'LTR was amplified from plasma samples of 41 study participants acutely infected with HIV-1C (Fiebig stages I and V/VI). Paired longitudinal samples were also available at one year post-infection for 31 of the 41 participants. 3' LTR amplicons were cloned into a pGL3-basic luciferase expression vector, and transfected alone or together with Transactivator of transcription (tat) into Jurkat cells in the absence or presence of cell activators (TNF-α, PMA, Prostratin and SAHA). Inter-patient T/F LTR sequence diversity was 5.7% (Renge: 2-12) with subsequent intrahost viral evolution observed in 48.4% of the participants analyzed at 12 months post-infection. T/F LTR variants exhibited differential basal transcriptional activity, with significantly higher Tat-mediated transcriptional activity compared to basal (p<0.001). Basal and Tat-mediated T/F LTR transcriptional activity showed significant positive correlation with contemporaneous viral loads and negative correlation with CD4 T cell counts (p<0.05) during acute infection respectively. Furthermore, Tat-mediated T/F LTR transcriptional activity significanly correlated positively with viral load set point and viral load; and negatively with CD4 T cell counts at one year post infection (all p<0.05). Lastly, PMA, Prostratin, TNF-α and SAHA cell stimulation resulted in enhanced yet heterologous transcriptional activation of different T/F LTR variants. Our data suggest that T/F LTR variants may influence viral transcriptional activity, disease outcomes and sensitivity to cell activation, with potential implications for therapeutic interventions.
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Affiliation(s)
- Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zakithi Mkhize
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shamara Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Samukelisiwe P Khathi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shreyal Maikoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kasmira Gopee
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Africa Health Research Institute (AHRI), Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
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Enhanced Transcriptional Strength of HIV-1 Subtype C Minimizes Gene Expression Noise and Confers Stability to the Viral Latent State. J Virol 2023; 97:e0137622. [PMID: 36533949 PMCID: PMC9888270 DOI: 10.1128/jvi.01376-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Stochastic fluctuations in gene expression emanating from the HIV-1 long terminal repeat (LTR), amplified by the Tat positive feedback circuit, determine the choice between viral infection fates: active transcription (ON) or transcriptional silence (OFF). The emergence of several transcription factor binding site (TFBS) variant strains in HIV-1 subtype C (HIV-1C), especially those containing the duplication of the NF-κB motif, mandates the evaluation of the effect of enhanced transcriptional strength on gene expression noise and its influence on viral fate selection switch. Using a panel of subgenomic LTR-variant strains containing different copy numbers of the NF-κB motif (ranging from 0 to 4), we used flow cytometry, mRNA quantification, and pharmacological perturbations to demonstrate an inverse correlation between promoter strength and gene expression noise in Jurkat T cells and primary CD4+ T cells. The inverse correlation is consistent in clonal cell populations at constant intracellular concentrations of Tat and when NF-κB levels were regulated pharmacologically. Further, we show that strong LTRs containing at least two copies of the NF-κB motif in the enhancer establish a more stable latent state and demonstrate more rapid latency reversal than weak LTRs containing fewer motifs. We also demonstrate a cooperative binding of NF-κB to the motif cluster in HIV-1C LTRs containing two, three, or four NF-κB motifs (Hill coefficient [H] = 2.61, 3.56, and 3.75, respectively). The present work alludes to a possible evolution of the HIV-1C LTR toward gaining transcriptional strength associated with attenuated gene expression noise with implications for viral latency. IMPORTANCE Over the past two consecutive decades, HIV-1 subtype C (HIV-1C) has been undergoing directional evolution toward augmenting the transcriptional strength of the long terminal repeat (LTR) by adding more copies of the existing transcription factor binding site (TFBS) by sequence duplication. Additionally, the duplicated elements are genetically diverse, suggesting broader-range signal receptivity by variant LTRs. The HIV-1 promoter is inherently noisy, and the stochastic fluctuations in gene expression of variant LTRs may influence the active transcription (ON)/transcriptional silence (OFF) latency decisions. The evolving NF-κB motif variations of HIV-1C offer a powerful opportunity to examine how the transcriptional strength of the LTR might influence gene expression noise. Our work here shows that the augmented transcriptional strength of the HIV-1C LTR leads to concomitantly reduced gene expression noise, consequently leading to stabler latency maintenance and rapid latency reversal. The present work offers a novel lead toward appreciating the molecular mechanisms governing HIV-1 latency.
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Bhange D, Prasad N, Singh S, Prajapati HK, Maurya SP, Gopalan BP, Nadig S, Chaturbhuj D, Jayaseelan B, Dinesha TR, Ahamed SF, Singh N, Brahmaiah A, Mehta K, Gohil Y, Balakrishnan P, Das BK, Dias M, Gangakhedkar R, Mehendale S, Paranjape RS, Saravanan S, Shet A, Solomon SS, Thakar M, Ranga U. The Evolution of Regulatory Elements in the Emerging Promoter-Variant Strains of HIV-1 Subtype C. Front Microbiol 2021; 12:779472. [PMID: 34899661 PMCID: PMC8660095 DOI: 10.3389/fmicb.2021.779472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
In a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naïve subjects, we identified nine different promoter variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not the coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1α/LEF-1, RBEIII, AP-1, and NF-κB, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but no significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a coinfection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy.
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Affiliation(s)
- Disha Bhange
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Nityanand Prasad
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Swati Singh
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Harshit Kumar Prajapati
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Shesh Prakash Maurya
- HIV Immunology Laboratory, Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Bindu Parachalil Gopalan
- Division of Microbiology/Infectious Diseases Unit, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Sowmya Nadig
- Division of Microbiology/Infectious Diseases Unit, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Devidas Chaturbhuj
- Department of Serology and Immunology, National AIDS Research Institute (NARI), Pune, India
| | - Boobalan Jayaseelan
- Department of Molecular Biology and Genotyping, Y. R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Thongadi Ramesh Dinesha
- Department of Molecular Biology and Genotyping, Y. R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Syed Fazil Ahamed
- Division of Microbiology/Infectious Diseases Unit, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Navneet Singh
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Anangi Brahmaiah
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Kavita Mehta
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Yuvrajsinh Gohil
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Pachamuthu Balakrishnan
- Infectious Diseases Laboratory, Y. R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Bimal Kumar Das
- HIV Immunology Laboratory, Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Mary Dias
- Division of Microbiology/Infectious Diseases Unit, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Raman Gangakhedkar
- Department of Clinical Sciences, National AIDS Research Institute (NARI), Pune, India
| | - Sanjay Mehendale
- Department of Research, P. G. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - Ramesh S Paranjape
- Department of Clinical Sciences, National AIDS Research Institute (NARI), Pune, India
| | - Shanmugam Saravanan
- Department of Molecular Biology and Genotyping, Y. R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Anita Shet
- Division of Microbiology/Infectious Diseases Unit, St. John's National Academy of Health Sciences, Bengaluru, India
| | - Sunil Suhas Solomon
- YRGCARE Suniti Solomon Outpatient Clinic, Y. R. Gaitonde Center for AIDS Research and Education (YRG CARE), Chennai, India.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Madhuri Thakar
- Department of Serology and Immunology, National AIDS Research Institute (NARI), Pune, India
| | - Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
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A Stronger Transcription Regulatory Circuit of HIV-1C Drives the Rapid Establishment of Latency with Implications for the Direct Involvement of Tat. J Virol 2020; 94:JVI.00503-20. [PMID: 32669338 DOI: 10.1128/jvi.00503-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The magnitude of transcription factor binding site variation emerging in HIV-1 subtype C (HIV-1C), especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong long terminal repeat (LTR)? We constructed panels of subgenomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. Surprisingly, we found that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.IMPORTANCE Over the past 10 to 15 years, HIV-1 subtype C (HIV-1C) has been evolving rapidly toward gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive to HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and concomitant strong, positive transcriptional feedback is the primary question that we attempted to address in the present manuscript. The role that Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype, HIV-1C, offers crucial leads toward Tat possessing a dual role in serving as both a transcriptional activator and repressor at different phases of viral infection of the cell. The leads that we offer through the present work have significant implications for HIV-1 cure research.
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Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms. Sci Rep 2020; 10:13214. [PMID: 32764600 PMCID: PMC7411029 DOI: 10.1038/s41598-020-70083-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/03/2020] [Indexed: 11/08/2022] Open
Abstract
The critical role of the regulatory elements at the 5′ end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13–17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strain-specific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5ʹ UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5′ end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA–protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection.
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Gartner MJ, Roche M, Churchill MJ, Gorry PR, Flynn JK. Understanding the mechanisms driving the spread of subtype C HIV-1. EBioMedicine 2020; 53:102682. [PMID: 32114391 PMCID: PMC7047180 DOI: 10.1016/j.ebiom.2020.102682] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C (C-HIV) is the most prevalent form of HIV-1 globally, accounting for approximately 50% of infections worldwide. C-HIV is the predominant and near-exclusive subtype in the low resource regions of India and Southern Africa. Given the vast diversity of HIV-1 subtypes, it is curious as to why C-HIV constitutes such a large proportion of global infections. This enriched prevalence may be due to phenotypic differences between C-HIV isolates and other viral strains that permit enhanced transmission efficiency or, pathogenicity, or might due to the socio-demographics of the regions where C-HIV is endemic. Here, we compare the mechanisms of C-HIV pathogenesis to less prominent HIV-1 subtypes, including viral genetic and phenotypic characteristics, and host genetic variability, to understand whether evolutionary factors drove C-HIV to predominance.
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Affiliation(s)
- Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Melissa J Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; Department of Microbiology, Monash University, Melbourne, Australia
| | - Paul R Gorry
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.
| | - Jacqueline K Flynn
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia; The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia.
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Obasa AE, Ashokkumar M, Neogi U, Jacobs GB. Mutations in Long Terminal Repeats κB Transcription Factor Binding Sites in Plasma Virus Among South African People Living with HIV-1. AIDS Res Hum Retroviruses 2019; 35:572-576. [PMID: 30793917 DOI: 10.1089/aid.2018.0293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
HIV-1 subtype C (HIV-1C) is responsible for the majority of infections in sub-Saharan Africa. We selected 63 plasma-derived samples and generated long terminal repeats (LTRs) amplicons from people living with HIV in South Africa to identify transcription factor binding sites. NF-κB plays an important role in regulating the viral gene expression from the viral promoter and controlling viral latency. LTR amplicons were sequenced and phylogenetically analyzed. In our data set, we identified F-κB sites (n = 4; 6%) at position II and (n = 1; 1%) at position I among 63 sequences analyzed. The majority of the sequences identified with H-κB at position II (n = 50; 79%) and position I (n = 55; 87%). Forty-nine (n = 49; 78%) sequences were found to exhibit C-κB site. ZA_LTR052 was identified with a single point mutation. We identified all three NF-κB-binding sites in (n = 44; 70%) the viral promoter-enhancer regions in South African patients.
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Affiliation(s)
- Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Manickam Ashokkumar
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
- HIV/AIDS Division, Department of Clinical Research, National Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai, India
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, University of Stockholm, Stockholm, Sweden
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Sharma S, Arunachalam PS, Menon M, Ragupathy V, Satya RV, Jebaraj J, Aralaguppe SG, Rao C, Pal S, Saravanan S, Murugavel KG, Balakrishnan P, Solomon S, Hewlett I, Ranga U. PTAP motif duplication in the p6 Gag protein confers a replication advantage on HIV-1 subtype C. J Biol Chem 2018; 293:11687-11708. [PMID: 29773649 DOI: 10.1074/jbc.m117.815829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 04/30/2018] [Indexed: 11/06/2022] Open
Abstract
HIV-1 subtype C (HIV-1C) may duplicate longer amino acid stretches in the p6 Gag protein, leading to the creation of an additional Pro-Thr/Ser-Ala-Pro (PTAP) motif necessary for viral packaging. However, the biological significance of a duplication of the PTAP motif for HIV-1 replication and pathogenesis has not been experimentally validated. In a longitudinal study of two different clinical cohorts of select HIV-1 seropositive, drug-naive individuals from India, we found that 8 of 50 of these individuals harbored a mixed infection of viral strains discordant for the PTAP duplication. Conventional and next-generation sequencing of six primary viral quasispecies at multiple time points disclosed that in a mixed infection, the viral strains containing the PTAP duplication dominated the infection. The dominance of the double-PTAP viral strains over a genetically similar single-PTAP viral clone was confirmed in viral proliferation and pairwise competition assays. Of note, in the proximity ligation assay, double-PTAP Gag proteins exhibited a significantly enhanced interaction with the host protein tumor susceptibility gene 101 (Tsg101). Moreover, Tsg101 overexpression resulted in a biphasic effect on HIV-1C proliferation, an enhanced effect at low concentration and an inhibitory effect only at higher concentrations, unlike a uniformly inhibitory effect on subtype B strains. In summary, our results indicate that the duplication of the PTAP motif in the p6 Gag protein enhances the replication fitness of HIV-1C by engaging the Tsg101 host protein with a higher affinity. Our results have implications for HIV-1 pathogenesis, especially of HIV-1C.
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Affiliation(s)
- Shilpee Sharma
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Prabhu S Arunachalam
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Malini Menon
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Viswanath Ragupathy
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | | | - Joshua Jebaraj
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | | | - Chaitra Rao
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Sreshtha Pal
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Shanmugam Saravanan
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | | | | | - Suniti Solomon
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | - Indira Hewlett
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Udaykumar Ranga
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India,
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Suryawanshi P, Godbole S, Pawar J, Thakar M, Shete A. Higher expression of human telomerase reverse transcriptase in productively-infected CD4 cells possibly indicates a mechanism for persistence of the virus in HIV infection. Microbiol Immunol 2018; 62:317-326. [PMID: 29577368 DOI: 10.1111/1348-0421.12585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 12/01/2022]
Abstract
Mechanisms involved in survival of productively-infected memory CD4+cells after initial antigenic stimulation and their subsequent reversion to the resting state are critical for the development of a predominant replication-competent HIV reservoir. These mechanisms may also counter their elimination after HIV reactivation through latency-reversing agents (LRA). Thus, their evaluation is critical when using an appropriate HIV latency model that recapitulates the predominant replication-competent HIV reservoir to develop strategies for HIV eradication. The model for evaluating the possible survival mechanisms after T cell receptor (TCR) stimulation was developed by infecting memory CD4+cells with an HIV-1C primary isolate and cytokine secretion and gene expression patterns determined. Infected cells showed compromised functionality as evident from 6.8-fold lower secretion of IL-2 than from uninfected control cells. After TCR stimulation, the infected cells showed significantly higher fold increases in CD27 and CCR5 and smaller increases in CD5 mRNA over baseline values. Because CD27 expression may influence telomerase activity through AKT phosphorylation, CD27, human telomerase reverse transcriptase (hTERT) and pAKT expression in productively-infected cells from HIV-infected patients was evaluated by flow cytometry. HIV harbored in memory CD4+ cells was reactivated by HIV-1 envelope peptides, which have been shown to act as effective LRA. P24+CD4+cell showed significantly higher expression of CD27, hTERT and pAKT than P24-CD4+cells. These findings indicate compromised functionality of HIV-infected cells after TCR stimulation, which may interfere with their elimination by the immune system. They also indicate that pAKT and hTERT induction are possible survival mechanisms of productively-infected CD4+cells.
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Affiliation(s)
- Poonam Suryawanshi
- National AIDS Research Institute, Plot No 73, G Block, Maharashtra Industrial Development Corporation, Bhosari, Pune-411026, Maharashtra, India
| | - Sheela Godbole
- National AIDS Research Institute, Plot No 73, G Block, Maharashtra Industrial Development Corporation, Bhosari, Pune-411026, Maharashtra, India
| | - Jyoti Pawar
- National AIDS Research Institute, Plot No 73, G Block, Maharashtra Industrial Development Corporation, Bhosari, Pune-411026, Maharashtra, India
| | - Madhuri Thakar
- National AIDS Research Institute, Plot No 73, G Block, Maharashtra Industrial Development Corporation, Bhosari, Pune-411026, Maharashtra, India
| | - Ashwini Shete
- National AIDS Research Institute, Plot No 73, G Block, Maharashtra Industrial Development Corporation, Bhosari, Pune-411026, Maharashtra, India
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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The PTAP sequence duplication in HIV-1 subtype C Gag p6 in drug-naive subjects of India and South Africa. BMC Infect Dis 2017; 17:95. [PMID: 28118816 PMCID: PMC5259826 DOI: 10.1186/s12879-017-2184-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/04/2017] [Indexed: 11/29/2022] Open
Abstract
Background HIV-1 subtype C demonstrates several biological properties distinct from other viral subtypes. One such variation is the duplication of PTAP motif in p6 Gag. PTAP motif is a key player in viral budding. Here, we studied the prevalence of PTAP motif duplication in subtype C viral strains in a longitudinal study. Methods In a prospective follow-up study, 65 HIV-1 seropositive drug-naive subjects were monitored in two different clinical cohorts of India for 2 years with repeated sampling at 6-month intervals. The viral RNA was extracted from plasma, the gag segment was amplified and sequenced. From a subset of viral isolates the sequences of pol, env and LTR were sequenced. Using HIV-1 gag amino acid sequences available from public databases and additional sequences derived from the Indian and South-African cohorts, we examined the nature of PTAP motif duplication in subtype C. Results In 16% (8 of 50) of the primary viral strains of India, we identified a sequence duplication of the PTAP motif in Gag p6. The length of the sequence duplication varied from 6 to 14 amino acids in the viral isolates but remained fixed within a subject over a period of 24–36 month follow-up. In the duplicated motif, the core PTAP motif was invariable, but the flanking residues were highly variable. In an acute phase clinical cohort of South Africa, in a subset of 75 subjects, we found the presence of the PTAP duplication at a frequency of 29.3%. An analysis of the gag sequences from the extant databases showed that unlike other subtypes of HIV-1, subtype C has a natural propensity to generate the PTAP motif duplication at a significantly higher frequency and of greater length. Additionally, the global prevalence of PTAP duplication in subtype C appears to be increasing progressively over the past 30 years. Conclusion We showed that in subtype C, the duplication of the PTAP motif in p6 Gag involves sequence stretches of greater length, and at a much higher frequency as compared to other HIV-1 subtypes. Given that subtype C naturally lacks the Alix binding motif, the acquisition of an additional PTAP motif may confer replication advantage on this HIV-1 subtype. Further investigation is warranted to examine the significance of PTAP motif duplication on the replicative fitness of HIV-1.
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Jiang G, Dandekar S. Targeting NF-κB signaling with protein kinase C agonists as an emerging strategy for combating HIV latency. AIDS Res Hum Retroviruses 2015; 31:4-12. [PMID: 25287643 DOI: 10.1089/aid.2014.0199] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) is very effective in suppressing HIV-1 replication and restoring immune functions in HIV-infected individuals. However, it fails to eradicate the latent viral reservoirs and fully resolve chronic inflammation in HIV infection. The "shock-and-kill" strategy was recently proposed to induce latent HIV expression in the presence of HAART. Recent studies have shown that the protein kinase C (PKC) agonists are highly potent in inducing latent HIV expression from the viral reservoirs in vitro and ex vivo and in protecting primary CD4(+) T cells from HIV infection through down-modulation of their HIV coreceptor expression. The PKC agonists are excellent candidates for advancing to clinical HIV eradication strategies. This article will present a critical review of the structure and function of known PKC agonists, their mechanisms for the reactivation of latent HIV expression, and the potential of these compounds for advancing clinical HIV eradication strategies.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology, University of California, Davis, California
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, University of California, Davis, California
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Boullosa J, Bachu M, Bila D, Ranga U, Süffert T, Sasazawa T, Tanuri A. Genetic diversity in HIV-1 subtype C LTR from Brazil and Mozambique generates new transcription factor-binding sites. Viruses 2014; 6:2495-504. [PMID: 24960272 PMCID: PMC4074939 DOI: 10.3390/v6062495] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/12/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 subtype C has been substituting the subtype B population in southern Brazil. This phenomenon has been previously described in other countries, suggesting that subtype C may possess greater fitness than other subtypes. The HIV-1 long-terminal repeat (LTR) is an important regulatory region critical for the viral life cycle. Sequence insertions immediately upstream of the viral enhancer are known as the most frequent naturally occurring length polimorphisms (MFNLP). Previous reports demonstrated that the MFNLP could lead to the duplication of transcription factor binding sites (TFBS) enhancing the activity of the HIV-1 subtype C LTR. Here, we amplified and sequenced the LTR obtained from proviral DNA samples collected from patients infected with subtype C from the Southern Region of Brazil (naïve or treatment failure) and Mozambique (only naïve). We confirm the presence of different types of insertions in the LTR sequences of both the countries leading to the creation of additional TFBS. In the Brazilian clinical samples, the frequency of the sequence insertion was significantly higher in subjects experiencing treatment failure than in antiretroviral naïve patients.
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Affiliation(s)
- José Boullosa
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
| | - Mahesh Bachu
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560 064, Jakkur Post, Bangalore, India.
| | - Dulce Bila
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
| | - Udaykumar Ranga
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560 064, Jakkur Post, Bangalore, India.
| | - Theodoro Süffert
- Prefeitura Municipal de Porto Alegre, Rio Grande do Sul, 90010-170, Brazil.
| | - Tomoko Sasazawa
- Prefeitura Municipal de Curitiba, Paraná, 80000-000, Brazil.
| | - Amilcar Tanuri
- Department of Genetics, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373. Edifício do Centro de Ciências da Saúde, Bloco A, sala A2-121, Cidade Universitária, Cep: 21.941-902, Brazil.
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Mamik MK, Ghorpade A. Chemokine CXCL8 promotes HIV-1 replication in human monocyte-derived macrophages and primary microglia via nuclear factor-κB pathway. PLoS One 2014; 9:e92145. [PMID: 24662979 PMCID: PMC3963875 DOI: 10.1371/journal.pone.0092145] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Chemokine CXCL8 is an important neutrophil chemoattractant implicated in various neurodegenerative disorders. Cytokine/chemokine imbalance, with an increase in proinflammatory cytokines like interleukin-1β and tumor necrosis factor-α within the central nervous system, is a hallmark of human immunodeficiency virus (HIV)-1 infection. We previously reported that HIV-1 infection is linked to upregulation of CXCL8 in brain tissues and human astrocytes. Chemokines play crucial roles in trafficking of leukocytes and trafficking of HIV-1-infected across the blood-brain barrier play an important role in HIV-1 central nervous system disease. In the post-antiretroviral therapy era, low level of productive replication of HIV-1 in brain is a critical component of neuropathogenesis regulation. The present study investigated the effect of CXCL8 on productive infection of HIV-1 in human monocytes-derived macrophages (MDM) and primary human microglia. RESULTS Human MDM and microglia were infected with the blood or brain derived HIV-1 isolates, HIV-1ADA or HIV-1JRFL. Treatment with CXCL8 significantly upregulated HIV-1p24 levels in supernatants of both HIV-1-infected MDM as well as microglia. In addition, the formation of 2-long terminal repeat (LTR) circles, a measure of viral genome integration, was significantly higher in CXCL8-treated, HIV-1-infected MDM and microglia. Transient transfection of U937 cells with HIV-1 LTR luciferase reporter construct resulted in increased promoter activity when treated with CXCL8. Moreover, increased nuclear translocation of nuclear factor-κB was seen in HIV-1-infected MDM following CXCL8 treatment. Blocking CXCL8 receptors CXCR1 and CXCR2 abrogated the CXCL8-mediated enhanced HIV-1 replication. CONCLUSION Our results show that CXCL8 mediates productive infection of HIV-1 in MDM and microglia via receptors CXCR1 and CXCR2. These results demonstrate that CXCL8 exerts its downstream effects by increasing translocation of nuclear factor-κB into the nucleus, thereby promoting HIV-1 LTR activity.
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Affiliation(s)
- Manmeet K. Mamik
- Department of Cell Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Anuja Ghorpade
- Department of Cell Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
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Bachu M, Yalla S, Asokan M, Verma A, Neogi U, Sharma S, Murali RV, Mukthey AB, Bhatt R, Chatterjee S, Rajan RE, Cheedarla N, Yadavalli VS, Mahadevan A, Shankar SK, Rajagopalan N, Shet A, Saravanan S, Balakrishnan P, Solomon S, Vajpayee M, Satish KS, Kundu TK, Jeang KT, Ranga U. Multiple NF-κB sites in HIV-1 subtype C long terminal repeat confer superior magnitude of transcription and thereby the enhanced viral predominance. J Biol Chem 2012; 287:44714-35. [PMID: 23132857 DOI: 10.1074/jbc.m112.397158] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We demonstrate that at least three different promoter variant strains of HIV-1 subtype C have been gradually expanding and replacing the standard subtype C viruses in India, and possibly in South Africa and other global regions, over the past decade. The new viral strains contain an additional NF-κB, NF-κB-like, or RBEIII site in the viral promoter. Although the acquisition of an additional RBEIII site is a property shared by all the HIV-1 subtypes, acquiring an additional NF-κB site remains an exclusive property of subtype C. The acquired κB site is genetically distinct, binds the p50-p65 heterodimer, and strengthens the viral promoter at the levels of transcription initiation and elongation. The 4-κB viruses dominate the 3-κB "isogenic" viral strains in pairwise competition assays in T-cell lines, primary cells, and the ecotropic human immunodeficiency virus mouse model. The dominance of the 4-κB viral strains is also evident in the natural context when the subjects are coinfected with κB-variant viral strains. The mean plasma viral loads, but not CD4 counts, are significantly different in 4-κB infection suggesting that these newly emerging strains are probably more infectious. It is possible that higher plasma viral loads underlie selective transmission of the 4-κB viral strains. Several publications previously reported duplication or deletion of diverse transcription factor-binding sites in the viral promoter. Unlike previous reports, our study provides experimental evidence that the new viral strains gained a potential selective advantage as a consequence of the acquired transcription factor-binding sites and importantly that these strains have been expanding at the population level.
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Affiliation(s)
- Mahesh Bachu
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
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