CD8 CTL responses in vaccines: emerging patterns of HLA restriction and epitope recognition

Antigen-specific T-cell-mediated immunity after HIV-1 infection: implications for vaccine control of HIV development

The definition of immune correlates of protection in HIV-1 infection is pivotal to the design of successful vaccine candidates and strategies. Although significant methodological and conceptual strides have been made in our understanding of HIV-specific cellular immunity, we have not yet defined those parameters that have a role in controlling the spread of HIV infection. This review discusses the basis of our understanding of HIV-specific cellular immunity and identifies its shortcomings. Furthermore, potential protective characteristics will be proposed that may ultimately be required for an effective vaccine designed to stimulate cellular immunity against HIV-1.

HIV-specific CD8+ T cell responses to HXB2 Gag and Nef peptide pools in Chinese HIV/AIDS patients

HXB2 is primarily used as a template strain in developing HIV vaccines in Europe and the US. However, it is not yet known whether the strain can induce strong HIV-specific CD8+ T cell responses in Chinese HIV/AIDS patients. In the present study, two groups of subjects were investigated: 9 AIDS patients and 7 long-term nonprogressors (LTNPs). HIV-specific CD8+ T cell responses were examined in all patients through the ELISPOT assay. CD4+ T cell counts, CD8+ T cell counts, viral load and HIV subtype of each patient were also measured. Thailand B virus strain was identified among all the patients. The breadth and magnitude of HIV-specific CD8+ T cell responses in the LTNPs group are greater than those in the AIDS group (P<0.01). There is a positive correlation between magnitude of HIV-specific CD8+ T cell responses and CD4+ T cells, and a negative correlation between HIV-specific CD8+ T cell responses and mean viral load. In summary, the HIV-specific CD8+ T cell responses to the HXB2 Gag and Nef peptide pools are considerable in Chinese HIV/AIDS patients infected with Thailand B virus strain. HIV-1 vaccines based on HXB2 strain that can induce extensive immunity may be helpful for Chinese.

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1)-infected persons who maintain plasma viral loads of <50 copies RNA/ml without treatment have been termed elite controllers (EC). Factors contributing to durable control of HIV in EC are unknown, but an HLA-dependent mechanism is suggested by overrepresentation of "protective" class I alleles, such as B*27, B*51, and B*57. Here we investigated the relative replication capacity of viruses (VRC) obtained from EC (n = 54) compared to those from chronic progressors (CP; n = 41) by constructing chimeric viruses using patient-derived gag-protease sequences amplified from plasma HIV RNA and inserted into an NL4-3 backbone. The chimeric viruses generated from EC displayed lower VRC than did viruses from CP (P < 0.0001). HLA-B*57 was associated with lower VRC (P = 0.0002) than were other alleles in both EC and CP groups. Chimeric viruses from B*57(+) EC (n = 18) demonstrated lower VRC than did viruses from B*57(+) CP (n = 8, P = 0.0245). Differences in VRC between EC and CP were also observed for viruses obtained from individuals expressing no described "protective" alleles (P = 0.0065). Intriguingly, two common HLA alleles, A*02 and B*07, were associated with higher VRC (P = 0.0140 and 0.0097, respectively), and there was no difference in VRC between EC and CP sharing these common HLA alleles. These findings indicate that cytotoxic T-lymphocyte (CTL) selection pressure on gag-protease alters VRC, and HIV-specific CTLs inducing escape mutations with fitness costs in this region may be important for strict viremia control in EC of HIV.

Cross-clade CD8 T-cell responses to HIV(IIIB) and Chinese B' and C/B' viruses in North American and Chinese HIV-seropositive donors

HIV variation presents an obstacle to a global AIDS vaccine. Viral diversity and host variations in MHC expression both affect vaccine responses. Whether CD8 T cells from HIV-infected donors in 1 part of the world cross-recognize isolates from other regions will provide guidance about whether country-specific vaccines are needed. We compared recognition of HIV(IIIB) and representative B' (Thai B) and recombinant C/B' virus strains endemic in China by CD8 T cells from 7 HIV-infected North American donors and 4 Chinese donors. IFN-gamma production in response to HIV(IIIB) or the Chinese viruses was comparable. Although 1.6 +/- 0.8% of American donor CD8 T cells produced IFN-gamma above the background level in response to IIIB virus, 1.5 +/- 0.8% responded to B' virus, and 1.4 +/- 0.7% responded to C/B' virus. Responses to adherent cells infected with vaccinia viruses expressing B' and C/B' virus gag and env were also comparable in magnitude with responses to IIIB virus. Cytolysis of CD4 T cells infected with B' virus was comparable with lysis of cells infected with IIIB virus, but lysis of the more divergent C/B' virus was somewhat reduced. T cells, selected for IFN-gamma production to IIIB virus, also efficiently lysed cells infected with Chinese viruses. Therefore, cross-clade CD8 T-cell responses to IIIB virus and prevalent Chinese viral strains are common.

Development of a synthetic consensus sequence scrambled antigen HIV-1 vaccine designed for global use

Induction of high levels of broadly reactive cytotoxic T lymphocytes (CTL) remains a promising approach for an effective HIV-1 vaccine. We have developed a novel genetic-based vaccine strategy that encodes consensus overlapping peptide sets from all HIV-1 proteins scrambled together. This synthetic scrambled antigen vaccine (SAVINE) strategy has significant advantages, e.g. capacity to encode more antigens safely and is very flexible compared to traditional isolate-based strategies. The SAVINE vaccine strategy is clearly immunogenic, being able to restimulate a range of human HIV-1 specific responses in vitro and induce HIV-1 specific immunity in vivo in mice. Interestingly, different in vivo delivery strategies affected the resulting immunity and immunodominance pattern in mice. This platform strategy could be used for other infections and cancers where T cell responses are important for protection.

Studies on the cross-clade and cross-species conservation of HIV-1 Gag-specific CD8 and CD4 T cell responses elicited by a clade B DNA/MVA vaccine in macaques

Here, we evaluate the T cell responses raised by our HIV-1 clade B DNA/MVA vaccine for recognition of a HIV-1 circulating recombinant form (CRF) AG Gag sequence (CRF-02). The cross-clade activity for the AG sequence was better conserved for CD8 than CD4 T cells. CD8 T cells exhibited 75% conservation for height and 83% conservation for breadth, whereas CD4 responses exhibited 45% conservation for height and 50% conservation for breadth. Five CD8 epitopes and 8 CD4 epitopes were mapped. Three of the 5 CD8 epitopes and 2 of the 8 CD4 epitopes were conserved across multiple HIV-1 clades. Impressively, all of the CD8 epitopes and half of the CD4 epitopes have been reported for human infections. Our results demonstrate that the clade B DNA/MVA HIV vaccine elicits T cell responses against epitopes that are conserved in multiple clades and recognized by humans and macaques.

Modified vaccinia Ankara expressing HIVA antigen stimulates HIV-1-specific CD8 T cells in ELISpot assays of HIV-1 exposed infants

Recombinant modified vaccinia virus Ankara expressing HIV-1 antigens (MVA.HIVA) was used in ELISpot assays to monitor HIV-1-specific T cell responses in infants. Responses to MVA.HIVA and HIV-1 peptides were examined in 13 infected and 81 exposed uninfected infants in Nairobi, Kenya. Responses to MVA.HIVA (38%) and peptide stimulation (38%) were similar in frequency (p=1.0) and magnitude (mean 176 versus 385 HIVSFU/10(6), p=0.96) in HIV-1 infected infants. In exposed uninfected infants, MVA.HIVA detected more positive responses and higher magnitude responses as compared to peptide. MVA.HIVA ELISpot is a sensitive method for quantification of HIV-1-specific CD8+ T cell responses in HIV-1 exposed infants. These results demonstrate the relevance of HIV-1 clade A consensus-derived immunogen HIVA for the viruses currently circulating in Nairobi.

Insights into the role of host genetic and T-cell factors in resistance to HIV transmission from studies of highly HIV-exposed Thais

Studies of resistance to HIV-1 transmission are likely to be valuable for the design of vaccines and other efforts to prevent HIV. Here, we review the T-cell and genetic factors associated with resistance to HIV-1 transmission in studies of highly exposed but persistently seronegative (HEPS) women from northern Thailand. Women were enrolled in two sex-worker studies and in a discordant couple study. We performed Cr51 cytotoxic T lymphocyte (CTL), interferon-gamma (IFN-gamma) ELISPOT, and proliferation assays as well as genetic studies, including HLA-class I typing. CTL and ELISPOT studies showed a skewing of T-cell responses to conserved HIV-1 proteins in HEPS, but not in HIV-1-seropositive women. T-cell responses were extremely long-lived in some HEPS women. In the two sex-worker studies, HLA-A11 was associated with resistance to HIV-1 transmission. These data provide promise for the ability of CTL to control HIV and emphasize the importance of developing HIV vaccines that stimulate strong, long-lasting Tcell responses.

Absence of immunodominant anti-Gag p17 (SL9) responses among Gag CTL-positive, HIV-uninfected vaccine recipients expressing the HLA-A*0201 allele

According to a number of previous reports, control of HIV replication in humans appears to be linked to the presence of anti-HIV-1 Gag-specific CD8 responses. During the chronic phase of HIV-1 infection, up to 75% of the HIV-infected individuals who express the histocompatibility leukocyte Ag (HLA)-A*0201 recognize the Gag p17 SLYNTVATL (aa residues 77-85) epitope (SL9). However, the role of the anti-SL9 CD8 CTL in controlling HIV-1 infection remains controversial. In this study we determined whether the pattern of SL9 immunodominance in uninfected, HLA-A*0201 HIV vaccine recipients is similar to that seen in chronically HIV-infected subjects. The presence of anti-SL9 responses was determined using a panel of highly sensitive cellular immunoassays, including peptide:MHC tetramer binding, IFN-gamma ELISPOT, and cytokine flow cytometry. Thirteen HLA-A*0201 vaccinees with documented anti-Gag CD8 CTL reactivities were tested, and none had a detectable anti-SL9 response. These findings strongly suggest that the pattern of SL9 epitope immunodominance previously reported among chronically infected, HLA-A*0201-positive patients is not recapitulated in noninfected recipients of Gag-containing canarypox-based candidate vaccines and may be influenced by the relative immunogenicity of these constructs.

HLA class I serotypes and cytotoxic T-lymphocyte responses among human immunodeficiency virus-1-uninfected Thai volunteers immunized with ALVAC-HIV in combination with monomeric gp120 or oligomeric gp160 protein boosting

Antigen-induced cellular immunogenicity may vary between populations due to differences in human leukocyte antigen (HLA) diversity and, hence, may play a critical role in the protection afforded by vaccines. In the setting of two, phase I/II human immunodeficiency virus-1 vaccine trials of a recombinant canarypox prime, and boosting with either recombinant monomeric gp120 or oligomeric gp160, we assessed the association between specific human leukocyte antigen (HLA) class I serotypes and the presence of cytotoxic T-lymphocyte response measured by 51Cr-release assay. HLA class I serotypes A11, A24, A33, B46, and B75 were the most common, present in 10% or more of 245 individuals studied. Forty of 187 (21.4%) Thai adults who received either ALVAC-HIV with gp120 or oligomeric gp160 or ALVAC alone had a precursor cytolytic CD8 T-cell response (pCTL). HLA-B44 was positively and significantly associated with a pCTL response (odds ratio 7.6, 95% CI: 2.7-21.2), whereas B46 was negatively associated but not robust when adjusted for multiple comparisons. Responses to Env proteins accounted for the majority (nine of 11) of pCTL activity among those persons with B44. This HLA class I serotype occurred in 9.4% of participants overall (including the placebo group), less commonly than what is reported from populations of European ancestry. These results strengthen the importance of assessing HLA class I distributions in conjunction with studies of vaccines designed to elicit cellular immunity in different populations.

Screening for HIV-specific T-cell responses using overlapping 15-mer peptide pools or optimized epitopes

The IFN-y enzyme-linked immunospot (ELI-Spot) assay is often used to map HIV-specific CD8 T-cell responses. We compared overlapping 15-mer pools with optimized CD8 epitopes to screen ELISpot responses in HIV-infected individuals. The 15-mer pools detected responses to previously undefined epitopes, but often missed low-level responses to predefined epitopes, particularly when the epitope was central in the 15-mer, rather than at the N-terminus or C-terminus. These factors should be considered in the monitoring of HIV vaccine trials.

HLA-A and -B allele expression and ability to develop anti-Gag cross-clade responses in subtype C HIV-1–infected Ethiopians

A cohort of 35 human immunodeficiency virus type 1 (HIV-1) subtype C-infected Ethiopians was studied to define the HLA phenotype in all 35 subjects and highly conserved Gag protein regions involved in cross-clade cell-mediated immunity. Full-length Gag virus sequences were determined in 15 individuals. CD8 cell-mediated immune responses were detected by interferon-gamma ELISpot assay. HLA-A*03, -B*49, and -B*57 allelic frequencies were relatively higher than in other African populations. Anti-p17 (aa 1-60) CD8+ were detectable in the highest number of individuals. Anti-p17 (aa 1-60 and 51-110) cross-clade responses against subtype B and C were detected in 50% of the tested subjects. The p24 KF11 (aa 162-172) epitope was found to be immunodominant among the HLA-B*5703--positive individuals. These data represent the first report of correlating HLA phenotype and HIV-specific cell-mediated immune responses among infected Ethiopians and may be useful in designing cytotoxic T lymphocyte-inducing vaccines for this part of Africa.

Cross-reactivity between HLA-A2-restricted FLU-M1:58-66 and HIV p17 GAG:77-85 epitopes in HIV-infected and uninfected individuals

BACKGROUND: The matrix protein of the influenza A virus and the matrix and capsid proteins of the human immunodeficiency virus (HIV) share striking structural similarities which may have evolutionary and biological significance. These similarities led us to hypothesize the existence of cross-reactivity between HLA-A2-restricted FLU-M1:58-66 and HIV-1 p17 GAG:77-85 epitopes. METHODS: The hypothesis that these two epitopes are cross-reactive was tested by determining the presence and extent of FLU/GAG immune cross-reactivity in lymphocytes from HIV-seropositive and seronegative HLA-A2+ donors by cytotoxicity assays and tetramer analyses. Moreover, the molecular basis for FLU/GAG cross-reactivity in HIV-seropositive and seronegative donors was studied by comparing lymphocyte-derived cDNA sequences corresponding to the TCR-beta variable regions, in order to determine whether stimulation of lymphocytes with either peptide results in the expansion of identical T-cell clonotypes. RESULTS: Here, we report evidence of cross-reactivity between FLU-M1:58-66 and HIV-1 p17 GAG:77-85 epitopes following in vitro stimulation of PBMC derived from either HIV-seropositive or seronegative HLA-A2+ donors as determined by cytotoxicity assays, tetramer analyses, and molecular clonotyping. CONCLUSION: These results suggest that immunity to the matrix protein of the influenza virus may drive a specific immune response to an HLA-A2-restricted HIV gag epitope in HIV-infected and uninfected donors vaccinated against influenza.

Cross-reactive CD8+ T cell epitopes identified in US adolescent minorities

Vaccines designed to bring forth CD8+ T cell responses in different racial and ethnic groups will require inclusion of T cell epitopes presented by various MHC class I molecules. This study was designed to identify new CD8+ T cell epitopes in HIV-infected African American and Hispanic youth as well as to determine the frequency of responses to both novel and previously described HIV-1 epitopes in a cohort of racially and ethnically diverse individuals. We found 8 MHC class I-restricted CD8+ T cell epitopes that had not been previously described, another 8 epitopes that were restricted by class I alleles not previously associated with these epitopes, and 8 additional epitopes that have been described previously. In a larger cohort, we demonstrated that 11 (69%) of these 16 newly described immunogens were recognized by individuals of different race or ethnicity. Most HIV-1-specific CD8+ T cell epitopes identified were either novel or restricted by alternative MHC class I alleles. Frequent recognition of several of these CTL epitopes in persons of diverse racial backgrounds bodes well for the development of a broadly reactive HIV-1 vaccine.

Comparison of overlapping peptide sets for detection of antiviral CD8 and CD4 T cell responses

Increasing efforts are directed towards the development of effective vaccines through induction of virus-specific T cell responses. Although emerging data indicate a significant role of these cells in determining viral set point in infections such as HIV, there is as yet no consensus as to the best methods for assaying the breadth of these responses. In this study, we used sensitive interferon gamma-based intracellular cytokine staining (ICS) and Elispot assays to determine the optimal overlapping peptide set to screen for these responses. Twenty persons with established HIV infection were studied, focusing on responses to the highly immunogenic Nef protein. Six different HIV-1 Nef peptide sets were used, ranging in length from 15 to 20 amino acids (aa), in overlap from 10 to 11 amino acids, and derived from two different B clade sequences. A total of 54 CD8 T cell responses to Nef peptides were found in this cohort, of which only 12 were detected using previously defined Nef optimal epitopes. No single peptide set detected all responses. Though there was a trend of the shorter peptides detecting more CD8 T cell responses than the 20 amino acid long peptides and longer peptides detecting more CD4 T cell responses, neither was statistically significant. There was no difference between an overlap of 10 or 11 amino acids. All responses detected with the six different sets of overlapping peptides were towards the more highly conserved regions of Nef. We conclude that peptides ranging from 15 to 20 amino acids yield similar results in IFN-gamma-based Elispot and ICS assays, and that all are likely to underestimate the true breadth of responses to a given reference strain of virus.

Comparison between env-specific T-cell epitopic responses in HIV-1-uninfected adults immunized with combination of ALVAC-HIV(vCP205) plus or minus rgp160MN/LAI-2 and HIV-1-infected adults

In this study, we investigated the CD4 T-helper response induced by ALVAC-HIV(vCP205) +/- rgp160MN/LAI-2 using a series of 15 overlapping amino acid peptides spanning the entire gp160MN/LAI-2 antigen. CD4 Env-specific T-cell lines were established from three groups of HIV-1-negative HIV vaccine recipients: vCP205 + gp160MN/LAI-2, vCP205 only, and gp160MN/LAI-2 only. CD4 Env-specific T-cell lines established from individuals who received the prime-boost vCP205 + rgp160MN/LAI-2 generated strong and broad T-helper responses scattered across the Env sequence, whereas Env-specific T-cell lines from individuals receiving the vCP205 vaccine alone generated reactivity to only a few peptides. CD4 -specific T-cell lines were also established from HIV-1-infected individuals and demonstrated poor reactogenicity to Env peptides in both breadth and amplitude of response. These results highlight the complexity of major histocompatibility complex class II presentation and CD4 antigen-specific reactivity, emphasizing the need to better understand these crucial T-helper cell responses in the setting of HIV infection and HIV vaccine development.

The ELISPOT assay: an easily transferable method for measuring cellular responses and identifying T cell epitopes

Characterization of human leukocyte antigen (HLA) class I restricted epitopes derived from viral pathogens is imperative for formulating therapeutic interventions, as well as for vaccine design and monitoring. Sensitive, easy and cost-effective assays that measure the frequency of antigen-specific T lymphocytes are crucial for evaluating and improving vaccines and therapies. This paper reviews the ELISPOT technique that allows for quantifying HIV-specific T lymphocytes at the single cell level from peripheral blood by detection of antigen-induced cytokine secretion. The assay can be used successfully to quantify T cell immune responses in humans infected with different pathogens and to assess T cell immunogenicity of vaccines in phase I/II and III clinical trials. This review focuses on the ELISPOT methodology and discusses how it can be standardized and potentially used by multiple international laboratories attached to clinical trial sites.

HIV Vaccines: Biological and Clinical Considerations

The discovery of an HIV-1 vaccine is a high priority. Recent advances in HIV vaccine development include an improved understanding about virus biology and structure, and the development of quantitative techniques that enable a detailed analysis of vaccine-induced immune responses in humans. The preclinical vaccine pipeline looks healthy, and a common feature of the new vaccine strategies is their ability to attenuate clinical disease rather than prevent HIV infection in nonhuman primates. Human clinical trials to evaluate the safety and immunogenicity of these vaccine candidates and strategies are being actively pursued.

Diversity considerations in HIV-1 vaccine selection

Globally, human immunodeficiency virus-type 1 (HIV-1) is extraordinarily variable, and this diversity poses a major obstacle to AIDS vaccine development. Currently, candidate vaccines are derived from isolates, with the hope that they will be sufficiently cross-reactive to protect against circulating viruses. This may be overly optimistic, however, given that HIV-1 envelope proteins can differ in more than 30% of their amino acids. To contend with the diversity, country-specific vaccines are being considered, but evolutionary relationships may be more useful than regional considerations. Consensus or ancestor sequences could be used in vaccine design to minimize the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half.

Large-scale computational identification of HIV T-cell epitopes

Bioinformatics-driven T-cell epitope-identification methods can enhance vaccine target selection significantly. We evaluated three unrelated computational methods to screen Pol, Gag and Env sequences extracted from the Los Alamos HIV database for HLA-A*0201 and HLA-B*3501 T-cell epitope candidates. The hidden Markov model predicted 389 HLA-B*3501-restricted candidates from 374 HIV-1 and 97 HIV-2 sequences. The artificial neural network (ANN) model, and Bioinformatics and Molecular Analysis Section (BIMAS) quantitative matrix predictions for A*0201 yielded 1122 HIV-1 and 548 HIV-2 candidates. The overall sequence coverage of the predicted A*0201 T-cell epitopes was 2.7% (HIV-1)and 3.0% (HIV-2). HLA-B*3501-predicted epitopes covered 0.9% (HIV-1) and 1.4% (HIV-2) of the total sequence. Comparison of 890 ANN- and 397 BIMAS-derived HIV-1 A*0201- restricted epitope candidates showed that only 13-19% of the predicted and 26% of the experimentally confirmed T-cell epitopes were captured by both methods. Extrapolating these results, we estimated that at least 247 predicted HIV-1 epitopes are yet to be discovered as active A*0201-restricted T-cell epitopes. Adequate comparison and combined usage of various predictive bioinformatics methods, rather than uncritical use of any single prediction method, will enable cost-effective and efficient T-cell epitope screening.