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Caetano DG, Napoleão-Pêgo P, Villela LM, Côrtes FH, Cardoso SW, Hoagland B, Grinsztejn B, Veloso VG, De-Simone SG, Guimarães ML. Patterns of Diversity and Humoral Immunogenicity for HIV-1 Antisense Protein (ASP). Vaccines (Basel) 2024; 12:771. [PMID: 39066409 PMCID: PMC11281420 DOI: 10.3390/vaccines12070771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
HIV-1 has an antisense gene overlapping env that encodes the ASP protein. ASP functions are still unknown, but it has been associated with gp120 in the viral envelope and membrane of infected cells, making it a potential target for immune response. Despite this, immune response patterns against ASP are poorly described and can be influenced by the high genetic variability of the env gene. To explore this, we analyzed 100k HIV-1 ASP sequences from the Los Alamos HIV sequence database using phylogenetic, Shannon entropy (Hs), and logo tools to study ASP variability in worldwide and Brazilian sequences from the most prevalent HIV-1 subtypes in Brazil (B, C, and F1). Data obtained in silico guided the design and synthesis of 15-mer overlapping peptides through spot synthesis on cellulose membranes. Peptide arrays were screened to assess IgG and IgM responses in pooled plasma samples from HIV controllers and individuals with acute or recent HIV infection. Excluding regions with low alignment accuracy, several sites with higher variability (Hs > 1.5) were identified among the datasets (25 for worldwide sequences, 20 for Brazilian sequences). Among sites with Hs < 1.5, sequence logos allowed the identification of 23 other sites with subtype-specific signatures. Altogether, amino acid variations with frequencies > 20% in the 48 variable sites identified were included in 92 peptides, divided into 15 sets, representing near full-length ASP. During the immune screening, the strongest responses were observed in three sets, one in the middle and one at the C-terminus of the protein. While some sets presented variations potentially associated with epitope displacement between IgG and IgM targets and subtype-specific signatures appeared to impact the level of response for some peptides, signals of cross-reactivity were observed for some sets despite the presence of B/C/F1 signatures. Our data provides a map of ASP regions preferentially targeted by IgG and IgM responses. Despite B/C/F1 subtype signatures in ASP, the amino acid variation in some areas preferentially targeted by IgM and IgG did not negatively impact the response against regions with higher immunogenicity.
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Affiliation(s)
- Diogo Gama Caetano
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
| | - Paloma Napoleão-Pêgo
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Larissa Melo Villela
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Fernanda Heloise Côrtes
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
| | - Sandra Wagner Cardoso
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Brenda Hoagland
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Valdilea Gonçalves Veloso
- Instituto Nacional de Infectologia Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
| | - Salvatore Giovanni De-Simone
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil
- Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói 22040-036, Brazil
| | - Monick Lindenmeyer Guimarães
- AIDS and Molecular Immunology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil (M.L.G.)
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Pavesi A, Romerio F. Creation of the HIV-1 antisense gene asp coincided with the emergence of the pandemic group M and is associated with faster disease progression. Microbiol Spectr 2024; 12:e0380223. [PMID: 38230940 PMCID: PMC10846101 DOI: 10.1128/spectrum.03802-23] [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: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
Despite being first identified more than three decades ago, the antisense gene asp of HIV-1 remains an enigma. asp is present uniquely in pandemic (group M) HIV-1 strains, and it is absent in all non-pandemic (out-of-M) HIV-1 strains and virtually all non-human primate lentiviruses. This suggests that the creation of asp may have contributed to HIV-1 fitness or worldwide spread. It also raises the question of which evolutionary processes were at play in the creation of asp. Here, we show that HIV-1 genomes containing an intact asp gene are associated with faster HIV-1 disease progression. Furthermore, we demonstrate that the creation of a full-length asp gene occurred via the evolution of codon usage in env overlapping asp on the opposite strand. This involved differential use of synonymous codons or conservative amino acid substitution in env that eliminated internal stop codons in asp, and redistribution of synonymous codons in env that minimized the likelihood of new premature stops arising in asp. Nevertheless, the creation of a full-length asp gene reduced the genetic diversity of env. The Luria-Delbruck fluctuation test suggests that the interrupted asp open reading frame (ORF) is the progenitor of the intact ORF, rather than a descendant under random genetic drift. Therefore, the existence of group-M isolates with a truncated asp ORF indicates an incomplete transition process. For the first time, our study links the presence of a full-length asp ORF to faster disease progression, thus warranting further investigation into the cellular processes and molecular mechanisms through which the ASP protein impacts HIV-1 replication, transmission, and pathogenesis.IMPORTANCEOverlapping genes engage in a tug-of-war, constraining each other's evolution. The creation of a new gene overlapping an existing one comes at an evolutionary cost. Thus, its conservation must be advantageous, or it will be lost, especially if the pre-existing gene is essential for the viability of the virus or cell. We found that the creation and conservation of the HIV-1 antisense gene asp occurred through differential use of synonymous codons or conservative amino acid substitutions within the overlapping gene, env. This process did not involve amino acid changes in ENV that benefited its function, but rather it constrained the evolution of ENV. Nonetheless, the creation of asp brought a net selective advantage to HIV-1 because asp is conserved especially among high-prevalence strains. The association between the presence of an intact asp gene and faster HIV-1 disease progression supports that conclusion and warrants further investigation.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Epigenetic Regulation of HIV-1 Sense and Antisense Transcription in Response to Latency-Reversing Agents. Noncoding RNA 2023; 9:ncrna9010005. [PMID: 36649034 PMCID: PMC9844351 DOI: 10.3390/ncrna9010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Nucleosomes positioned on the HIV-1 5' long terminal repeat (LTR) regulate sense transcription as well as the establishment and maintenance of latency. A negative-sense promoter (NSP) in the 3' LTR expresses antisense transcripts with coding and non-coding activities. Previous studies identified cis-acting elements that modulate NSP activity. Here, we used the two chronically infected T cell lines, ACH-2 and J1.1, to investigate epigenetic regulation of NSP activity. We found that histones H3 and H4 are present on the 3' LTR in both cell lines. Following treatment with histone deacetylase inhibitors (HDACi), the levels of H3K27Ac increased and histone occupancy declined. HDACi treatment also led to increased levels of RNA polymerase II (RNPII) at NSP, and antisense transcription was induced with similar kinetics and to a similar extent as 5' LTR-driven sense transcription. We also detected H3K9me2 and H3K27me3 on NSP, along with the enzymes responsible for these epigenetic marks, namely G9a and EZH2, respectively. Treatment with their respective inhibitors had little or no effect on RNPII occupancy at the two LTRs, but it induced both sense and antisense transcription. Moreover, the increased expression of antisense transcripts in response to treatment with a panel of eleven latency-reversing agents closely paralleled and was often greater than the effect on sense transcripts. Thus, HIV-1 sense and antisense RNA expression are both regulated via acetylation and methylation of lysine 9 and 27 on histone H3. Since HIV-1 antisense transcripts act as non-coding RNAs promoting epigenetic silencing of the 5' LTR, our results suggest that the limited efficacy of latency-reversing agents in the context of 'shock and kill' cure strategies may be due to concurrent induction of antisense transcripts thwarting their effect on sense transcription.
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Kuniholm J, Coote C, Henderson AJ. Defective HIV-1 genomes and their potential impact on HIV pathogenesis. Retrovirology 2022; 19:13. [PMID: 35764966 PMCID: PMC9238239 DOI: 10.1186/s12977-022-00601-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Defective HIV-1 proviruses represent a population of viral genomes that are selected for by immune pressures, and clonally expanded to dominate the persistent HIV-1 proviral genome landscape. There are examples of RNA and protein expression from these compromised genomes which are generated by a variety of mechanisms. Despite the evidence that these proviruses are transcribed and translated, their role in HIV pathogenesis has not been fully explored. The potential for these genomes to participate in immune stimulation is particularly relevant considering the accumulation of cells harboring these defective proviruses over the course of antiretroviral therapy in people living with HIV. The expression of defective proviruses in different cells and tissues could drive innate sensing mechanisms and inflammation. They may also alter antiviral T cell responses and myeloid cell functions that directly contribute to HIV-1 associated chronic comorbidities. Understanding the impact of these defective proviruses needs to be considered as we advance cure strategies that focus on targeting the diverse population of HIV-1 proviral genomes.
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Affiliation(s)
- Jeffrey Kuniholm
- Department of Microbiology, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA
| | - Carolyn Coote
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA
| | - Andrew J Henderson
- Department of Microbiology, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA. .,Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA.
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Gholizadeh Z, Iqbal MS, Li R, Romerio F. The HIV-1 Antisense Gene ASP: The New Kid on the Block. Vaccines (Basel) 2021; 9:vaccines9050513. [PMID: 34067514 PMCID: PMC8156140 DOI: 10.3390/vaccines9050513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 01/14/2023] Open
Abstract
Viruses have developed incredibly creative ways of making a virtue out of necessity, including taking full advantage of their small genomes. Indeed, viruses often encode multiple proteins within the same genomic region by using two or more reading frames in both orientations through a process called overprinting. Complex retroviruses provide compelling examples of that. The human immunodeficiency virus type 1 (HIV-1) genome expresses sixteen proteins from nine genes that are encoded in the three positive-sense reading frames. In addition, the genome of some HIV-1 strains contains a tenth gene in one of the negative-sense reading frames. The so-called Antisense Protein (ASP) gene overlaps the HIV-1 Rev Response Element (RRE) and the envelope glycoprotein gene, and encodes a highly hydrophobic protein of ~190 amino acids. Despite being identified over thirty years ago, relatively few studies have investigated the role that ASP may play in the virus lifecycle, and its expression in vivo is still questioned. Here we review the current knowledge about ASP, and we discuss some of the many unanswered questions.
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, Pazgier M, Ray K, Latinovic OS, Romerio F. The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope. J Virol 2019; 93:e00574-19. [PMID: 31434734 PMCID: PMC6803264 DOI: 10.1128/jvi.00574-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
The negative strand of HIV-1 encodes a highly hydrophobic antisense protein (ASP) with no known homologs. The presence of humoral and cellular immune responses to ASP in HIV-1 patients indicates that ASP is expressed in vivo, but its role in HIV-1 replication remains unknown. We investigated ASP expression in multiple chronically infected myeloid and lymphoid cell lines using an anti-ASP monoclonal antibody (324.6) in combination with flow cytometry and microscopy approaches. At baseline and in the absence of stimuli, ASP shows polarized subnuclear distribution, preferentially in areas with low content of suppressive epigenetic marks. However, following treatment with phorbol 12-myristate 13-acetate (PMA), ASP translocates to the cytoplasm and is detectable on the cell surface, even in the absence of membrane permeabilization, indicating that 324.6 recognizes an ASP epitope that is exposed extracellularly. Further, surface staining with 324.6 and anti-gp120 antibodies showed that ASP and gp120 colocalize, suggesting that ASP might become incorporated in the membranes of budding virions. Indeed, fluorescence correlation spectroscopy studies showed binding of 324.6 to cell-free HIV-1 particles. Moreover, 324.6 was able to capture and retain HIV-1 virions with efficiency similar to that of the anti-gp120 antibody VRC01. Our studies indicate that ASP is an integral protein of the plasma membranes of chronically infected cells stimulated with PMA, and upon viral budding, ASP becomes a structural protein of the HIV-1 envelope. These results may provide leads to investigate the possible role of ASP in the virus replication cycle and suggest that ASP may represent a new therapeutic or vaccine target.IMPORTANCE The HIV-1 genome contains a gene expressed in the opposite, or antisense, direction to all other genes. The protein product of this antisense gene, called ASP, is poorly characterized, and its role in viral replication remains unknown. We provide evidence that the antisense protein, ASP, of HIV-1 is found within the cell nucleus in unstimulated cells. In addition, we show that after PMA treatment, ASP exits the nucleus and localizes on the cell membrane. Moreover, we demonstrate that ASP is present on the surfaces of viral particles. Altogether, our studies identify ASP as a new structural component of HIV-1 and show that ASP is an accessory protein that promotes viral replication. The presence of ASP on the surfaces of both infected cells and viral particles might be exploited therapeutically.
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Affiliation(s)
- Yvonne Affram
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Juan C Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Zahra Gholizadeh
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - William D Tolbert
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Wei Zhou
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Maria D Iglesias-Ussel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marzena Pazgier
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olga S Latinovic
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Fabio Romerio
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Peng BJ, Carlson JM, Liu MKP, Gao F, Goonetilleke N, McMichael AJ, Borrow P, Gilmour J, Heath SL, Hunter E, Bansal A, Goepfert PA. Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection. J Virol 2018; 92:e00711-18. [PMID: 30021907 PMCID: PMC6146806 DOI: 10.1128/jvi.00711-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/31/2023] Open
Abstract
While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Of the 66 predicted CE, 10 were recognized in 8/32 and 4/11 patients with chronic and acute infections, respectively. The immunogenic CE were all derived from a single antisense reading frame within pol However, when these CE were tested using longitudinal study samples, CE-specific T cell responses were detected but did not consistently select for viral escape mutations. Thus, while we demonstrated that CE are immunogenic in acute infection, the immune responses to CE are not major drivers of viral escape in the initial stages of HIV infection. The latter finding may be due to either the subdominant nature of CE-specific responses, the low antigen sensitivity, or the magnitude of CE responses during acute infections.IMPORTANCE Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question following acute infection. In this comprehensive study, we utilized longitudinal viral sequencing data obtained from three separate acute infection cohorts to predict potential cryptic epitopes based on HLA-I-associated viral escape. Our data show that cryptic epitopes are immunogenic during acute infection and that many of the responses they elicit are toward translation products of HIV-1 antisense reading frames. However, despite cryptic epitope targeting, our study did not find any evidence of early CD8-mediated immune escape. Nevertheless, improving cryptic epitope-specific CD8 T cell responses may still be beneficial in both preventative and therapeutic HIV-1 vaccines.
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Affiliation(s)
- Binghao J Peng
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Michael K P Liu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Feng Gao
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Nilu Goonetilleke
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Starck SR, Shastri N. Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. Immunol Rev 2017; 272:8-16. [PMID: 27319338 DOI: 10.1111/imr.12434] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Effective immune surveillance by CD8(+) cytotoxic T cells of intracellular microbes and cancer depends on the antigen presentation pathway. This pathway produces an optimal peptide repertoire for presentation by major histocompatibility (MHC) class I molecules (pMHCs I) on the cell surface. We have known for years that the pMHC I repertoire is a reflection of the intracellular protein pool. However, many studies have revealed that pMHCs I present peptides not only from precursors encoded in open-reading frames of mRNA transcripts but also cryptic peptides encoded in apparently 'untranslated' regions. These sources vastly increase the availability of peptides for presentation and immune evasion. Here, we review studies on the composition of the cryptic pMHC I repertoire, the immunological significance of these pMHC I, and the novel translational mechanisms that generate cryptic peptides from unusual sources.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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10
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Zapata JC, Campilongo F, Barclay RA, DeMarino C, Iglesias-Ussel MD, Kashanchi F, Romerio F. The Human Immunodeficiency Virus 1 ASP RNA promotes viral latency by recruiting the Polycomb Repressor Complex 2 and promoting nucleosome assembly. Virology 2017; 506:34-44. [PMID: 28340355 PMCID: PMC5505171 DOI: 10.1016/j.virol.2017.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/04/2023]
Abstract
Various epigenetic marks at the HIV-1 5′LTR suppress proviral expression and promote latency. Cellular antisense transcripts known as long noncoding RNAs (lncRNAs) recruit the polycomb repressor complex 2 (PRC2) to gene promoters, which catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), thus promoting nucleosome assembly and suppressing gene expression. We found that an HIV-1 antisense transcript expressed from the 3′LTR and encoding the antisense protein ASP promotes proviral latency. Expression of ASP RNA reduced HIV-1 replication in Jurkat cells. Moreover, ASP RNA expression promoted the establishment and maintenance of HIV-1 latency in Jurkat E4 cells. We show that this transcript interacts with and recruits PRC2 to the HIV-1 5′LTR, increasing accumulation of the suppressive epigenetic mark H3K27me3, while reducing RNA Polymerase II and thus proviral transcription. Altogether, our results suggest that the HIV-1 ASP transcript promotes epigenetic silencing of the HIV-1 5′LTR and proviral latency through the PRC2 pathway.
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Affiliation(s)
- Juan C Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Federica Campilongo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert A Barclay
- Laboratory of Molecular Virology, George Mason University, Manassas, VA, USA
| | - Catherine DeMarino
- Laboratory of Molecular Virology, George Mason University, Manassas, VA, USA
| | - Maria D Iglesias-Ussel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, George Mason University, Manassas, VA, USA
| | - Fabio Romerio
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA.
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11
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Bansal A, Mann T, Sterrett S, Peng BJ, Bet A, Carlson JM, Goepfert PA. Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome. J Acquir Immune Defic Syndr 2015; 70:1-8. [PMID: 26322665 DOI: 10.1097/qai.0000000000000700] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cryptic epitopes (CEs) are peptides derived from the translation of 1 or more of the 5 alternative reading frames (ARFs; 2 sense and 3 antisense) of genes. Here, we compared response rates to HIV-1-specific CE predicted to be restricted by HLA-I alleles associated with protection against disease progression to those without any such association. METHODS Peptides (9mer to 11mer) were designed based on HLA-I-binding algorithms for B*27, B*57, or B*5801 (protective alleles) and HLA-B*5301 or B*5501 (nonprotective allele) in all 5 ARFs of the 9 HIV-1 encoded proteins. Peptides with >50% probability of being an epitope (n = 231) were tested for T-cell responses in an IFN-γ enzyme-linked immunosorbent spot (ELISpot) assay. Peripheral blood mononuclear cell samples from HIV-1 seronegative donors (n = 42) and HIV-1 seropositive patients with chronic clade B infections (n = 129) were used. RESULTS Overall, 16%, 2%, and 2% of chronic HIV infected patients had CE responses by IFN-γ ELISpot in the protective, nonprotective, and seronegative groups, respectively (P = 0.009, Fischer exact test). Twenty novel CE-specific responses were mapped (median magnitude of 95 spot forming cells/10 peripheral blood mononuclear cells), and most were both antisense derived (90%) and represented ARFs of accessory proteins (55%). CE-specific CD8 T cells were multifunctional and proliferated when assessed by intracellular cytokine staining. CONCLUSIONS CE responses were preferentially restricted by the protective HLA-I alleles in HIV-1 infection, suggesting that they may contribute to viral control in this group of patients.
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Affiliation(s)
- Anju Bansal
- *Department of Medicine, University of Alabama at Birmingham, Birmingham, AL; and †Microsoft Research, Redmond, WA
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12
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Bet A, Maze EA, Bansal A, Sterrett S, Gross A, Graff-Dubois S, Samri A, Guihot A, Katlama C, Theodorou I, Mesnard JM, Moris A, Goepfert PA, Cardinaud S. The HIV-1 antisense protein (ASP) induces CD8 T cell responses during chronic infection. Retrovirology 2015; 12:15. [PMID: 25809376 PMCID: PMC4335690 DOI: 10.1186/s12977-015-0135-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
Background CD8+ T cells recognize HIV-1 epitopes translated from a gene’s primary reading frame (F1) and any one of its five alternative reading frames (ARFs) in the forward (F2, F3) or reverse (R1-3) directions. The 3’ end of HIV-1’s proviral coding strand contains a conserved sequence that is directly overlapping but antiparallel to the env gene (ARF R2) and encodes for a putative antisense HIV-1 protein called ASP. ASP expression has been demonstrated in vitro using HIV-transfected cell lines or infected cells. Although antibodies to ASP were previously detected in patient sera, T cell recognition of ASP-derived epitopes has not been evaluated. We therefore investigated the ex vivo and in vitro induction of ASP-specific T cell responses as a measure of immune recognition and protein expression during HIV-1 infection. Results A panel of overlapping peptides was initially designed from the full-length ASP sequence to perform a global assessment of T cell responses. Recognition of ASP-derived antigens was evaluated in an IFN-γELISpot assay using PBMCs from HIV-1 seropositive and seronegative individuals. Eight of 25 patients had positive responses to ASP antigens and none of the seronegative donors responded. As a complimentary approach, a second set of antigens was designed using HLA-I binding motifs and affinities. Two ASP-derived peptides with high predicted binding affinities for HLA-A*02 (ASP-YL9) and HLA-B*07 (ASP-TL10) were tested using PBMCs from HIV-1 seropositive and seronegative individuals who expressed the matching HLA-I-restricting allele. We found that HLA-I-restricted ASP peptides were only recognized by CD8+ T cells from patients with the relevant HLA-I and did not induce responses in any of the seronegative donors or patients who do not express the restrictive HLA alleles. Further, ASP-YL9-specific CD8+ T cells had functional profiles that were similar to a previously described HLA-A*02-restricted epitope (Gag-SL9). Specific recognition of ASP-YL9 by CD8+ T cells was also demonstrated by tetramer staining using cells from an HLA-A*02 HIV-infected patient. Conclusion Our results provide the first description of CD8+ T cell-mediated immune responses to ASP in HIV-1-infected patients, demonstrating that ASP is expressed during infection. Our identification of epitopes within ASP has implications for designing HIV vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0135-y) contains supplementary material, which is available to authorized users.
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Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1. J Virol 2015; 89:4015-9. [PMID: 25589651 DOI: 10.1128/jvi.03435-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytotoxic-T lymphocyte (CTL) responses to epitopes in alternative HIV reading frames have been reported. However, the extent of CTL responses to putative proteins encoded in antisense reading frames is unknown. Using sequence alignments and computational approaches, we here predict five potential antisense HIV proteins and characterize common CTL responses against them. Results suggest that antisense-derived sequences are commonly transcribed and translated and could encode functional proteins that contain important targets of anti-HIV cellular immunity.
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Bet A, Sterret S, Sato A, Bansal A, Goepfert PA. Characterization of T-cell responses to cryptic epitopes in recipients of a noncodon-optimized HIV-1 vaccine. J Acquir Immune Defic Syndr 2014; 65:142-50. [PMID: 24442221 PMCID: PMC3896890 DOI: 10.1097/qai.0b013e3182a9917e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Cryptic epitopes (CEs) can be encoded by any of the 5 alternative reading frames (ARFs, 2 sense and 3 antisense) of a known gene. Although CE responses are commonly detected during HIV-1 infection, it is not known whether these responses are induced after vaccination. METHODS Using a bioinformatic approach, we determined that vaccines with codon-optimized HIV inserts significantly skewed CE sequences and are not likely to induce crossreactive responses to natural HIV CE. We then evaluated the CE- and protein-specific T-cell responses using Gag, Pol, and ARF peptide pools among participants immunized with a non-codon optimized vaccine regimen of 2 pGA2/JS7 DNA primes followed by 2 MVA/HIV62 Gag-Pol-Env vector boosts or 4 saline injections. RESULTS Vaccinees had significantly more interferon gamma enzyme-linked immunosorbent spot (IFNγ ELISpot) responses toward Gag (P = 0.003) but not toward Pol protein than did placebo recipients. However, CE-specific T-cell responses were low in magnitude, and their frequencies did not differ significantly between vaccine and placebo recipients. Additionally, most positive CE responses could not be mapped to individual peptides. After expanding responses in a cultured assay, however, the frequency and the median magnitude of responses to ARF peptides were significantly greater in vaccinees (P < 0.0001), indicating that CE-specific T-cell responses are present but below an ex vivo assay's limit of detection. CONCLUSIONS Our data demonstrate that HIV-1 vaccines currently in clinical trials are poorly immunogenic with regard to CE-specific T-cell responses. Therefore, the context of HIV-1 immunogens may need to be modified as a comprehensive strategy to broaden vaccine-induced T-cell responses.
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Affiliation(s)
- Anne Bet
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL USA 35294
| | - Sarah Sterret
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL USA 35294
| | - Alicia Sato
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL USA 35294
| | - Paul A. Goepfert
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL USA 35294
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL USA 35294
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Walsh AD, Bimber BN, Das A, Piaskowski SM, Rakasz EG, Bean AT, Mudd PA, Ericsen AJ, Wilson NA, Hughes AL, O'Connor DH, Maness NJ. Acute phase CD8+ T lymphocytes against alternate reading frame epitopes select for rapid viral escape during SIV infection. PLoS One 2013; 8:e61383. [PMID: 23671565 PMCID: PMC3645990 DOI: 10.1371/journal.pone.0061383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 03/07/2013] [Indexed: 12/13/2022] Open
Abstract
CD8+ T Lymphocytes (CTL) can control AIDS virus replication. However, natural selection favoring viral variants that escape CTL recognition is a common feature of both simian immunodeficiency virus (SIV) infection of macaques and HIV infection of humans. Emerging data indicate that CTL directed against alternate reading frame (ARF)-derived epitopes (a.k.a. cryptic epitopes) are important components of the total virus-specific response in SIV and HIV infection but the contributions of these responses during the critical first several weeks of infection have not been determined. We used a focused deep sequencing approach to examine acute phase viral evolution in response to CTL targeting two polypeptides encoded by ARFs of SIVmac239 in SIV-infected rhesus macaques. We report high magnitude CTL responses as early as three weeks post-infection against epitopes within both ARFs, which both overlap the 5′ end of the env gene. Further, mutations accumulated in the epitopes by three to four weeks post infection consistent with viral escape. Interestingly, these mutations largely maintained the primary amino acid sequence of the overlapping Envelope protein. Our data show that high frequency CTL target cryptic epitopes and exert selective pressure on SIV during the acute phase, underscoring the importance of these unique immune responses.
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Affiliation(s)
- Andrew D. Walsh
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Benjamin N. Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Arpita Das
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Shari M. Piaskowski
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eva G. Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander T. Bean
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Philip A. Mudd
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Medical Scientist Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Adam J. Ericsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nancy A. Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- * E-mail:
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