Broadening of Virus-Specific CD8+ T-Cell Responses Is Indicative of Residual Viral Replication in Aviremic SIV Controllers

The quality of SIV-specific fCD8 T cells limits SIV RNA production in Tfh cells during antiretroviral therapy

The attack and defense of infected cells and cytotoxic CD8 T cells occur in germinal centers in lymphoid tissue in chronic persistent HIV/SIV infection. Latently infected cells, the therapeutic target of HIV infection, accumulate in follicular helper T (Tfh) cells in lymphoid tissue; the impact of HIV-specific follicular CD8 (fCD8) T cells in lymphoid tissue on the latently infected cells remains unknown. We infected 15 cynomolgus macaques with SIVmac239 and examined the contribution of SIV-Gag-specific fCD8 T cells, defined by activation-induced markers (AIMs), to SIV-infected cells. Eight out of the 15 infected macaques served as progressors; a chronic phase combination antiretroviral therapy (cART) model was established for the eight macaques (progressors) with chronic persistent infection status, wherein cART was started in the chronic phase and discontinued after 27 weeks. Seven macaques that naturally controlled the viremia served as natural controllers. The frequency of SIV-Gag-specific fCD8 T cells was inversely correlated with the amount of cell-associated SIV-gag RNA in the Tfh only under cART or in the controllers but not in untreated progressors. scRNA-seq of SIV-Gag-specific fCD8 T cells in various conditions revealed that the gene expression pattern of SIV-Gag-specific fCD8 T cells in the controllers was closer to that of those under cART than the untreated progressors. Comparing the SIV-Gag-specific fCD8 T cells of those under cART to the controllers revealed their more exhausted and immunosenescent nature under cART. Improving the HIV/SIV-specific fCD8 T cells under cART by targeting those pathways might contribute to the development of potential curative strategies.IMPORTANCEWe infected cynomolgus macaques with SIVmac239 to establish an SIV-chronically infected cART model. We performed an in-depth characterization of Tfh and fCD8 T cells in three conditions-chronic stage of untreated, cART-treated, and natural controller cynomolgus macaques-by combining tissue section analysis and single-cell analyses of sorted cells. We revealed the inverse relationship between Tfh infection and SIV-Gag-specific fCD8 T cell frequencies as observed in HIV-infected individuals, thereby establishing the cynomolgus macaque as a relevant animal model to study the determinants of HIV/SIV persistence in lymphoid tissue. Additionally, scRNA-seq analysis of SIV-Gag-specific fCD8 T cells revealed an enrichment of exhausted or senescent transcriptomic signatures under cART. These data will provide the basic insights into virus-host CD8 T cell interactions, particularly within the follicular region, during latent HIV infection under ART.

Late-phase dominance of a single epitope-specific CD8+ T-cell response in passive neutralizing antibody-infused simian immunodeficiency virus controllers

OBJECTIVE

Analysis of the quantity and quality of epitope-specific CD8+ T-cell responses is crucial for understanding the mechanism of HIV/simian immunodeficiency virus (SIV) replication control. We have previously shown that acute-phase passive infusion of neutralizing antibodies (NAbs) results in augmented broad T-cell responses and robust SIVmac239 control in rhesus macaques. Analyzing long-term dynamics of CD8+ T-cell responses in these SIV controllers provides important insights into designing lasting anti-HIV immunity.

DESIGN

We analyzed dynamics and metabolic/functional profiles of SIV-specific CD8+ T-cell responses in rhesus macaques that controlled SIVmac239 replication following acute-phase passive NAb infusion.

METHODS

SIV epitope-specific CD8+ T-cell responses in peripheral blood at multiple chronic-phase time points were investigated in four passive NAb-infused SIV controllers. In particular, expression patterns of Eomesodermin (Eomes), phosphorylated AMP kinase (pAMPK), CD28 and programmed death-1 (PD-1) were examined.

RESULTS

In the NAb-infused SIV controllers, a single epitope-specific CD8+ T-cell response detected from acute infection and maintaining low levels up to year 1 showed a surge thereafter, up to year 2 postchallenge. Retention of an effector-skewed and unexhausted Eomes-high/pAMPK-low/CD28-negative/PD-1-low subpopulation in these epitope-specific CD8+ T cells implicated their front-line commitment in residual viral replication control.

CONCLUSION

In long-term SIV control following acute-phase passive NAb infusion, a single-epitope, high-quality CTL response was dominantly induced in the chronic phase. These results likely describe one favorable pattern of immunodominant epitope-specific CD8+ T-cell preservation and suggest the importance of incorporating metabolic marker signatures for understanding NAb/T-cell synergism-based HIV/SIV control.

Nef-specific CD107a+ CD4+ T-cell responses in a rhesus macaque (Macaca mulatta) showing partial simian immunodeficiency virus control following passive neutralizing antibody infusion

Acute-phase neutralizing antibody (NAb) passive immunization in simian immunodeficiency virus (SIV)-infected rhesus macaques (Macaca mulatta) can confer stringent viremia control with T-cell augmentation. In one NAb-infused SIV partial controller, we identify chronic-phase Nef-specific CD107a⁺ CD4⁺ T-cell response maintenance, implicating that NAb infusion modulates long-term T-cell responses even within viremic control.

Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques

SARS-CoV-2 infection presents clinical manifestations ranging from asymptomatic to fatal respiratory failure. Despite the induction of functional SARS-CoV-2-specific CD8⁺ T-cell responses in convalescent individuals, the role of virus-specific CD8⁺ T-cell responses in the control of SARS-CoV-2 replication remains unknown. In the present study, we show that subacute SARS-CoV-2 replication can be controlled in the absence of CD8⁺ T cells in cynomolgus macaques. Eight macaques were intranasally inoculated with 10⁵ or 10⁶ TCID₅₀ of SARS-CoV-2, and three of the eight macaques were treated with a monoclonal anti-CD8 antibody on days 5 and 7 post-infection. In these three macaques, CD8⁺ T cells were undetectable on day 7 and thereafter, while virus-specific CD8⁺ T-cell responses were induced in the remaining five untreated animals. Viral RNA was detected in nasopharyngeal swabs for 10–17 days post-infection in all macaques, and the kinetics of viral RNA levels in pharyngeal swabs and plasma neutralizing antibody titers were comparable between the anti-CD8 antibody treated and untreated animals. SARS-CoV-2 RNA was detected in the pharyngeal mucosa and/or retropharyngeal lymph node obtained at necropsy on day 21 in two of the untreated group but undetectable in all macaques treated with anti-CD8 antibody. CD8⁺ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but our results indicate possible containment of subacute viral replication in the absence of CD8⁺ T cells, implying that CD8⁺ T-cell dysfunction may not solely lead to viral control failure.

SARS-CoV-2 infection presents a wide spectrum of clinical manifestations ranging from asymptomatic to fatal respiratory failure. The determinants for failure in viral control and/or fatal disease progression have not been elucidated fully. Both acquired immune effectors, antibodies and CD8⁺ T cells, are considered to contribute to viral control. However, it remains unknown whether a deficiency in either of these two arms is directly linked to failure in the control of SARS-CoV-2 replication. In the present study, to know the requirement of CD8⁺ T cells for viral control after the establishment of infection, we examined the effect of CD8⁺ cell depletion by monoclonal anti-CD8 antibody administration in the subacute phase on SARS-CoV-2 replication in cynomolgus macaques. Unexpectedly, our analysis revealed no significant impact of CD8⁺ cell depletion on viral replication, indicating that subacute SARS-CoV-2 replication can be controlled in the absence of CD8⁺ T cells. CD8⁺ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but this study suggests that CD8⁺ T-cell dysfunction may not solely lead to viral control failure or fatal disease progression.

[In vivo protective mechanisms of neutralizing antibodies against simian immunodeficiency virus replicatio]

Identifying protective adaptive immune responses against human immunodeficiency virus type 1 (HIV-1), mainly comprising CD8+ cytotoxic T lymphocyte (CTL) and neutralizing antibody (NAb) responses, is crucial for understanding in vivo mechanisms of viral persistence and developing prophylactic/intervention strategies. In HIV-1 and pathogenic simian immunodeficiency virus (SIV) infections, CTL responses play the canonical role in primary viral replication control, whereas NAb responses are impaired. This NAb impairment in early infection conversely highlights the necessity of elucidating anti-HIV/SIV antibody defense/induction mechanisms, and one approach to analyze the impact of NAbs on HIV/SIV infection is passive immunization. We have analyzed a simian AIDS model of highly pathogenic SIVmac239-infected rhesus macaques, and characterized that a single acute-phase passive infusion of SIV-specific polyclonal NAbs drives a synergistic qualitative boosting of virus-specific T-cell responses, resulting in sustained SIV replication control. This in vivo functional augmentation of virus-specific T cells by NAbs in the SIV model provides insights into the design of protective immunity against HIV-1 infection.

A Novel Immunogen Selectively Eliciting CD8+ T Cells but Not CD4+ T Cells Targeting Immunodeficiency Virus Antigens

Optimization of immunogen is crucial for induction of effective T-cell responses in the development of a human immunodeficiency virus (HIV) vaccine. Conventional T-cell-based vaccines have been designed to induce virus-specific CD4⁺ T as well as CD8⁺ T cells. However, it has been indicated that induction of HIV-specific CD4⁺ T cells, preferential targets for HIV infection, by vaccination may be detrimental and accelerate viral replication after HIV exposure. In the present study, we present a novel immunogen to selectively induce CD8⁺ T cells but not CD4⁺ T cells targeting viral antigens. The immunogen, CaV11, was constructed by tandem connection of overlapping 11-mer peptides spanning simian immunodeficiency virus (SIV) Gag capsid (CA) and Vif. Prime-boost immunization with DNA and Sendai virus (SeV) vectors expressing CaV11 efficiently induced Gag/Vif-specific CD8⁺ T-cell responses with inefficient Gag/Vif-specific CD4⁺ T-cell induction in rhesus macaques (n = 6). None of the macaques exhibited the enhancement of acute viral replication after an intravenous high-dose SIV challenge, which was observed in those immunized with DNA and SeV expressing the whole Gag protein in our previous study. Set point viral control postinfection was associated with SeV-specific CD4⁺ T-cell responses postimmunization, suggesting contribution of SeV-specific helper responses to effective Gag/Vif-specific CD8⁺ T-cell induction by vaccination. This immunogen design could be a promising method for selective induction of effective anti-HIV CD8⁺ T-cell responses.IMPORTANCE Induction of effective CD8⁺ T-cell responses is an important HIV vaccine strategy. Several promising vaccine delivery tools have been developed, and immunogen optimization is now crucial for effective T-cell induction. Conventional immunogens have been designed to induce virus-specific CD4⁺ T cells as well as CD8⁺ T cells, but induction of virus-specific CD4⁺ T cells that are preferential targets for HIV infection could enhance acute HIV proliferation. Here, we designed a novel immunogen to induce HIV-specific CD8⁺ T cells without HIV-specific CD4⁺ T-cell induction but with non-HIV antigen-specific CD4⁺ T-cell help. Our analysis in a macaque AIDS model showed that our immunogen can efficiently elicit effective CD8⁺ T but not CD4⁺ T cells targeting viral antigens, resulting in no enhancement of acute viral replication after virus exposure. This immunogen design, also applicable for other currently developed immunogens, could be a promising method for selective induction of effective anti-HIV CD8⁺ T-cell responses.

Determination of a T cell receptor of potent CD8+ T cells against simian immunodeficiency virus infection in Burmese rhesus macaques

Cumulative studies on human immunodeficiency virus (HIV)-infected individuals have shown association of major histocompatibility complex class I (MHC-I) polymorphisms with lower viral load and delayed AIDS progression, suggesting that HIV replication can be controlled by potent CD8⁺ T-cell responses. We have previously established an AIDS model of simian immunodeficiency virus (SIV) infection in Burmese rhesus macaques and found a potent CD8⁺ T cell targeting the Mamu-A1*065:01-restricted Gag_241-249 epitope, which is located in a region corresponding to the HIV Gag_240-249 TW10 epitope restricted by a protective MHC-I allele, HLA-B*57. In the present study, we determined a T cell receptor (TCR) of this Gag_241-249 epitope-specific CD8⁺ T cell. cDNA clones encoding TCR-α and TCR-β chains were obtained from a Gag_241-249-specific CD8⁺ T-cell clone. Coexpression of these TCR-α and TCR-β cDNAs resulted in reconstitution of a functional TCR specifically detected by Gag_241-249 epitope-Mamu-A1*065:01 tetramer. Two of three previously-reported CD8⁺ T-cell escape mutations reduced binding affinity of Gag_241-249 peptide to Mamu-A1*065:01 but the remaining one not. This is consistent with the data obtained by molecular modeling of the epitope-MHC-I complex and TCR. These results would contribute to understanding how viral CD8⁺ T-cell escape mutations are selected under structural constraint of viral proteins.

CD8+ T cell-based strong selective pressure on multiple simian immunodeficiency virus targets in macaques possessing a protective MHC class I haplotype

In human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections, host major histocompatibility complex class I (MHC-I) genotypes have a great impact on viral replication and MHC-I-associated viral genome mutations are selected under CD8⁺ T-cell pressure. Association of MHC-I genotypes with HIV/SIV control has been investigated at MHC-I allele levels but not fully at haplotype levels. We previously established groups of rhesus macaques sharing individual MHC-I haplotypes. In the present study, we compared viral genome diversification after SIV infection in macaques possessing a protective MHC-I haplotype, 90-010-Id, with those possessing a non-protective MHC-I haplotype, 90-010-Ie. These two MHC-I haplotypes are associated with immunodominant CD8⁺ T-cell responses targeting similar regions of viral Nef antigen. Analyses of viral genome sequences and antigen-specific T-cell responses showed four and two candidates of viral CD8⁺ T-cell targets associated with 90-010-Id and 90-010-Ie, respectively, in addition to the Nef targets. In these CD8⁺ T-cell target regions, higher numbers of mutations were detected at the setpoint after SIV infection in macaques possessing 90-010-Id than those possessing 90-010-Ie. These results indicate higher selective pressure on overall CD8⁺ T-cell targets associated with the protective MHC-I haplotype, suggesting a pattern of HIV/SIV control by multiple target-specific CD8⁺ T-cell responses.

In vivo virulence of MHC-adapted AIDS virus serially-passaged through MHC-mismatched hosts

CD8⁺ T-cell responses exert strong suppressive pressure on HIV replication and select for viral escape mutations. Some of these major histocompatibility complex class I (MHC-I)-associated mutations result in reduction of in vitro viral replicative capacity. While these mutations can revert after viral transmission to MHC-I-disparate hosts, recent studies have suggested that these MHC-I-associated mutations accumulate in populations and make viruses less pathogenic in vitro. Here, we directly show an increase in the in vivo virulence of an MHC-I-adapted virus serially-passaged through MHC-I-mismatched hosts in a macaque AIDS model despite a reduction in in vitro viral fitness. The first passage simian immunodeficiency virus (1pSIV) obtained 1 year after SIVmac239 infection in a macaque possessing a protective MHC-I haplotype 90-120-Ia was transmitted into 90-120-Ia^- macaques, whose plasma 1 year post-infection was transmitted into other 90-120-Ia^- macaques to obtain the third passage SIV (3pSIV). Most of the 90-120-Ia-associated mutations selected in 1pSIV did not revert even in 3pSIV. 3pSIV showed lower in vitro viral fitness but induced persistent viremia in 90-120-Ia^- macaques. Remarkably, 3pSIV infection in 90-120-Ia⁺ macaques resulted in significantly higher viral loads and reduced survival compared to wild-type SIVmac239. These results indicate that MHC-I-adapted SIVs serially-transmitted through MHC-I-mismatched hosts can have higher virulence in MHC-I-matched hosts despite their lower in vitro viral fitness. This study suggests that multiply-passaged HIVs could result in loss of HIV-specific CD8⁺ T cell responses in human populations and the in vivo pathogenic potential of these escaped viruses may be enhanced.

CD8⁺ T-cell responses exert considerable control over replication of HIV and select for viral escape mutations. Recent studies have suggested that these major histocompatibility complex class I (MHC-I)-associated mutations accumulate in populations and make viruses less pathogenic in vitro. Other studies have shown that some of these escape mutations can revert after passage to MHC-I-disparate hosts. In an attempt to reconcile these apparently conflicting results, we serially passaged a virus isolate through MHC-I-mismatched hosts in the macaque AIDS model of simian immunodeficiency virus (SIV) infection. Here we show an increase in the in vivo virulence of an MHC-I-adapted virus despite a reduction in in vitro viral replication capacity. Only a few of the selected escape mutations reverted after transmission to MHC-I-disparate recipients. Results clearly showed that MHC-I-adapted SIVs that have been serially-transmitted through MHC-I-mismatched hosts can have higher in vivo virulence in MHC-I-matched hosts despite their lower in vitro viral fitness. This study suggests that HIVs may become less sensitive to CD8⁺ T cell responses and could have increased in vivo virulence by adaptation to MHC-I in human populations.

Biphasic CD8+ T-Cell Defense in Simian Immunodeficiency Virus Control by Acute-Phase Passive Neutralizing Antibody Immunization

Identifying human immunodeficiency virus type 1 (HIV-1) control mechanisms by neutralizing antibodies (NAbs) is critical for anti-HIV-1 strategies. Recent in vivo studies on animals infected with simian immunodeficiency virus (SIV) and related viruses have shown the efficacy of postinfection NAb passive immunization for viremia reduction, and one suggested mechanism is its occurrence through modulation of cellular immune responses. Here, we describe SIV control in macaques showing biphasic CD8(+) cytotoxic T lymphocyte (CTL) responses following acute-phase NAb passive immunization. Analysis of four SIVmac239-infected rhesus macaque pairs matched with major histocompatibility complex class I haplotypes found that counterparts receiving day 7 anti-SIV polyclonal NAb infusion all suppressed viremia for up to 2 years without accumulating viral CTL escape mutations. In the first phase of primary viremia control attainment, CD8(+) cells had high capacities to suppress SIVs carrying CTL escape mutations. Conversely, in the second, sustained phase of SIV control, CTL responses converged on a pattern of immunodominant CTL preservation. During this sustained phase of viral control, SIV epitope-specific CTLs showed retention of phosphorylated extracellular signal-related kinase (ERK)(hi)/phosphorylated AMP-activated protein kinase (AMPK)(lo) subpopulations, implying their correlation with SIV control. The results suggest that virus-specific CTLs functionally boosted by acute-phase NAbs may drive robust AIDS virus control.

IMPORTANCE

In early HIV infection, NAb responses are lacking and CTL responses are insufficient, which leads to viral persistence. Hence, it is important to identify immune responses that can successfully control such HIV replication. Here, we show that monkeys receiving NAb passive immunization in early SIV infection strictly control viral replication for years. Passive infusion of NAbs with CTL cross-priming capacity resulted in induction of functionally boosted early CTL responses showing enhanced suppression of CTL escape mutant virus replication. Accordingly, the NAb-infused animals did not show accumulation of viral CTL escape mutations during sustained SIV control, and immunodominant CTL responses were preserved. This early functional augmentation of CTLs by NAbs provides key insights into the design of lasting and viral escape mutation-free protective immunity against HIV-1 infection.