Human immunodeficiency virus-specific responses in adult Ugandans: patterns of cross-clade recognition

Macrophage Inflammatory Protein-1 Beta and Interferon Gamma Responses in Ugandans with HIV-1 Acute/Early Infections

Control of HIV replication through CD4(+) and CD8(+) T cells might be possible, but the functional and phenotypic characteristics of such cells are not defined. Among cytokines produced by T cells, CCR5 ligands, including macrophage inflammatory protein-1 beta (MIP-1β), compete for the CCR5 coreceptor with HIV, promoting CCR5 internalization and decreasing its availability for virus binding. Interferon (IFN)-γ also has some antiviral activity and has been used as a read-out for T cell immunogenicity. We used cultured ELISpot assays to compare the relative contribution of MIP-1β and IFN-γ to HIV-specific responses. The magnitude of responses was 1.36 times higher for MIP-1β compared to IFN-γ. The breadth of the MIP-1β response (45.41%) was significantly higher than IFN-γ (36.88%), with considerable overlap between the peptide pools that stimulated both MIP-1β and IFN-γ production. Subtype A and D cross-reactive responses were observed both at stimulation and test level, but MIP-1β and IFN-γ responses displayed different effect patterns. We conclude that the MIP-1β ELISpot would be a useful complement to the evaluation of the immunogenicity of HIV vaccines and the activity of adjuvants.

Cross-reactive potential of human T-lymphocyte responses in HIV-1 infection

An effective HIV-1 vaccine should elicit sufficient breadth of immune recognition to protect against the genetically diverse forms of the circulating virus. Evaluation of the breadth and magnitude of cellular immune responses to epitope variants is important for HIV-1 vaccine assessment. We compared HIV-1 Gag-specific T-lymphocyte responses in 20 HIV-1-infected individuals representing two different HIV-1 subtypes, B and C. By assessing T lymphocyte responses with peptides based on natural HIV-1 variants, we found evidence for limited cross-reactivity and significantly enhanced within-clade responses among clade B-infected subjects, and not among clade C-infected subjects.

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.

Enrichment of HIV-1 subtype AD recombinants in a Ugandan cohort of severely septic patients

Background

Several population-wide HIV-1 subtype distribution studies in Uganda have evaluated relatively healthy clinic patients. Given the differences in HIV-1 disease progression based on subtype, we examined HIV-1 subtype distribution and disease outcomes among hospitalized patients with severe sepsis.

Methods

Patients with severe sepsis were enrolled at two hospitals in Uganda. Data collected included demographics, Karnofsky scores, highly active antiretroviral therapy (HAART) use, HIV-1 serostatus, CD4+ T cell concentration, whole blood lactate concentration, and blood cultures. HIV-1 subtypes were determined by sequencing parts of the gag and env genes, followed by phylogenetic analysis.

Results

Of the 267 patients evaluated, 228 (85.4%) were HIV infected. The predominant HIV-1 subtypes were A (46%), D (17%), and AD recombinants (30%). HIV-1 subtypes B, C, and other recombinants were uncommon. Patients infected with HIV-1 subtypes A, D and AD viruses were similar in demographics, CD4⁺ T cell concentration, HAART use, Karnofsky scores, whole blood lactate concentration, and positive blood cultures. There was no difference in 30-day mortality from severe sepsis between the 3 groups (p = 0.99).

Conclusion

A high proportion of HIV-1 subtypes A and AD recombinants was observed in this cohort of severely septic patients. The proportion of AD recombinants was higher in this cohort than in previous cohorts of Ugandan HIV-1 patients. No difference in baseline demographics, clinical factors or 30-day mortality was seen across HIV-subtypes.

Clade-specific evolution mediated by HLA-B*57/5801 in human immunodeficiency virus type 1 clade A1 p24

HLA-B*57-mediated selection pressure leads to a typical escape pathway in human immunodeficiency virus type 1 (HIV-1) CD8 epitopes such as TW10. Whether this T242N pathway is shared by all clades remains unknown. We therefore assessed the nature of HLA-B*57 selection in a large, observational Kenyan cohort where clades A1 and D predominate. While T242N was ubiquitous in clade D HLA-B*57(+) subjects, this mutation was rare (15%) in clade A1. Instead, P243T and I247L were selected by clade A1-infected HLA-B*57 subjects but not by HLA-B*5801(+) subjects. Our data suggest that clade A1 consensus proline at Gag residue 243 might represent an inherent block to T242N escape in clade A1. We confirmed immunologically that P243T and I247L likely represent escape mutations. HLA-B*57 evolution also differed between clades in the KF11 and IW9 epitopes. A better understanding of clade-specific evolution is important for the development of HIV vaccines in regions with multiple clades.

Epitope mapping of HIV-specific CD8+ T cells in a cohort dominated by clade A1 infection

BACKGROUND

CD8+ T cell responses are often detected at large magnitudes in HIV-infected subjects, and eliciting these responses is the central aim of many HIV-1 vaccine strategies. Population differences in CD8+ T cell epitope specificity will need to be understood if vaccines are to be effective in multiple geographic regions.

METHODOLOGY/PRINCIPAL FINDINGS

In a large Kenyan cohort, we compared responsive CD8+ T cell HIV-1 Env overlapping peptides (OLPs) to Best Defined Epitopes (BDEs), many of which have been defined in clade B infection. While the majority of BDEs (69%) were recognized in this population, nearly half of responsive OLPs (47%) did not contain described epitopes. Recognition frequencies of BDEs were inversely correlated to epitopic sequence differences between clade A1 and BDE (P = 0.019), and positively selected residues were more frequent in "new" OLPs (without BDEs). We assessed the impact of HLA and TAP binding on epitope recognition frequencies, focusing on predicted and actual epitopes in the HLA B7 supertype.

CONCLUSIONS/SIGNIFICANCE

Although many previously described CD8 epitopes were recognized, several novel CD8 epitopes were defined in this population, implying that epitope mapping efforts have not been completely exhausted. Expansion of these studies will be critical to understand population differences in CD8 epitope recognition.

Host HLA B*allele-associated multi-clade Gag T-cell recognition correlates with slow HIV-1 disease progression in antiretroviral therapy-naïve Ugandans

BACKGROUND

Some HIV infected individuals remain asymptomatic for protracted periods of time in the absence of antiretroviral therapy (ART). Virological control, CD4 T cell loss and HIV-specific responses are some of the key interrelated determinants of HIV-1 disease progression. In this study, possible interactions between viral load, CD4 T cell slopes, host genetics and HIV-specific IFN-gamma responses were evaluated in chronically HIV-1-infected adults.

METHODOLOGY/PRINCIPAL FINDINGS

Multilevel regression modeling was used to stratify clade A or D HIV-infected individuals into disease progression groups based on CD4 T cell slopes. ELISpot assays were used to quantify the frequency and magnitude of HIV-induced IFN-gamma responses in 7 defined rapid progressors (RPs) and 14 defined slow progressors (SPs) at a single time point. HLA typing was performed using reference strand conformational analysis (RSCA). Although neither the breadth nor the magnitude of the proteome-wide HIV-specific IFN-gamma response correlated with viral load, slow disease progression was associated with over-representation of host immunogenetic protective HLA B* alleles (10 of 14 SPs compared to 0 of 7; p = 0.004, Fisher's Exact) especially B*57 and B*5801, multiclade Gag T-cell targeting (71%, 10 of 14 SPs compared to 14%, 1 of 7 RPs); p = 0.029, Fisher's Exact test and evident virological control (3.65 compared to 5.46 log10 copies/mL in SPs and RPs respectively); p<0.001, unpaired student's t-test

CONCLUSIONS

These data are consistent with others that associated protection from HIV disease with inherent host HLA B allele-mediated ability to induce broader Gag T-cell targeting coupled with apparent virological control. These immunogenetic features of Gag-specific immune response which could influence disease progression may provide useful insight in future HIV vaccine design.

Cross-reactive T cell responses in HIV CRF01_AE and B'-infected intravenous drug users: implications for superinfection and vaccines

Abstract We previously observed limited cross-reactive T cell responses in two HIV-1-superinfected injection drug users (IDUs) before superinfection [Ramos A, et al.: J Virol 2002;76(15):7444-7452]. To elucidate the role of such responses in superinfection we examined cross-reactive T cell responses in IDUs infected with a single HIV-1 subtype. In this study, IFN-gamma ELISPOT assays were performed using recombinant vaccinia constructs and peripheral blood mononuclear cells (PBMCs) from 43 IDUs singly infected with CRF01_AE or B' from the same cohort as the superinfected IDUs. PBMCs were from time points corresponding to pre- (early) or post- (late) superinfection in the superinfected IDUs. We observed that most singly infected IDUs had cross-reactivity in samples from early (84% of CRF01_AE and 78% of B'-infected IDUs) and late (96% of CRF_01AE and 77% of B'-infected IDUs) time points. Frequent homologous reactivity at early (67% of CRF-01AE and 100% of B') and late (84% of CRF01_AE-infected and 100% of B'-infected IDUs) time points was also observed. Cross-reactive responses were predominantly to Pol and were broader and higher in CRF01_AE than in B'-infected IDUs (medians of 825 vs. 90 and 585 vs. 60 spot-forming units/10(6) PBMCs at early and late time points, respectively). Our results show that cross-reactive responses were more prevalent with greater height and breadth in singly infected IDUs than previously observed in corresponding collection time points of superinfected IDU. Thus, low or absent cross-reactivity may have contributed to the previously observed superinfections. These data are relevant for understanding superinfection and improving vaccine design.

The Distribution and Immune Profile of T Cell Subsets in HIV-Infected Children from Uganda

Abstract T cell activation is an important mechanism in HIV-associated immune depletion. We have previously demonstrated an association between the hyperactivation of CD4(+) and CD8(+) T cells and low CD4 status in HIV-infected Ugandan children. In this study, we explore differences in activation between naive and memory T cells in HIV-infected Ugandan children. A significant correlation between CD4- and CD8-mediated immune activation and CD4 status was observed only in the memory T cells. Antiretroviral (ART) untreated and treated HIV-positive and HIV-negative children displayed similar profiles of activation and distribution within the CD4(+) naive T cells. In contrast, significantly higher immune activation of the memory CD4(+) T cell subset was seen in ART-untreated children when compared to ART-treated or HIV-negative children. ART-mediated viral suppression led to the correction of CD4(+) immune activation to levels seen in uninfected children but did not increase the size of the memory CD4(+) T cell population. High levels of CD8(+) immune activation were also found in both naive and memory cell subsets. Antiretroviral treatment led to the normalization of CD8(+) T cell activation but did not correct the distribution of naive CD8(+) T cells. We also assessed PD-1 expression on CD8(+) T cells as a measure of immune dysfunction. Upregulation of PD-1 was highest in untreated children but persisted in ART-treated children compared to uninfected children. The mechanisms of immunopathogenesis in pediatric HIV infection likely involve distinct contributions from individual naive and memory T cells subsets.

Cross-clade detection of HIV-1-specific cytotoxic T lymphocytes does not reflect cross-clade antiviral activity

The genetic divergence of human immunodeficiency virus (HIV)-1 into distinct clades is a serious consideration for cytotoxic T lymphocyte (CTL)-based vaccine development. Demonstrations that CTLs can cross-recognize epitope sequences from different clades has been proposed as offering hope for a single vaccine. Cross-clade CTL data, however, have been generated by assessing recognition of exogenous peptides. The present study compares HIV-1-specific CTL cross-clade epitope recognition of exogenously loaded peptides with suppression of HIV-1-infected cells. Despite apparently broad cross-clade reactivity of CTLs against the former, CTL suppression of HIV-1 strains with corresponding epitope sequences is significantly impaired. The functional avidity of CTLs for nonautologous clade epitope sequences is diminished, suggesting that CTLs can fail to recognize levels of infected endogenously derived cell-surface epitopes despite recognizing supraphysiologic exogenously added epitopes. These data strongly support clade-specific antiviral activity of CTLs and call into question the validity of standard methods for assessing cross-clade CTL activity or CTL antiviral activity in general.

HIV subtypes induce distinct profiles of HIV-specific CD8(+) T cell responses

CD8(+) T cells play an important role in controlling HIV infection and qualitative differences in HIV-specific CD8(+) responses may determine the degree of immune control. We studied 56 HIV-infected, ARV-naive Ugandans and examined the role of subtypes in modulating their HIV-specific T cell responses. Gag-specific responses were readily detectable in our study population. Interestingly, we found significantly decreased Gag-specific cytolysis (as measured by CD107 expression) in subtype D (n = 21) compared to subtype A (n = 35) HIV infection. Sequence analyses within identified epitopes suggest patterns of conservation that are subtype specific. We conclude that HIV subtypes may promote distinct profiles of T cells responses and immune control.

An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort

Human immunodeficiency virus type 1 (HIV-1) is able to evade the host cytotoxic T-lymphocyte (CTL) response through a variety of escape avenues. Epitopes that are presented to CTLs are first processed in the presenting cell in several steps, including proteasomal cleavage, transport to the endoplasmic reticulum, binding by the HLA molecule, and finally presentation to the T-cell receptor. An understanding of the potential of the virus to escape CTL responses can aid in designing an effective vaccine. To investigate such a potential, we analyzed HIV-1 gag from 468 HIV-1-positive Kenyan women by using several bioinformatic approaches that allowed the identification of positively selected amino acids in the HIV-1 gag region and study of the effects that these mutations could have on the various stages of antigen processing. Correlations between positively selected residues and mean CD4 counts also allowed study of the effect of mutation on HIV disease progression. A number of mutations that could create or destroy proteasomal cleavage sites or reduce binding affinity of the transport antigen processing protein, effectively hindering epitope presentation, were identified. Many mutations correlated with the presence of specific HLA alleles and with lower or higher CD4 counts. For instance, the mutation V190I in subtype A1-infected individuals is associated with HLA-B*5802 (P = 4.73 x 10(-4)), a rapid-progression allele according to other studies, and also to a decreased mean CD4 count (P = 0.019). Thus, V190I is a possible HLA escape mutant. This method classifies many positively selected mutations across the entire gag region according to their potential for immune escape and their effect on disease progression.

Profile of immunologic recovery in HIV-infected Ugandan adults after antiretroviral therapy

HIV infection is characterized by a decrease in total CD4 cell count, rising viral load, as well as an increase in immune activation levels. Increased activation can lead to an increase in apoptosis and contribute to CD4 depletion. We evaluated the clinical and immunologic responses of 23 HIV-positive Ugandan volunteers following initiation of antiretroviral therapy (ART). All volunteers achieved and maintained complete viral suppression within the first 3 months of therapy (p > 0.05). CD4+ and CD8+ T cell activation also decreased significantly, although it never reached the level of HIV negative Ugandan volunteers. Viral suppression and CD4 cell recovery were also associated with an improved profile in CD8+ T cell functional markers, but had no effect on HIV-specific proliferation. We conclude that ART in a cohort of therapy-naive Ugandans with AIDS partially restores but does not fully reverse the immune dysfunction observed in chronic HIV infection.

HIV viral diversity and escape from cellular immunity

Immune control of HIV often fails due to viral escape from cellular and humoral host immune responses. Vaccine development is a daunting task because of the ability of HIV to adapt rapidly to different selection pressures and quickly restore viral fitness when transmitted to new hosts. In addition, the global viral diversity poses significant difficulties for accurate and standardized testing of immune responses in the infected host, slowing the generation of data that are crucial to defining relevant immune correlates of controlled HIV infection. Many recent studies have shed light on some of the potentially important factors of protective immune responses and have provided further insight into the viral kinetics determining immune control, viral adaptation, and immune escape. This knowledge will likely further guide the design of broadly applicable HIV vaccine candidates.

In a mixed subtype epidemic, the HIV-1 Gag-specific T-cell response is biased towards the infecting subtype

OBJECTIVES

Southwest Tanzania is affected by an HIV-1 epidemic consisting of subtypes A, C, and D, and their recombinant forms. This study was designed to assess whether the Gag- and Nef-specific T-cell response is biased towards recognizing the infecting subtype.

METHODS

The infecting subtypes were characterized with a Multi-hybridization assay that discriminates between subtypes A, C and D. The interferon-gamma ELISPOT assay was used to detect the Gag- and Nef-specific T-cell responses in freshly isolated peripheral blood mononuclear cells in 56 seropositive patients. To study the HIV-specific T-cell responses, isolate-based Gag and Nef peptide sets representative of the locally occurring subtypes were used. The results were analysed at the total protein and single peptide level.

RESULTS

In the study population, 35% were infected with a pure C subtype, 24% and 23% with ACD or AC recombinant forms, respectively. The total magnitude (P < 0.01) and breadth (P < 0.01) of the Gag-specific T-cell response detected with the subtype C-Gag peptide set was significantly greater than that detected with either the subtype A-Gag or D-Gag peptide sets. No significant difference was observed in the Nef-specific response. In 85% of responses targeting the most immunodominant Gag epitopes with subtype-specific sequence differences, the best recognized epitope variant corresponded to the infecting subtype.

CONCLUSIONS

The Gag-specific T-cell response had a preference for recognizing peptides related to the infecting subtype.

Presence of distinct subsets of cytolytic CD8+ T cells in chronic HIV infection

Cytolytic T lymphocytes (CTL) play an important role in the control of HIV infection. The eventual failure to contain HIV-1 infection may arise because of a functional impairment of HIV-specific CTL. We evaluated Gag-specific cytotoxicity in HIV-1-positive Ugandans. Expression of CD107, a marker for cytolytic activity, was present in CD45RA(bright) and CD45RA(dim) CD8(+) T cell populations in HIV-infected individuals. The frequency of Gag-specific CD107(+)CD45RA(bright)CD28(-)CCR7(-) CD8(+) T cells decreased with CD4 cell depletion and correlated with the presence of Gag-specific T helper response. In contrast, the frequency of Gag-specific CD107(+)CD45RA(dim)CD28(-)CCR7(-) CD8(+) T cells within the same individuals has no significant association with viral load or CD4 cell count. The ratio of CD45RA(bright) to CD45RA(dim) CTL correlates significantly with CD4 cell count. This positive association decreases with antiretroviral treatment (ARV), indicating that suppression of viral replication alters the balance of circulating Gag-specific CD8(+) effector T cells. Subsets of cytolytic T cells may have distinct antiviral functions and further characterization of these effector CD8(+) T cells may yield important information on T cell regulation and dysfunction in HIV infection.

The promise and challenge of anti-HIV cellular immunity

PURPOSE OF REVIEW

We discuss recent studies giving insight into the promise of cell-mediated immunity for prophylactic HIV vaccine strategies, and challenges to be overcome for this approach to succeed.

RECENT FINDINGS

Advances in understanding of events in very early HIV infection and their importance in viral pathogenesis emphasize the rapidity with which vaccine-induced T-cell responses must act to modulate CD4 cell destruction, but also reveal an early window of opportunity when foci of infection are limited and could potentially be eliminated. Super-infection with diverse HIV strains is now appreciated to be relatively common, indicating that cell-mediated responses in most infected individuals do not confer protection. Recent studies suggest that T-cell correlates of good control of HIV replication may be a consequence rather than a cause of containment of viraemia. Analysis of features of HIV-specific T-cell responses restricted by human leukocyte antigen alleles associated with differential prognosis of infection is giving insight into correlates of protection. The importance of efficacious responses, escape from which incurs high fitness costs, is increasingly appreciated.

SUMMARY

There are many challenges to be overcome before the promise of cell-mediated immunity for HIV vaccines is realized.

CTL epitope distribution patterns in the Gag and Nef proteins of HIV-1 from subtype A infected subjects in Kenya: use of multiple peptide sets increases the detectable breadth of the CTL response

Background

Subtype A is a major strain in the HIV-1 pandemic in eastern Europe, central Asia and in certain regions of east Africa, notably in rural Kenya. While considerable effort has been focused upon mapping and defining immunodominant CTL epitopes in HIV-1 subtype B and subtype C infections, few epitope mapping studies have focused upon subtype A.

Results

We have used the IFN-γ ELIspot assay and overlapping peptide pools to show that the pattern of CTL recognition of the Gag and Nef proteins in subtype A infection is similar to that seen in subtypes B and C. The p17 and p24 proteins of Gag and the central conserved region of Nef were targeted by CTL from HIV-1-infected Kenyans. Several epitope/HLA associations commonly seen in subtype B and C infection were also observed in subtype A infections. Notably, an immunodominant HLA-C restricted epitope (Gag 296–304; YL9) was observed, with 8/9 HLA-C_W0304 subjects responding to this epitope. Screening the cohort with peptide sets representing subtypes A, C and D (the three most prevalent HIV-1 subtypes in east Africa), revealed that peptide sets based upon an homologous subtype (either isolate or consensus) only marginally improved the capacity to detect CTL responses. While the different peptide sets detected a similar number of responses (particularly in the Gag protein), each set was capable of detecting unique responses not identified with the other peptide sets.

Conclusion

Hence, screening with multiple peptide sets representing different sequences, and by extension different epitope variants, can increase the detectable breadth of the HIV-1-specific CTL response. Interpreting the true extent of cross-reactivity may be hampered by the use of 15-mer peptides at a single concentration and a lack of knowledge of the sequence that primed any given CTL response. Therefore, reagent choice and knowledge of the exact sequences that prime CTL responses will be important factors in experimentally defining cross-reactive CTL responses and their role in HIV-1 disease pathogenesis and validating vaccines aimed at generating broadly cross-reactive CTL responses.

HIV-specific IL-10-positive CD8+ T cells are increased in advanced disease and are associated with decreased HIV-specific cytolysis

IL-10-producing T cells have been shown to inhibit Ag-specific CD8+ T cell responses, and may play a role in the immune dysregulation observed in HIV-1 infection. We characterized the Gag-specific IL-10 responses by CD8+ T cells in HIV-1-positive volunteers from Uganda. HIV-specific IL-10 responses were detected in 32 of 61 (52.4%) antiretroviral naive and 2 of 15 (13.3%) volunteers with a complete virologic response on antiretroviral therapy (< 400 copies/ml). The frequency of HIV-specific IL-10-positive cells was significantly higher in volunteers with advanced disease (CD4+ T cell count <200 cells/mm3; p = 0.0004), and correlated positively with plasma HIV RNA (r = 0.43, p = 0.0004). Interestingly, the frequency of Gag-specific CD107a/b-, but not IFN-gamma-, positive cells was significantly lower in individuals with detectable IL-10-positive CD8+ T cells (p = 0.004). Gag-specific IL-10-positive CD8+ T cells demonstrated a pattern of surface memory marker expression that is distinct compared with CD107a/b- and IFN-gamma-positive CD8+ T cell populations (p < 0.0001). Our study describes a distinct population of IL-10-positive CD8+ T cells that may play a role in HIV-associated immune dysfunction.

Cross-clade CD8(+) T-cell responses with a preference for the predominant circulating clade

Human immunodeficiency virus (HIV) genetic diversity is a major impediment to the design of a successful vaccine. Even if an HIV vaccine is proven effective, it remains to be seen whether this protection will extend to inter-clade, intra-clade, and recombinant strains. We used recombinant vaccinia-based interferon gamma (IFN) Elispot assays to test the inter-clade crossreactivity of clades A, B, C, and D HIV Env in two cohorts of HIV-infected Kenyans. Despite the tremendous diversity in this HIV protein, a substantial proportion of multi-clade responses were observed. Although these multi-clade responses correlated well with each other in regression analyses, clade A responses were seen at a higher frequency and at greater relative magnitudes in a proportion of these patients, when compared to the other three clades. Epitope mapping indicates CD8(+) T cell recognition of conserved regions of Env, accounting for the high degree of cross-reactivity but not the clade A preference. A better understanding of cross-clade CD8(+) T cell responses to HIV may help to predict whether a successful vaccine could be used to stop geographically and genetically distinct HIV epidemics.