HLA-A*2402-restricted HIV-1-specific cytotoxic T lymphocytes and escape mutation after ART with structured treatment interruptions

Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors

Cross-recognized public TCRs against HIV epitopes have been proposed to be important for the control of AIDS disease progression and HIV variants. The overlapping Nef138-8 and Nef138-10 peptides from the HIV Nef protein are HLA-A24-restricted immunodominant T cell epitopes, and an HIV mutant strain with a Y139F substitution in Nef protein can result in immune escape and is widespread in Japan. Here, we identified a pair of public TCRs specific to the HLA-A24-restricted Nef-138-8 epitope using PBMCs from White and Japanese patients, respectively, namely TD08 and H25-11. The gene use of the variable domain for TD08 and H25-11 is TRAV8-3, TRAJ10 for the α-chain and TRBV7-9, TRBD1*01, TRBJ2-5 for the β-chain. Both TCRs can recognize wild-type and Y2F-mutated Nef138-8 epitopes. We further determined three complex structures, including TD08/HLA-A24-Nef138-8, H25-11/HLA-A24-Nef138-8, and TD08/HLA-A24-Nef138-8 (2F). Then, we revealed the molecular basis of the public TCR binding to the peptide HLA, which mostly relies on the interaction between the TCR and HLA and can tolerate the mutation in the Nef138-8 peptide. These findings promote the molecular understanding of T cell immunity against HIV epitopes and provide an important basis for the engineering of TCRs to develop T cell-based immunotherapy against HIV infection.

N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations

We have applied our advanced multicanonical molecular dynamics (McMD)-based dynamic docking methodology to investigate the binding mechanism of an HIV-1 Nef protein epitope to the Asian-dominant allele human leukocyte antigen (HLA)-A*2402. Even though pMHC complex formation [between a Major histocompatibility complex (MHC) class I molecule, which is encoded by an HLA allele, and an antigen peptide] is one of the fundamental processes of the adaptive human immune response, its binding mechanism has not yet been well studied, partially due to the high allelic variation of HLAs in the population. We have used our developed McMD-based dynamic docking method and have successfully reproduced the native complex structure, which is located near the free energy global minimum. Subsequent path sampling MD simulations elucidated the atomic details of the binding process and indicated that the peptide binding is initially driven by the highly positively charged N-terminus of the peptide that is attracted to the various negatively charged residues on the MHC molecule's surface. Upon nearing the pocket, the second tyrosine residue of the peptide anchors the peptide by strongly binding to the B-site of the MHC molecule via hydrophobic driven interactions, resulting in a very strong bound complex structure. Our methodology can be effectively used to predict the bound complex structures between MHC molecules and their antigens to study their binding mechanism in close detail, which would help with the development of new vaccines against cancers, as well as viral infections such as HIV and COVID-19.

Clinical trials of antiretroviral treatment interruption in HIV-infected individuals

: Despite the benefits of antiretroviral therapy (ART) for people living with HIV, there has been a long-standing research interest in interrupting ART as a strategy to minimize adverse effects of ART as well as to test interventions aiming to achieve a degree of virological control without ART. We performed a systematic review of HIV clinical studies involving treatment interruption from 2000 to 2017 to describe the differences between treatment interruption in studies that contained and didn't contain an intervention. We assessed differences in monitoring strategies, threshold to restart ART, duration and adverse outcomes of treatment interruption, and factors aimed at minimizing transmission. We found that treatment interruption has been incorporated into 159 clinical studies since 2000 and is increasingly being included in trials to assess the efficacy of interventions to achieve sustained virological remission off ART. Great heterogeneity was noted in immunological, virological and clinical monitoring strategies, as well as in thresholds to recommence ART. Treatment interruption in recent intervention studies were more closely monitored, had more conservative thresholds to restart ART and had a shorter treatment interruption duration, compared with older treatment interruption studies that didn't include an intervention.

Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation

The mechanistic basis for the progressive accumulation of Y(135)F Nef mutant viruses in the HIV-1-infected population remains poorly understood. Y(135)F viruses carry the 2F mutation within RW8 and RF10, which are two HLA-A(∗)24:02-restricted superimposed Nef epitopes recognized by distinct and adaptable CD8(+) T cell responses. We combined comprehensive analysis of the T cell receptor repertoire and cross-reactive potential of wild-type or 2F RW8- and RF10-specific CD8(+) T cells with peptide-MHC complex stability and crystal structure studies. We find that, by affecting direct and water-mediated hydrogen bond networks within the peptide-MHC complex, the 2F mutation reduces both TCR and HLA binding. This suggests an advantage underlying the evolution of the 2F variant with decreased CD8(+) T cell efficacy. Our study provides a refined understanding of HIV-1 and CD8(+) T cell co-adaptation at the population level.

Variable processing and cross-presentation of HIV by dendritic cells and macrophages shapes CTL immunodominance and immune escape

Dendritic cells (DCs) and macrophages (Møs) internalize and process exogenous HIV-derived antigens for cross-presentation by MHC-I to cytotoxic CD8⁺ T cells (CTL). However, how degradation patterns of HIV antigens in the cross-presentation pathways affect immunodominance and immune escape is poorly defined. Here, we studied the processing and cross-presentation of dominant and subdominant HIV-1 Gag-derived epitopes and HLA-restricted mutants by monocyte-derived DCs and Møs. The cross-presentation of HIV proteins by both DCs and Møs led to higher CTL responses specific for immunodominant epitopes. The low CTL responses to subdominant epitopes were increased by pretreatment of target cells with peptidase inhibitors, suggestive of higher intracellular degradation of the corresponding peptides. Using DC and Mø cell extracts as a source of cytosolic, endosomal or lysosomal proteases to degrade long HIV peptides, we identified by mass spectrometry cell-specific and compartment-specific degradation patterns, which favored the production of peptides containing immunodominant epitopes in all compartments. The intracellular stability of optimal HIV-1 epitopes prior to loading onto MHC was highly variable and sequence-dependent in all compartments, and followed CTL hierarchy with immunodominant epitopes presenting higher stability rates. Common HLA-associated mutations in a dominant epitope appearing during acute HIV infection modified the degradation patterns of long HIV peptides, reduced intracellular stability and epitope production in cross-presentation-competent cell compartments, showing that impaired epitope production in the cross-presentation pathway contributes to immune escape. These findings highlight the contribution of degradation patterns in the cross-presentation pathway to HIV immunodominance and provide the first demonstration of immune escape affecting epitope cross-presentation.

Pathogens such as HIV can enter cells by fusion at the plasma membrane for delivery in the cytosol, or by internalization in endolysosomal vesicles. Pathogens can be degraded in these various compartments into peptides (epitopes) displayed at the cell surface by MHC-I. The presentation of pathogen-derived peptides triggers the activation of T cell immune responses and the clearance of infected cells. How the diversity of compartments in which HIV traffics combined with the diversity of HIV sequences affects the degradation of HIV and the recognition of infected cells by immune cells is not understood. We compared the degradation of HIV proteins in subcellular compartments of dendritic cells and macrophages, two cell types targeted by HIV and the subsequent presentation of epitopes to T cells. We show variable degradation patterns of HIV according to compartments, and the preferential production and superior intracellular stability of immunodominant epitopes corresponding to stronger T cell responses. Frequent mutations in immunodominant epitopes during acute infection resulted in decreased production and intracellular stability of these epitopes. Together these results demonstrate the importance of protein degradation patterns in shaping immunodominant epitopes and the contribution of impaired epitope production in all cellular compartments to immune escape during HIV infection.

Superimposed epitopes restricted by the same HLA molecule drive distinct HIV-specific CD8+ T cell repertoires

Superimposed epitopes, in which a shorter epitope is embedded within a longer one, can be presented by the same HLA class I molecule. CD8(+) CTL responses against such epitopes and the contribution of this phenomenon to immune control are poorly characterized. In this study, we examined HLA-A*24:02-restricted CTLs specific for the superimposed HIV Nef epitopes RYPLTFGWCF (RF10) and RYPLTFGW (RW8). Unexpectedly, RF10-specific and RW8-specific CTLs from HIV-1-infected HLA-A*24:02+ individuals had no overlapping Ag reactivity or clonotypic compositions. Single-cell TCR sequence analyses demonstrated that RF10-specific T cells had a more diverse TCR repertoire than did RW8-specific T cells. Furthermore, RF10-specific CTLs presented a higher Ag sensitivity and HIV suppressive capacity compared with RW8-specific CTLs. Crystallographic analyses revealed important structural differences between RF10- and RW8-HLA-A*24:02 complexes as well, with featured and featureless conformations, respectively, providing an explanation for the induction of distinct T cell responses against these epitopes. The present study shows that a single viral sequence containing superimposed epitopes restricted by the same HLA molecule could elicit distinct CD8+ T cell responses, therefore enhancing the control of HIV replication. This study also showed that a featured epitope (e.g., RF10) could drive the induction of T cells with high TCR diversity and affinity.

Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes

Strong statistical associations between polymorphisms in HIV-1 population sequences and carriage of HLA class I alleles have been widely used to identify possible sites of CD8 T cell immune selection in vivo. However, there have been few attempts to prospectively and systematically test these genetic hypotheses arising from population-based studies at a cellular, functional level. We assayed CD8 T cell epitope-specific IFN-γ responses in 290 individuals from the same cohort, which gave rise to 874 HLA-HIV associations in genetic analyses, taking into account autologous viral sequences and individual HLA genotypes. We found immunological evidence for 58% of 374 associations tested as sites of primary immune selection and identified up to 50 novel HIV-1 epitopes using this reverse-genomics approach. Many HLA-adapted epitopes elicited equivalent or higher-magnitude IFN-γ responses than did the nonadapted epitopes, particularly in Nef. At a population level, inclusion of all of the immunoreactive variant CD8 T cell epitopes in Gag, Pol, Nef, and Env suggested that HIV adaptation leads to an inflation of Nef-directed immune responses relative to other proteins. We concluded that HLA-HIV associations mark viral epitopes subject to CD8 T cell selection. These results can be used to guide functional studies of specific epitopes and escape mutations, as well as to test, train, and evaluate analytical models of viral escape and fitness. The inflation of Nef and HLA-adapted variant responses may have negative effects on natural and vaccine immunity against HIV and, therefore, has implications for diversity coverage approaches in HIV vaccine design.

Clinical symptoms and courses of primary HIV-1 infection in recent years in Japan

BACKGROUND

The natural course of HIV-1 infection includes 10 years of an asymptomatic period before the development of AIDS. However, in Japan, the disease progression process seems faster in recent years.

METHODS

The study subjects were 108 new patients with primary HIV-1 infection during the period from 1997 through 2007. We evaluated their clinical symptoms and laboratory data, and then analyzed disease progression in 82 eligible patients. Disease progression was defined as a fall in CD4 count below 350/µL and/or initiation of antiretroviral therapy.

RESULTS

Ninety percent of the patients were infected via homosexual intercourse. All patients had at least one clinical symptom (mean; 4.75±1.99) related to primary HIV-1 infection, with a mean duration of 23.2 days (±14.8) and 53.3% of them had to be hospitalized due to severe symptoms. The mean CD4 count and viral load at first visit were 390/µL (±220.1) and 4.81 log10/mL (±0.78), respectively. None developed AIDS during the study period. Estimates of risk of disease progression were 61.0% at 48 weeks and 82.2% at 144 weeks. In patients who required antiretroviral therapy, the median CD4 count was 215/µL (range, 52-858) at initiation of such therapy. Among the patients with a CD4 count of <350/µL at first visit, 53% never showed recovery of CD4 count (>350/µL) without antiretroviral therapy.

CONCLUSION

Despite possible bias in patient population, disease progression seemed faster in symptomatic Japanese patients with recently acquired primary HIV-1 infection than the previously defined natural course of the disease.