HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection

ABSTRACT Immune control of human immunodeficiency virus type 1 (HIV) infection is typically associated with effective Gag-specific CD8+ T-cell responses. We here focus on HLA-B*14, which protects against HIV disease progression, but the immunodominant HLA-B*14-restricted anti-HIV response is Env specific (ERYLKDQQL, HLA-B*14-EL9). A subdominant HLA-B*14-restricted response targets Gag (DRYFKTLRA, HLA-B*14-DA9). Using HLA-B*14/peptide-saporin-conjugated tetramers, we show that HLA-B*14-EL9 is substantially more potent at inhibiting viral replication than HLA-B*14-DA9. HLA-B*14-EL9 also has significantly higher functional avidity (P < 0.0001) and drives stronger selection pressure on the virus than HLA-B*14-DA9. However, these differences were HLA-B*14 subtype specific, applying only to HLA-B*14:02 and not to HLA-B*14:01. Furthermore, the HLA-B*14-associated protection against HIV disease progression is significantly greater for HLA-B*14:02 than for HLA-B*14:01, consistent with the superior antiviral efficacy of the HLA-B*14-EL9 response. Thus, although Gag-specific CD8+ T-cell responses may usually have greater anti-HIV efficacy, factors independent of protein specificity, including functional avidity of individual responses, are also critically important to immune control of HIV. IMPORTANCE In HIV infection, although cytotoxic T lymphocytes (CTL) play a potentially critical role in eradication of viral reservoirs, the features that constitute an effective response remain poorly defined. We focus on HLA-B*14, unique among HLAs associated with control of HIV in that the dominant CTL response is Env specific, not Gag specific. We demonstrate that Env-specific HLA-B*14-restricted activity is substantially more efficacious than the subdominant HLA-B*14-restricted Gag response. Env immunodominance over Gag and strong Env-mediated selection pressure on HIV are observed only in subjects expressing HLA-B*14:02, and not HLA-B*14:01. This reflects the increased functional avidity of the Env response over Gag, substantially more marked for HLA-B*14:02. Finally, we show that HLA-B*14:02 is significantly more strongly associated with viremic control than HLA-B*14:01. These findings indicate that, although Gag-specific CTL may usually have greater anti-HIV efficacy than Env responses, factors independent of protein specificity, including functional avidity, may carry greater weight in mediating effective control of HIV.

[1]  D. Follmann,et al.  CD8+ T-cell Cytotoxic Capacity Associated with Human Immunodeficiency Virus-1 Control Can Be Mediated through Various Epitopes and Human Leukocyte Antigen Types , 2014, EBioMedicine.

[2]  Angela R. McLean,et al.  Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence , 2014, Proceedings of the National Academy of Sciences.

[3]  P. Goulder,et al.  Impact of HLA-B*35 subtype differences on HIV disease outcome in Mexico , 2014, AIDS.

[4]  Des C. Jones,et al.  LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection , 2014, PLoS genetics.

[5]  Todd M. Allen,et al.  How a single patient influenced HIV research--15-year follow-up. , 2014, The New England journal of medicine.

[6]  J. Frelinger,et al.  Deletion of naïve T cells recognizing the minor histocompatibility antigen HY with toxin-coupled peptide-MHC class I tetramers inhibits cognate CTL responses and alters immunodominance. , 2013, Transplant immunology.

[7]  Jessica Prince,et al.  Selection bias at the heterosexual HIV-1 transmission bottleneck , 2013, Science.

[8]  C. Rouzioux,et al.  Both HLA-B*57 and Plasma HIV RNA Levels Contribute to the HIV-Specific CD8+ T Cell Response in HIV Controllers , 2013, Journal of Virology.

[9]  N. Frahm,et al.  Vaccine-induced gag-specific T cells are associated with reduced viremia after HIV-1 infection. , 2013, The Journal of infectious diseases.

[10]  Klaus Schulten,et al.  Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics , 2013, Nature.

[11]  B. Clotet,et al.  Expansion of antibody secreting cells and modulation of neutralizing antibody activity in HIV infected individuals undergoing structured treatment interruptions , 2013, Journal of Translational Medicine.

[12]  David Heckerman,et al.  Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins , 2013, Journal of Virology.

[13]  J. Prado,et al.  Early Antigen Presentation of Protective HIV-1 KF11Gag and KK10Gag Epitopes from Incoming Viral Particles Facilitates Rapid Recognition of Infected Cells by Specific CD8+ T Cells , 2012, Journal of Virology.

[14]  Todd M. Allen,et al.  Vaccine-induced CD8+ T cells control AIDS virus replication , 2012, Nature.

[15]  B. Walker,et al.  HIV and HLA class I: an evolving relationship. , 2012, Immunity.

[16]  Andrew K. Sewell,et al.  Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope , 2012, Journal of Virology.

[17]  T. Ndung’u,et al.  HIV control through a single nucleotide on the HLA-I locus , 2012, Journal of Virology.

[18]  Todd M. Allen,et al.  TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection , 2012, Nature Immunology.

[19]  David Heckerman,et al.  Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1 , 2012, Journal of Virology.

[20]  D. Heckerman,et al.  CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control , 2012, PloS one.

[21]  B. Walker,et al.  HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control , 2011, Journal of Virology.

[22]  D. Heckerman,et al.  HLA-A*7401–Mediated Control of HIV Viremia Is Independent of Its Linkage Disequilibrium with HLA-B*5703 , 2011, The Journal of Immunology.

[23]  Jeffrey N. Martin,et al.  A Low T Regulatory Cell Response May Contribute to Both Viral Control and Generalized Immune Activation in HIV Controllers , 2011, PloS one.

[24]  O. Yang,et al.  Antiviral Activity of Human Immunodeficiency Virus Type 1 Gag-Specific Cytotoxic T Lymphocyte Targeting Is Not Necessarily Intrinsically Superior to Envelope Targeting , 2010, Journal of Virology.

[25]  Jack T Stapleton,et al.  The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation , 2010, Science.

[26]  S. Buus,et al.  Efficacious Early Antiviral Activity of HIV Gag- and Pol-Specific HLA-B*2705-Restricted CD8+ T Cells , 2010, Journal of Virology.

[27]  D. Heckerman,et al.  Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection , 2010, Journal of Virology.

[28]  Mark Connors,et al.  Long-term nonprogressive disease among untreated HIV-infected individuals: clinical implications of understanding immune control of HIV. , 2010, JAMA.

[29]  A. Sáez-Cirión,et al.  Ex vivo T cell–based HIV suppression assay to evaluate HIV-specific CD8+ T-cell responses , 2010, Nature Protocols.

[30]  T. Kepler,et al.  Toxin-Coupled MHC Class I Tetramers Can Specifically Ablate Autoreactive CD8+ T Cells and Delay Diabetes in Nonobese Diabetic Mice , 2010, The Journal of Immunology.

[31]  R. Ahmed,et al.  T‐cell reconstitution without T‐cell immunopathology in two models of T‐cell‐mediated tissue destruction , 2009, Immunology.

[32]  D. Watkins,et al.  Infection with “Escaped” Virus Variants Impairs Control of Simian Immunodeficiency Virus SIVmac239 Replication in Mamu-B*08-Positive Macaques , 2009, Journal of Virology.

[33]  C. Hallahan,et al.  Defective Human Immunodeficiency Virus-Specific CD8+ T-Cell Polyfunctionality, Proliferation, and Cytotoxicity Are Not Restored by Antiretroviral Therapy , 2009, Journal of Virology.

[34]  B. Autran,et al.  Antigen sensitivity is a major determinant of CD8+ T-cell polyfunctionality and HIV-suppressive activity. , 2009, Blood.

[35]  C. Rouzioux,et al.  Heterogeneity in HIV Suppression by CD8 T Cells from HIV Controllers: Association with Gag-Specific CD8 T Cell Responses1 , 2009, The Journal of Immunology.

[36]  Todd M. Allen,et al.  HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphocyte Recognition , 2009, Journal of Virology.

[37]  B. Walker,et al.  Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703–positive individuals and their transmission recipients , 2009, The Journal of experimental medicine.

[38]  Eric J. Arts,et al.  Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response , 2009, PLoS pathogens.

[39]  Todd M. Allen,et al.  Differential Neutralization of Human Immunodeficiency Virus (HIV) Replication in Autologous CD4 T Cells by HIV-Specific Cytotoxic T Lymphocytes , 2009, Journal of Virology.

[40]  Bin Li,et al.  HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphotye Recognition , 2008, Journal of Virology.

[41]  C. Hallahan,et al.  Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control. , 2008, Immunity.

[42]  D. Heckerman,et al.  Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point , 2008, Journal of Virology.

[43]  A. Hughes,et al.  Comprehensive Immunological Evaluation Reveals Surprisingly Few Differences between Elite Controller and Progressor Mamu-B*17-Positive Simian Immunodeficiency Virus-Infected Rhesus Macaques , 2008, Journal of Virology.

[44]  C. Sylvester-Hvid,et al.  One-Pot, Mix-and-Read Peptide-MHC Tetramers , 2008, PloS one.

[45]  D. Heckerman,et al.  Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure. , 2008, AIDS research and human retroviruses.

[46]  David A. Price,et al.  Superior control of HIV-1 replication by CD8+ T cells is reflected by their avidity, polyfunctionality, and clonal turnover , 2007, The Journal of experimental medicine.

[47]  Todd M. Allen,et al.  Escape from the Dominant HLA-B27-Restricted Cytotoxic T-Lymphocyte Response in Gag Is Associated with a Dramatic Reduction in Human Immunodeficiency Virus Type 1 Replication , 2007, Journal of Virology.

[48]  Todd M. Allen,et al.  Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A , 2007, Journal of Virology.

[49]  D. Watkins,et al.  Pol-Specific CD8+ T Cells Recognize Simian Immunodeficiency Virus-Infected Cells Prior to Nef-Mediated Major Histocompatibility Complex Class I Downregulation , 2007, Journal of Virology.

[50]  E. Rosenberg,et al.  Recognition of a Defined Region within p24 Gag by CD8+ T Cells during Primary Human Immunodeficiency Virus Type 1 Infection in Individuals Expressing Protective HLA Class I Alleles , 2007, Journal of Virology.

[51]  Asier Sáez-Cirión,et al.  HIV controllers exhibit potent CD8 T cell capacity to suppress HIV infection ex vivo and peculiar cytotoxic T lymphocyte activation phenotype , 2007, Proceedings of the National Academy of Sciences.

[52]  J. Frelinger,et al.  Selective deletion of antigen-specific CD8+ T cells by MHC class I tetramers coupled to the type I ribosome-inactivating protein saporin. , 2007, Blood.

[53]  D. Watkins,et al.  Gag-Specific CD8+ T Lymphocytes Recognize Infected Cells before AIDS-Virus Integration and Viral Protein Expression1 , 2007, The Journal of Immunology.

[54]  F. Pereyra,et al.  Control of Human Immunodeficiency Virus Type 1 Is Associated with HLA-B*13 and Targeting of Multiple Gag-Specific CD8+ T-Cell Epitopes , 2007, Journal of Virology.

[55]  M. Hoelscher,et al.  CD8 T-Cell Recognition of Multiple Epitopes within Specific Gag Regions Is Associated with Maintenance of a Low Steady-State Viremia in Human Immunodeficiency Virus Type 1-Seropositive Patients , 2006, Journal of Virology.

[56]  M. McElrath,et al.  Preservation of T Cell Proliferation Restricted by Protective HLA Alleles Is Critical for Immune Control of HIV-1 Infection1 , 2006, The Journal of Immunology.

[57]  Mario Roederer,et al.  HIV nonprogressors preferentially maintain highly functional HIV-specific CD8+ T cells. , 2006, Blood.

[58]  B. Walker,et al.  Fitness Cost of Escape Mutations in p24 Gag in Association with Control of Human Immunodeficiency Virus Type 1 , 2006, Journal of Virology.

[59]  Bette T. Korber,et al.  Relative Dominance of Gag p24-Specific Cytotoxic T Lymphocytes Is Associated with Human Immunodeficiency Virus Control , 2006, Journal of Virology.

[60]  A. Paradela,et al.  Two HLA-B14 Subtypes (B*1402 and B*1403) Differentially Associated with Ankylosing Spondylitis Differ Substantially in Peptide Specificity but Have Limited Peptide and T-cell Epitope Sharing with HLA-B27* , 2005, Journal of Biological Chemistry.

[61]  C. Rouzioux,et al.  HIV controllers: a homogeneous group of HIV-1-infected patients with spontaneous control of viral replication. , 2005, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[62]  Todd M. Allen,et al.  Limited Sequence Evolution within Persistently Targeted CD8 Epitopes in Chronic Human Immunodeficiency Virus Type 1 Infection , 2005, Journal of Virology.

[63]  Bette Korber,et al.  Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA , 2004, Nature.

[64]  D. Katzenstein,et al.  Hierarchical Targeting of Subtype C Human Immunodeficiency Virus Type 1 Proteins by CD8+ T Cells: Correlation with Viral Load , 2004, Journal of Virology.

[65]  Todd M. Allen,et al.  HIV evolution: CTL escape mutation and reversion after transmission , 2004, Nature Medicine.

[66]  Kenneth A. Taylor,et al.  Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Kristin Beaudry,et al.  Viral Escape from Dominant Simian Immunodeficiency Virus Epitope-Specific Cytotoxic T Lymphocytes in DNA-Vaccinated Rhesus Monkeys , 2003, Journal of Virology.

[68]  C. Hallahan,et al.  The Differential Ability of HLA B*5701+ Long-Term Nonprogressors and Progressors To Restrict Human Immunodeficiency Virus Replication Is Not Caused by Loss of Recognition of Autologous Viral gag Sequences , 2003, Journal of Virology.

[69]  Jeffrey N. Martin,et al.  T cell activation is associated with lower CD4+ T cell gains in human immunodeficiency virus-infected patients with sustained viral suppression during antiretroviral therapy. , 2003, The Journal of infectious diseases.

[70]  N. Jones,et al.  Evaluation of antigen-specific responses using in vitro enriched T cells. , 2003, Journal of immunological methods.

[71]  D. Strick,et al.  Comprehensive Epitope Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific T-Cell Responses Directed against the Entire Expressed HIV-1 Genome Demonstrate Broadly Directed Responses, but No Correlation to Viral Load , 2003, Journal of Virology.

[72]  T. Ndung’u,et al.  Association between Virus-Specific T-Cell Responses and Plasma Viral Load in Human Immunodeficiency Virus Type 1 Subtype C Infection , 2003, Journal of Virology.

[73]  J. Fernández-Morera,et al.  Association of ankylosing spondylitis with HLA-B*1403 in a West African population. , 2002, Arthritis and rheumatism.

[74]  C. Hallahan,et al.  HIV-specific CD8+ T cell proliferation is coupled to perforin expression and is maintained in nonprogressors , 2002, Nature Immunology.

[75]  M. Mulligan,et al.  Magnitude of Functional CD8+ T-Cell Responses to the Gag Protein of Human Immunodeficiency Virus Type 1 Correlates Inversely with Viral Load in Plasma , 2002, Journal of Virology.

[76]  B. Walker,et al.  Nef-Mediated Resistance of Human Immunodeficiency Virus Type 1 to Antiviral Cytotoxic T Lymphocytes , 2002, Journal of Virology.

[77]  Steven M. Wolinsky,et al.  Eventual AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes , 2002, Nature.

[78]  J J Goedert,et al.  Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. , 2001, The New England journal of medicine.

[79]  E. Rosenberg,et al.  Identification of Dominant Optimal HLA-B60- and HLA-B61-Restricted Cytotoxic T-Lymphocyte (CTL) Epitopes: Rapid Characterization of CTL Responses by Enzyme-Linked Immunospot Assay , 2000, Journal of Virology.

[80]  F. Marincola,et al.  HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[81]  S O'Brien,et al.  New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. , 1999, Journal of immunology.

[82]  B. Walker,et al.  Molecular and functional analysis of a conserved CTL epitope in HIV-1 p24 recognized from a long-term nonprogressor: constraints on immune escape associated with targeting a sequence essential for viral replication. , 1999, Journal of immunology.

[83]  M A Nowak,et al.  Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. , 1998, Science.

[84]  B. Walker,et al.  HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes , 1998, Nature.

[85]  R P Johnson,et al.  Suppression of human immunodeficiency virus type 1 replication by CD8+ cells: evidence for HLA class I-restricted triggering of cytolytic and noncytolytic mechanisms , 1997, Journal of virology.

[86]  J. Goedert,et al.  Influence of combinations of human major histocompatibility complex genes on the course of HIV–1 infection , 1996, Nature Medicine.

[87]  B. Walker,et al.  Cytotoxic T lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. , 1996, Journal of immunology.

[88]  P. Sansonetti,et al.  Gag-specific cytotoxic responses to HIV type 1 are associated with a decreased risk of progression to AIDS-related complex or AIDS. , 1995, AIDS research and human retroviruses.

[89]  H. Schuitemaker,et al.  Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics , 1995, The Journal of experimental medicine.

[90]  K. Parker,et al.  The HLA-B14 peptide binding site can accommodate peptides with different combinations of anchor residues. , 1994, The Journal of biological chemistry.

[91]  B. Walker,et al.  Longitudinal analysis of T cell receptor (TCR) gene usage by human immunodeficiency virus 1 envelope-specific cytotoxic T lymphocyte clones reveals a limited TCR repertoire , 1994, The Journal of experimental medicine.

[92]  P. Parham,et al.  B*1401 encodes the B64 antigen: the B64 and B65 splits of B14 differ only at residue 11, a buried amino acid. , 1993, Tissue antigens.

[93]  B. Walker,et al.  Identification of overlapping HLA class I-restricted cytotoxic T cell epitopes in a conserved region of the human immunodeficiency virus type 1 envelope glycoprotein: definition of minimum epitopes and analysis of the effects of sequence variation , 1992, The Journal of experimental medicine.

[94]  D. Wiley,et al.  Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution. , 1991, Journal of molecular biology.

[95]  M. A. Saper,et al.  Specificity pockets for the side chains of peptide antigens in HLA-Aw68 , 1990, Nature.

[96]  J. Goedert,et al.  A prospective study of human immunodeficiency virus type 1 infection and the development of AIDS in subjects with hemophilia. , 1989, The New England journal of medicine.

[97]  P. Parham,et al.  Nature of polymorphism in HLA-A, -B, and -C molecules. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[98]  M. A. Saper,et al.  Structure of the human class I histocompatibility antigen, HLA-A2 , 1987, Nature.

[99]  R. Colvin,et al.  Bi-specific monoclonal antibodies: selective binding and complement fixation to cells that express two different surface antigens. , 1987, Journal of immunology.

[100]  P. Klenerman,et al.  Increasing inflationary T-cell responses following transient depletion of MCMV-specific memory T cells. , 2015, European Journal of Immunology.

[101]  The Swiss,et al.  Cohort Profile: The Swiss HIV Cohort Study , 2010 .

[102]  Nicole Frahm,et al.  How to Optimally Define Optimal Cytotoxic T Lymphocyte Epitopes in HIV Infection , 2009 .

[103]  David Heckerman,et al.  CD8+ T-cell responses to different HIV proteins have discordant associations with viral load , 2007, Nature Medicine.

[104]  P. Cresswell,et al.  Genes regulating HLA class I antigen expression in T-B lymphoblast hybrids , 2004, Immunogenetics.

[105]  J. Phair,et al.  Acquired immune deficiency syndrome occurring within 5 years of infection with human immunodeficiency virus type-1: the Multicenter AIDS Cohort Study. , 1992, Journal of acquired immune deficiency syndromes.