Virus-specific CD8+ T cells are crucial in controlling chronic human viral infections such as HIV-1, but the effect of persistent antigen exposure on T cell repertoire formation is not well understood. In this study, we examined epitope-specific CD8+ T cell repertoires in people living with HIV-1, where duration of viremia following hyperacute infection was modulated by the time of initiation of continuous suppressive antiretroviral therapy (ART). After ART-induced suppression of viremia in persons expressing the same HLA class I allele, we analyzed the impact of early (n=6) versus delayed (n=6) ART initiation on the clonotypic composition, cross-reactivity, functional avidity and memory differentiation profile of the HIV-specific T cell repertoire restricted by HLA-B*58:01. Using a panel of barcoded tetramers, we mapped T cell receptor (TCR) clonotypes specific for three dominant epitopes and their variants. Both groups exhibited polyclonal TCR repertoires with evidence of cross-reactivity, which was significantly enriched in donors with prolonged antigen exposure. Within this cohort, broadly cross-reactive clonotypes capable of recognizing all autologous variants were identified, but these were rare (<1%). Early ART initiation preserved repertoires characterized by higher-avidity TCRs and a relative enrichment of transitional memory CD8+ T cell subsets. These functional differences were not associated with differences in TRBV gene sharing, indicating that ART timing shapes repertoire quality and memory differentiation without altering TRBV gene bias. These findings demonstrate how antigen suppression dynamics differentially shape the breadth, functional sensitivity, and memory composition of the HIV-specific TCR repertoire, with implications for T cell-directed immunotherapies and HIV cure strategies.

Immune reconstitution following the initiation of combination antiretroviral therapy (cART) significantly impacts the prognosis of individuals infected with human immunodeficiency virus (HIV). Our previous studies have indicated that the baseline CD4+ T cells count and percentage before cART initiation are predictors of immune recovery in TB-negative children infected with HIV, with TB co-infection potentially causing a delay in immune recovery. However, it remains unclear whether these predictors consistently impact immune reconstitution during long-term intensive cART treatment in TB-negative/positive children infected with HIV. We confirmed that the baseline CD4+ T cell count is a significant predictor of immune recovery following long-term intensive cART treatment among children aged 0 to 13 years. Children with lower CD4+ T cell count prior cART initiation did not show substantial immunological recovery during the follow-up period. Interestingly, children who were co-infected with TB and had higher baseline CD4+ T cell count eventually achieved good immunological recovery comparable to the TB-negative HIV-infected children. Hence, the baseline CD4+ T cell count at the onset of treatment serves as a reliable predictor of immunological reconstitution in HIV-infected children with or without TB co-infection. Taken together, this follow-up study validates our previous findings and further establishes that initiating cART early alongside early HIV testing can help prevent the diminished CD4+ T cell count associated with inadequate immunological reconstitution.

Immunogenetic studies have shown that specific HLA-B residues (67, 70, 97, and 156) mediate the impact of HLA class I on HIV infection, but the molecular basis is not well understood. Here we evaluate the function of these residues within the protective HLA-B∗5701 allele. While mutation of Met67, Ser70, and Leu156 disrupt CD8+ T cell recognition, substitution of Val97 had no significant impact. Thermal denaturation of HLA-B∗5701-peptide complexes revealed that Met67 and Leu156 maintain HLA-peptide stability, while Ser70 and Leu156 facilitate T cell receptor (TCR) interactions. Analyses of existing structures and structural models suggested that Val97 mediates HLA-peptide binding to inhibitory KIR3DL1 molecules, which was confirmed by experimental assays. These data thereby demonstrate that the genetic basis by which host immunity impacts HIV outcomes occurs by modulating HLA-B-peptide stability and conformation for interaction with TCR and killer immunoglobulin receptor (KIR) molecules. Moreover, they indicate a key role for epitope specificity and HLA-KIR interactions to HIV control.

BACKGROUND:The underrepresentation of historically marginalized groups in the HIV research workforce is a barrier to reaching national Ending the Epidemic goals.SETTING:The Harvard University Center for AIDS Research (HU CFAR) Diversity Equity and Inclusion Working Group (DEI WG) uses a multifaceted approach to enhance the field's diversity.METHODS:We established a DEI WG to improve the recruitment, inclusion, and retention of underrepresented minorities (URMs) in HIV research. We use community-based, participatory processes to establish and expand education and outreach programs about HIV care and research to better connect the HU CFAR to communities affected by HIV. This article reports on the development of the WG in July 2022, progress in its first year, and future plans.RESULTS:We have built a network of >50 investigators across the university for monthly meetings; partnered with existing research pathway programs for high school, undergraduate, and graduate students, directly supporting 7 new trainees and linking CFAR investigators to additional mentorship opportunities; and created 2-year Scholar Awards for 5 URM investigators in HIV. Planned work includes needs assessments for early-stage investigators to understand factors contributing to inclusion and retention and new pathway and outreach programming being developed with community partner minority-serving institutions.CONCLUSIONS:The HU CFAR DEI WG strives to ensure that individuals from underrepresented, marginalized, and minoritized communities have an opportunity to contribute to HIV research and that research is informed by the needs of the communities affected by the epidemic. An intersectional approach should be incorporated into HIV research pathway initiatives.

HIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV-infected cells and immune responses in native lymph node tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in lymph node biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated in Fiebig stages III-V and 17 late treated individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, we detect HIV RNA and/or protein in 12 of 14 Fiebig I/II treated persons on suppressive therapy for 1 to 55 months, and in late treated persons with persistent antigens. CXCR3 + T follicular helper cells harbor the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8 + T cells responses are associated with lower HIV antigen burden, suggesting that these responses may contribute to HIV suppression in lymph nodes during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.

Background HIV eradication efforts have been unsuccessful partly due to virus persistence in immune sanctuary sites such as germinal centres within lymph node (LN) tissues. Recent evidence suggests that LNs harbour a novel subset of regulatory T cells, termed follicular regulatory T cells (TFRs), but their role in HIV pathogenesis is not fully elucidated. Results Paired excisional LN and peripheral blood samples obtained from 20 HIV-uninfected and 31 HIV-infected treated and 7 chronic untreated, were used to determine if and how HIV infection modulate frequencies, function and spatial localization of TFRs within LN tissues. Imaging studies showed that most TFRs are localized in extra-follicular regions. Co-culture assays showed TFRs suppression of TFH help to B cells. Importantly, epigenetic and transcriptional studies identified DPP4 and FCRL3 as novel phenotypic markers that define four functionally distinct TFR subpopulations in human LNs regardless of HIV status. Imaging studies confirmed the regulatory phenotype of DPP4 + TFRs. Conclusion Together these studies describe TFRs dynamic changes during HIV infection and reveal previously underappreciated TFR heterogeneity within human LNs.

Polymorphisms in human leukocyte antigen ( HLA ) genes strongly influence outcomes to HIV infection. However, the underlying mechanisms by which certain alleles mediate protection is not well understood. Here we systematically investigate residues within HLA class I molecules (at positions 67, 70, 97 and 156) that have been demonstrated by genetic studies to explain the observed variation of HLA class I alleles on HIV infection. Through a detailed assessment of the protective HLA-B*5701 allele, we find that each of these residues has distinct effects on either HIV-specific CD8+ T cell recognition (67, 70, 156), stabilization of HLA class I-peptide complexes (67, 156), binding of HLA class I-peptide to HIV-specific T cell receptors (70, 156) or KIR3DL1 (97). Structural analyses illustrate that residue mutations uniquely affect the residue microenvironment of the class I binding groove to impact interactions between HLA-peptide complexes with TCR and KIR. These results thereby provide a structural and mechanistic basis for the HLA association with HIV disease outcome. Moreover, they definitively demonstrate that the major host genetic determinant of HIV control is modulation of the stability and conformation of viral peptides by HLA class I for recognition by both the innate and adaptive immune system.

Key Points A paucity of follicular CD8+ T cells in LN germinal centers contributes to HIV persistence during cART. CXCR5 expression in human CD8+ T cells is tightly regulated by epigenetic mechanisms.

HIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV infected cells and immune responses in native lymph node (LN) tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in LN biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated (Tx) in Fiebig stages III-V and 17 late Tx individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, HIV RNA and/or protein was detected in 12 of 14 Fiebig I/II Tx persons who were on suppressive therapy for 1 to 55 months, while all late Tx persons had persistent antigens. CXCR3+T follicular helper T cells harbored the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8+ T cells responses associated with lower HIV antigen burden in LNs, suggesting that these responses may contribute to HIV suppression in LNs during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.

CD8+ T cells play an important role in viral and tumour control. However, in human lymph nodes (LNs), only a small subset of CD8+ T cells called follicular CD8+ T cells (fCD8s) expresses CXCR5, the chemokine receptor required for cell migration into B cell follicles, thought to promote immune evasion. Here we obtained LNs from HIV infected persons to investigate regulation of CXCR5 expression in lymphoid CD8+ T cells, and compared this to the more abundant CXCR5 expressing T follicular CD4+ helper cells (GCTfh). Our results show that DNA hypermethylation and closed chromatin at the transcriptional start site (TSS) prevent CXCR5 expression in non-fCD8s. We also found that greater nucleosomal density at the CXCR5 TSS could be responsible for reduced CXCR5 expression in fCD8s relative to GCTfh. Together, these data provide critical insights into both the underlying molecular mechanisms that repress CXCR5 expression in non-fCD8s and the plausible mechanism responsible for the low CXCR5 expression in fCD8s, with implications for HIV cure strategies.Author Summary A paucity of CD8+ T cells that express CXCR5, the chemokine receptor critical for entering the B cell follicles of secondary lymphoid tissues have recently been described. Animal studies have revealed transcriptional networks that govern the expression of CXCR5 in CD8+ T cells. However, it is not known if similar or additional networks regulate the expression of CXCR5 in human CD8+ T cells. In this study, we demonstrated that DNA methylation coupled with chromatin compaction at the transcriptional start site (TSS) of CXCR5 gene prevent the expression CXCR5 in human CD8+ T cells. In addition, we observed greater nucleosomal occupancy at the TSS of CXCR5 gene which could impact expression levels of CXCR5 in human CXCR5+CD8+ T cells. This study revealed multitiered epigenetic mechanisms that repress CXCR5 expression in human CD8+ T cells, with implications for HIV cure strategy or eradication of B cell-derived tumours.

The class I human leucocyte antigen (HLA) gene is a major determinant of HIV disease progression. Some people have versions of the HLA gene that are associated with better HIV control. One such HLA gene is HLAB*81. However, HLA-B*42 which is closely related to HLA-B*81 genetically is unable to control HIV to the same extent despite targeting the same region of the HIV known as the TL9 epitope. This study sought to examine the mechanism for the observed difference in HIV control by the two HLA genes. We identified an unexpected population of immune cells that target TL9 when presented by B*81 and B*42, even in individuals who lacked one gene. This dual-HLA reactive response was more common in individuals possessing the B*81 gene and it was associated with lower viral loads, indicating that it contributes to control of HIV infection. An in-depth analysis of receptors on immune cells, known as T cell receptors (TCR), uncovered similarities between immune responses derived from B*81 and those from B*42 individuals with dual-HLA responses. Interestingly, we identified viral variants that selectively stimulated dual-reactive responses, suggesting that vaccination with these variants might be more effective for people who possess B*42.

Sustained viremia after acute HIV infection is associated with profound CD4+ T cell loss and exhaustion of HIV-specific CD8+ T cell responses. To determine the impact of combination antiretroviral therapy (cART) on these processes, we examined the evolution of immune responses in acutely infected individuals initiating treatment before peak viremia. Immediate treatment of Fiebig stages I and II infection led to a rapid decline in viral load and diminished magnitude of HIV-specific (tetramer+) CD8+ T cell responses compared to untreated donors. There was a strong positive correlation between cumulative viral antigen exposure before full cART-induced suppression and immune responses measured by MHC class I tetramers, IFN-γ ELISPOT, and CD8+ T cell activation. HIV-specific CD8+ T responses of early treated individuals were characterized by increased CD127 and BCL-2 expression, greater in vitro IFN-γ secretion, and enhanced differentiation into effector memory (Tem) cells. Transcriptional analysis of tetramer+ CD8+ T cells from treated persons revealed reduced expression of genes associated with activation and apoptosis, with concurrent up-regulation of prosurvival genes including BCL-2, AXL, and SRC Early treatment also resulted in robust HIV-specific CD4+ T cell responses compared to untreated HIV-infected individuals. Our data show that limiting acute viremia results in enhanced functionality of HIV-specific CD4+ and CD8+ T cells, preserving key antiviral properties of these cells.

Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8 + T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML 180–188 ) in the context of the protective allele B*81:01 and the less protective allele B*42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B*81:01 and B*42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B*42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation.

Despite decades of focused research, the field has yet to develop a prophylactic vaccine for HIV-1 infection. In the RV144 vaccine trial, nonneutralizing antibody responses were identified as a correlate for prevention of HIV acquisition. However, factors that predict the development of such antibodies are not fully elucidated. We sought to define the contribution of circulating T follicular helper (cTfh) subsets to the development of nonneutralizing antibodies in HIV-1 clade C infection. Study participants were recruited from an acute HIV-1 clade C infection cohort. Plasma anti-gp41, -gp120, -p24, and -p17 antibodies were screened using a customized multivariate Luminex assay. Phenotypic and functional characterizations of cTfh cells were performed using HLA class II tetramers and intracellular cytokine staining. In this study, we found that acute HIV-1 clade C infection skewed the differentiation of functional cTfh subsets toward increased Tfh1 (P = 0.02) and Tfh2 (P < 0.0001) subsets, with a concomitant decrease in overall Tfh1-17 (which shares both Tfh1 and Tfh17 properties) (P = 0.01) and Tfh17 (P < 0.0001) subsets, compared to the subsets found in HIV-negative subjects. Interestingly, the frequencies of Tfh1 cells during acute infection (5.0 to 8.0 weeks postinfection) correlated negatively with the set point viral load (P = 0.03, Spearman rho [r] = -60) and were predictive of p24-specific plasma IgG titers at 1 year of infection (P = 0.003, r = 0.85). Taken together, our results suggest that the circulating Tfh1 subset plays an important role in the development of anti-HIV antibody responses and contributes to HIV suppression during acute HIV-1 infection. These results have implications for vaccine studies aimed at inducing long-lasting anti-HIV antibody responses.IMPORTANCE The HIV epidemic in southern Africa accounts for almost half of the global HIV burden, with HIV-1 clade C being the predominant strain. It is therefore important to define immune correlates of clade C HIV control that might have implications for vaccine design in this region. T follicular helper (Tfh) cells are critical for the development of HIV-specific antibody responses and could play a role in viral control. Here we showed that the early induction of circulating Tfh1 cells during acute infection correlated positively with the magnitude of p24-specific IgG and was associated with a lower set point viral load. This study highlights a key Tfh cell subset that could limit HIV replication by enhancing antibody generation. This study underscores the importance of circulating Tfh cells in promoting nonneutralizing antibodies during HIV-1 infection.

Introduction Standard immunogenicity assays, such as ELISpot and intracellular cytokine staining, fail to correlate HIV-1-specific CD8+T-cells responses with HIV-1 replication in-vivo. Therefore, it is essential to develop assays that can determine antiviral potential of vaccine elicited CD8+T-cells. The current ELISA-VIA measures HIV-1-p24 production overtime in autologous CD4+T-cells. However, it is not designed to identify the class-I-HLA-allele involved in mediating the response. We developed a new FACS based VIA that can investigate CD8+T-cells antiviral potential in the context of restricting class-I-HLA alleles. The assay measures the ability of CD8+T-cells to kill HIV-1 infected GXR-cells over-expressing class-I-HLA allele of interest. The assay utilises a GXR-cell engineered to express GFP upon HIV-1 infection. Methods CD8+T-cells were co-cultured with HIV-1 infected GXR-cells for 3 days. Reduction in the infected GXR-cells expressing GFP measured by FACS was used to evaluate the CD8+T-cells killing activity. The assay was validated using a panel of 9 HIV-infected samples and were concurrently assayed with the ELISA-VIA. The tested results on each assay were categorised into four groups namely: true-inhibition (TI ≥50%), doubtful-inhibition (DI ≥20% to ≤49.99%), false-inhibition (FI ≥10% to ≤19.99%) and non-inhibition (NI≤ 9.99%). These results were used in a 2 by 2 table to compute sensitivity (TI/TI+DI) and specificity (FI/FI+NI). Results True inhibition was observed in 44% of samples analysed using GXR-VIA compared to 33% with ELISA-VIA. 11% with GXR-VIA had doubtful result compared to 33% with ELISA-VIA. 22% with GXR-VIA were categorised as false inhibition compared to 33% with ELISA-VIA. Interestingly, no sample showed non-inhibition with GXR-VIA whereas 22% showed no inhibition by ELISA-VIA. Collectively, GXR-VIA is very specific (100%) but less sensitive (57%) at detecting virus inhibition activity. Conclusion The specificity of GXR-VIA and its marginal sensitivity indicates that the assay is capable of identifying CD8+T-cells-mediated inhibition of HIV-1 replication. Overall, the GXR-VIA provides a platform to assess the influence of different restricting class-I-HLA alleles on HIV-1-specific CD8+T-cells antiviral function.

CD8+ T cells contribute to the control of HIV, but it is not clear whether initial immune responses modulate the viral set point. We screened high-risk uninfected women twice a week for plasma HIV RNA and identified 12 hyperacute infections. Onset of viremia elicited a massive HIV-specific CD8+ T cell response, with limited bystander activation of non-HIV memory CD8+ T cells. HIV-specific CD8+ T cells secreted little interferon-γ, underwent rapid apoptosis, and failed to upregulate the interleukin-7 receptor, known to be important for T cell survival. The rapidity to peak CD8+ T cell activation and the absolute magnitude of activation induced by the exponential rise in viremia were inversely correlated with set point viremia. These data indicate that rapid, high magnitude HIV-induced CD8+ T cell responses are crucial for subsequent immune control of acute infection, which has important implications for HIV vaccine design.

Master of Medical Sciences in Immunology. University of KwaZulu-Natal, Medical School 2015.