HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case-cohort analysis

BACKGROUND

In the Step Study, the MRKAd5 HIV-1 gag/pol/nef vaccine did not reduce plasma viraemia after infection, and HIV-1 incidence was higher in vaccine-treated than in placebo-treated men with pre-existing adenovirus serotype 5 (Ad5) immunity. We assessed vaccine-induced immunity and its potential contributions to infection risk.

METHODS

To assess immunogenicity, we characterised HIV-specific T cells ex vivo with validated interferon-gamma ELISPOT and intracellular cytokine staining assays, using a case-cohort design. To establish effects of vaccine and pre-existing Ad5 immunity on infection risk, we undertook flow cytometric studies to measure Ad5-specific T cells and circulating activated (Ki-67+/BcL-2(lo)) CD4+ T cells expressing CCR5.

FINDINGS

We detected interferon-gamma-secreting HIV-specific T cells (range 163/10(6) to 686/10(6) peripheral blood mononuclear cells) ex vivo by ELISPOT in 77% (258/354) of people receiving vaccine; 218 of 354 (62%) recognised two to three HIV proteins. We identified HIV-specific CD4+ T cells by intracellular cytokine staining in 58 of 142 (41%) people. In those with reactive CD4+ T cells, the median percentage of CD4+ T cells expressing interleukin 2 was 88%, and the median co-expression of interferon gamma or tumor necrosis factor alpha (TNFalpha), or both, was 72%. We noted HIV-specific CD8+ T cells (range 0.4-1.0%) in 117 of 160 (73%) participants, expressing predominantly either interferon gamma alone or with TNFalpha. Vaccine-induced HIV-specific immunity, including response rate, magnitude, and cytokine profile, did not differ between vaccinated male cases (before infection) and non-cases. Ad5-specific T cells were lower in cases than in non-cases in several subgroup analyses. The percentage of circulating Ki-67+BcL-2(lo)/CCR5+CD4+ T cells did not differ between cases and non-cases.

INTERPRETATION

Consistent with previous trials, the MRKAd5 HIV-1 gag/pol/nef vaccine was highly immunogenic for inducing HIV-specific CD8+ T cells. Our findings suggest that future candidate vaccines have to elicit responses that either exceed in magnitude or differ in breadth or function from those recorded in this trial.

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

Tumour-infiltrating lymphocytes are associated with a survival benefit in several tumour types and with the response to immunotherapy^1-8. However, the reason some tumours have high CD8 T cell infiltration while others do not remains unclear. Here we investigate the requirements for maintaining a CD8 T cell response against human cancer. We find that CD8 T cells within tumours consist of distinct populations of terminally differentiated and stem-like cells. On proliferation, stem-like CD8 T cells give rise to more terminally differentiated, effector-molecule-expressing daughter cells. For many T cells to infiltrate the tumour, it is critical that this effector differentiation process occur. In addition, we show that these stem-like T cells reside in dense antigen-presenting-cell niches within the tumour, and that tumours that fail to form these structures are not extensively infiltrated by T cells. Patients with progressive disease lack these immune niches, suggesting that niche breakdown may be a key mechanism of immune escape.

Dynamic T cell migration program provides resident memory within intestinal epithelium

Migration to intestinal mucosa putatively depends on local activation because gastrointestinal lymphoid tissue induces expression of intestinal homing molecules, whereas skin-draining lymph nodes do not. This paradigm is difficult to reconcile with reports of intestinal T cell responses after alternative routes of immunization. We reconcile this discrepancy by demonstrating that activation within spleen results in intermediate induction of homing potential to the intestinal mucosa. We further demonstrate that memory T cells within small intestine epithelium do not routinely recirculate with memory T cells in other tissues, and we provide evidence that homing is similarly dynamic in humans after subcutaneous live yellow fever vaccine immunization. These data explain why systemic immunization routes induce local cell-mediated immunity within the intestine and indicate that this tissue must be seeded with memory T cell precursors shortly after activation.

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses

Correlates of immune-mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of 40 volunteers followed for up to 1 yr after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity, including complement, the inflammasome, and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (modular immune in vitro construct [MIMIC] system), by the coordinated up-regulation of transcripts for specific transcription factors, including STAT1, IRF7, and ETS2, which are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of master transcription factors that lead to the development of a broad, polyfunctional, and persistent immune response that integrates all effector cells of the immune system.

Case of yellow fever vaccine--associated viscerotropic disease with prolonged viremia, robust adaptive immune responses, and polymorphisms in CCR5 and RANTES genes

BACKGROUND

The live attenuated yellow fever vaccine 17D (YF-17D) is one of the most effective vaccines. Despite its excellent safety record, some cases of viscerotropic adverse events develop, which are sometimes fatal. The mechanisms underlying such events remain a mystery. Here, we present an analysis of the immunologic and genetic factors driving disease in a 64-year-old male who developed viscerotropic symptoms.

METHODS

We obtained clinical, serologic, virologic, immunologic and genetic data on this case patient.

RESULTS

Viral RNA was detected in the blood 33 days after vaccination, in contrast to the expected clearance of virus by day 7 after vaccination in healthy vaccinees. Vaccination induced robust antigen-specific T and B cell responses, which suggested that persistent virus was not due to adaptive immunity of suboptimal magnitude. The genes encoding OAS1, OAS2, TLR3, and DC-SIGN, which mediate antiviral innate immunity, were wild type. However, there were heterozygous genetic polymorphisms in chemokine receptor CCR5, and its ligand RANTES, which influence the migration of effector T cells and CD14+CD16bright monocytes to tissues. Consistent with this, there was a 200-fold increase in the number of CD14+CD16bright monocytes in the blood during viremia and even several months after virus clearance.

CONCLUSION

In this patient, viscerotropic disease was not due to the impaired magnitude of adaptive immunity but instead to anomalies in the innate immune system and a possible disruption of the CCR5-RANTES axis.

Cardiac allograft rejection as a complication of PD-1 checkpoint blockade for cancer immunotherapy: a case report

INTRODUCTION

The increased availability of immunotherapeutic agents for the treatment of a wide array of cancer in the general oncology practice setting will reveal rare and unique toxicities.

MATERIALS AND METHODS

The mechanism of cardiac allograft rejection in the context of PD-1 antibody therapy was explored in a patient with cutaneous squamous cell cancer complicating long-standing cardiac allograft. Immune cell infiltrate in the myocardium and peripheral blood lymphocyte repertoire were assessed using myocardial biopsy and temporal analysis of peripheral blood samples. The efficacy of high-intensity immunosuppression to reverse graft rejection was explored.

RESULTS

Endomyocardial biopsy showed acute moderate diffuse cellular rejection with a predominant population of CD3+, CD8+ and CD4+ infiltrating lymphocytes; peripheral blood circulating lymphocytes showed a high frequency of proliferating and activated CD8+ T cells expressing PD-1 compared to a normal control. There was no difference in the activation and proliferation of CD4+ T cells compared to a normal control. Cardiac function improved following high-intensity immunosuppression and patient survived for up to 7 months after discontinuation of nivolumab.

CONCLUSIONS

Immune checkpoint inhibitors should be avoided in allograft recipients but high-intensity immunosuppression is effective to salvage allograft rejection induced by these agents.

HIV-DNA priming alters T cell responses to HIV-adenovirus vaccine even when responses to DNA are undetectable

Many candidate HIV vaccines are designed to primarily elicit T cell responses. Although repeated immunization with the same vaccine boosts Ab responses, the benefit for T cell responses is ill defined. We compared two immunization regimens that include the same recombinant adenoviral serotype 5 (rAd5) boost. Repeated homologous rAd5 immunization fails to increase T cell responses, but increases gp140 Ab responses 10-fold. DNA prime, as compared with rAd5 prime, directs long-term memory CD8(+) T cells toward a terminally differentiated effector memory phenotype with cytotoxic potential. Based on the kinetics of activated cells measured directly ex vivo, the DNA vaccination primes for both CD4(+) and CD8(+) T cells, despite the lack of detection of the latter until after the boost. These results suggest that heterologous prime-boost combinations have distinct immunological advantages over homologous prime-boosts and suggest that the effect of DNA on subsequent boosting may not be easily detectable directly after the DNA vaccination.

Distinctive TLR7 signaling, type I IFN production, and attenuated innate and adaptive immune responses to yellow fever virus in a primate reservoir host

Why cross-species transmissions of zoonotic viral infections to humans are frequently associated with severe disease when viruses responsible for many zoonotic diseases appear to cause only benign infections in their reservoir hosts is unclear. Sooty mangabeys (SMs), a reservoir host for SIV, do not develop disease following SIV infection, unlike nonnatural HIV-infected human or SIV-infected rhesus macaque (RM) hosts. SIV infections of SMs are characterized by an absence of chronic immune activation, in association with significantly reduced IFN-α production by plasmacytoid dendritic cells (pDCs) following exposure to SIV or other defined TLR7 or TLR9 ligands. In this study, we demonstrate that SM pDCs produce significantly less IFN-α following ex vivo exposure to the live attenuated yellow fever virus 17D strain vaccine, a virus that we show is also recognized by TLR7, than do RM or human pDCs. Furthermore, in contrast to RMs, SMs mount limited activation of innate immune responses and adaptive T cell proliferative responses, along with only transient antiviral Ab responses, following infection with yellow fever vaccine 17D strain. However, SMs do raise significant and durable cellular and humoral immune responses comparable to those seen in RMs when infected with modified vaccinia Ankara, a virus whose immunogenicity does not require TLR7/9 recognition. Hence, differences in the pattern of TLR7 signaling and type I IFN production by pDCs between primate species play an important role in determining their ability to mount and maintain innate and adaptive immune responses to specific viruses, and they may also contribute to determining whether disease follows infection.

Antigen-specific CD4+ T cells recognize epitopes of protective antigen following vaccination with an anthrax vaccine

Detection of antigen-specific CD4+ T cells is facilitated by the use of fluorescently labeled soluble peptide-major histocompatibility complex (MHC) multimers which mirror the antigen specificity of T-cell receptor recognition. We have used soluble peptide-MHC class II tetramers containing peptides from the protective antigen (PA) of Bacillus anthracis to detect circulating T cells in peripheral blood of subjects vaccinated with an anthrax vaccine. PA-specific HLA class II-restricted T lymphocytes were isolated which displayed both TH1- and TH2-like characteristics, indicating heterogeneity of the lymphocyte lineage within the CD4+ response. Presentation of antigen to these T-cell clones by HLA-matched antigen-presenting cells exposed to the intact PA protein confirmed that the identified epitopes are indeed naturally processed by the human immune system. Specific tetramer-derived T-cell profiling may be useful for monitoring helper CD4+ T-cell responses to anthrax vaccination.

Using epigenetics to define vaccine-induced memory T cells

Memory T cells generated from acute infection or vaccination have the potential to provide the host with life-long immunity against re-infection. Protection by memory T cells is achieved through their acquired ability to persist at anatomical sites of the primary infection as well as maintaining a heightened ability to recall effector functions. The maintenance of CD8 and CD4 T cell function in a state of readiness is key to life-long immunity and manifest through changes in transcriptional regulation. Yet, the ability to identify poised transcriptional programs at the maintenance stage of the response is lacking from most transcriptional profiling studies of memory T cells. Epigenetic profiling allows for the assessment of transcriptionally poised (promoters that are readily accessible for transcription) states of antigen-specific T cells without manipulation of the activation state of the cell. Here we review recent studies that have examined epigenetic programs of effector and memory T cell subsets. These reports demonstrate that acquisition of epigenetic programs during memory T cell differentiation to acute and chronic infections is coupled to, and potentially regulate, the cell's recall response. We discuss the usefulness of epigenetic profiling in characterizing T cell differentiation state and function for preclinical evaluation of vaccines and the current methodologies for single locus versus genome-wide epigenetic profiling.

Evidence of hepatitis E virus exposure among seronegative healthy residents of an endemic area

OBJECTIVE

Hepatitis E virus (HEV) infection is endemic in the Indian subcontinent. Detection of serum anti-HEV IgG has traditionally been used to determine prior exposure to this virus. We studied HEV-specific recall immune responses in healthy subjects with and without detectable anti-HEV IgG.

METHODS

Memory B and T cells specific for HEV recombinant proteins pORF2 and pORF3 were estimated among healthy subjects residing in an HEV-endemic region using enzyme-linked immunospot (ELISPOT) assays.

RESULTS

Anti-HEV IgG-negative and anti-HEV IgG-positive healthy subjects had a similar median (range) number of IgG-secreting memory B cells specific for HEV pORF2 [percent of total IgG-producing cells: 0.39 (0-13.63) vs. 0.83 (0-12.78)] and HEV pORF3 [0.33 (0.05-12.35) vs. 1.01 (0.08-9.48)], and of IFN-γ-secreting memory T cells specific for HEV pORF2 [per one million PBMCs: 16 (0-220) vs. 36.5 (0-474)] and HEV pORF3 [166 (0-957) vs. 70.5 (0-533)]. Eight healthy volunteers residing in the USA and studied as controls lacked detectable T cells specific for HEV pORF2.

CONCLUSION

ELISPOT assays may detect evidence of prior HEV infection in persons residing in areas endemic for this infection and lacking detectable anti-HEV IgG. Seroepidemiological studies that use the serum anti-HEV IgG test may underestimate the frequency of exposure to HEV.

Dependence of CD8 T Cell Response upon Antigen Load During Primary Infection : Analysis of Data from Yellow Fever Vaccination

A major question in immunology is what role antigen load plays in determining the size of the CD8 immune response. Is the amount of antigen important during recruitment, proliferation, and/or memory formation? Animal studies have shown that antigen is only strictly required early during activation of T cells, but the importance of antigen at later timepoints is unclear. Using data from 24 volunteers infected with the yellow fever vaccine virus (YFV), we analyzed the dependence of T cell proliferation upon viral load. We found that volunteers with high viral load initially have greater T cell responses, but by 28 days post-vaccination those with lower viral load are able to 'catch-up.' Using differential equation modeling we show that this pattern is consistent with viral load only affecting recruitment (i.e., programmed proliferation) as opposed to affecting recruitment and proliferation (i.e., antigen-dependent proliferation). A quantitative understanding of the dependence of T cell dynamics on antigen load will be of use to modelers studying not only vaccination, but also cancer immunology and autoimmune disorders.

What Controls the Acute Viral Infection Following Yellow Fever Vaccination?

Does target cell depletion, innate immunity, or adaptive immunity play the dominant role in controlling primary acute viral infections? Why do some individuals have higher peak virus titers than others? Answering these questions is a basic problem in immunology and can be particularly difficult in humans due to limited data, heterogeneity in responses in different individuals, and limited ability for experimental manipulation. We address these questions for infections following vaccination with the live attenuated yellow fever virus (YFV-17D) by analyzing viral load data from 80 volunteers. Using a mixed effects modeling approach, we find that target cell depletion models do not fit the data as well as innate or adaptive immunity models. Examination of the fits of the innate and adaptive immunity models to the data allows us to select a minimal model that gives improved fits by widely used model selection criteria (AICc and BIC) and explains why it is hard to distinguish between the innate and adaptive immunity models. We then ask why some individuals have over 1000-fold higher virus titers than others and find that most of the variation arises from differences in the initial/maximum growth rate of the virus in different individuals.

Abstract 1317: Biomarker evaluation for PD-1 targeted therapies in non-small cell lung cancer (NSCLC) patients

Sustained expression of programmed cell death (PD)-1 inhibitory receptor is a hallmark of exhausted T cells during chronic infections and cancer. PD-1 signaling inhibits T cell activation, and maintains T cells in a dysfunctional state. Notably, inhibition of PD-1 interactions with PD-L1 is able to restore function in exhausted T cells. Several clinical trials have now shown that PD-1 blockade therapy results in durable clinical benefits in advanced stage cancer patients refractory to other treatments, and efficacy has been reported in multiple tumor types. Nonetheless many patients do not respond to PD-1 targeted therapies, hence a better understanding of the immunological responses induced by PD-1 pathway blockade and identification of predictive biomarkers is imperative. In this ongoing study we have analyzed peripheral blood mononuclear cells (PBMC) from advanced stage NSCLC patients, before and during the course of PD-1 pathway blockade therapy. We find that CD8 T cell activation is observed in some patients following therapy, but it is not consistently associated with clinical response. Interestingly, treatment-induced CD8 T cell proliferation is not sustained in some patients even with continuation of therapy. After PD-1 pathway blockade, we find co-expression of CTLA-4 on proliferating PD-1+ CD8 T cells in the blood. Accordingly, we found that tumor infiltrating CD8 T cells expressing high levels of PD-1 also co-express CTLA-4 (and Tim-3) in surgical specimens of patients with NSCLC. We will present additional data on CD8 and CD4 T cells in NSCLC patients enrolled in PD-1 targeted therapies clinical trials and discuss potential biomarkers. We conclude that peripheral blood analysis can provide valuable insights into anti-cancer effects of PD-1 targeted therapy.

Citation Format: Alice O. Kamphorst, Rathi N. Pillai, Shu Yang, Rama Akondy, Lydia Koenig, Ke Yu, Megan McCausland, Gabriel Sica, Fadlo R. Khuri, Taofeek K. Owonikoko, Suresh S. Ramalingam, Rafi Ahmed. Biomarker evaluation for PD-1 targeted therapies in non-small cell lung cancer (NSCLC) patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1317. doi:10.1158/1538-7445.AM2015-1317

Characterization of long-lived human memory CD8 T cells specific to yellow fever virus (LYM5P.707)

The live yellow fever virus vaccine (YFV-17D) is a safe and effective vaccine that confers long-lasting protection after a single immunization. This vaccine results in the generation of virus memory T and B cells that persist for many years. We have used this vaccine to study the generation and maintenance of human memory CD8 T cells following an acute viral infection. Earlier studies using tetramers targeting an HLA-A2 restricted epitope have shown that YFV-specific CD8 T cells have polyfunctionality and recall potential - two hallmarks associated with effective T cell immunity. To better characterize these long-lived memory CD8 T cells we analyzed the peripheral blood mononuclear cells from HLA-A2+ individuals who had received a single dose of the vaccine 8 to 15 years previously. We will present data on the phenotype, function and epigenetic fingerprint of the YFV-specific memory CD8 T cells. Interestingly, these long-lived memory CD8 T cells had an epigenetic fingerprint that was consistent with their having passed through an effector stage during their differentiation.

Aberrant DNA demethylation of PD-1 during chronic viral infection (136.16)

Chronic infection results in CD8 T cell exhaustion characterized by reduced cytokine expression, cell proliferation and an inability to clear the source of antigen. Central to the development of exhausted CD8 T cells is the retained upregulation of the inhibitory receptor programmed death (PD)-1. It is now known that PD-1 upregulation in exhausted CD8 T cells is coincident with the progression of many chronic human diseases including human immunodeficiency virus (HIV), hepatitis C virus, (HCV), and Epstein Barr virus (EBV). To date, relatively little is known regarding PD-1 regulation. Using Lymphocytic Choriomeningitis virus (LCMV) infection to study anti-viral CD8 T cells in mice, we observe that DNA methylation of the PD-1 promoter is present in naïve (PD-1lo) and memory (PD-1lo) CD8 T cells, while effector cells (PD-1hi) are partially demethylated. Consistent with these observations, exhausted CD8 T cells from chronically infected mice have near complete demethylation of the PD-1 promoter. Resolution of the persistent LCMV infection results in a moderate reduction of PD-1 expression and a lack of promoter methylation. These findings provide insight into antigen induced expression of PD-1 associated with many human diseases. Moreover prolonged signals for demethylation in the antigen specific cells may result in heritable transcriptional dysregulation accounting for the deviant gene profile of functionally exhausted CD8 T cells.

Early proliferation of PD-1+ CD8 T cells in peripheral blood as predictive of response to PD-1 inhibition for patients with advanced NSCLC

e20648

Background: Anti PD-1 and PDL-1 antibodies are now established immune targeted therapies for a subset of patients with advanced non-small cell lung cancer (NSCLC). There is a need for predictive biomarkers to better guide patient selection. We profiled peripheral blood samples from patients receiving PD-1 pathway targeted antibodies for lymphocyte subsets and correlated temporal changes with clinical response. Methods: NSCLC patients treated at our institution with PD-1 or PDL-1 inhibitors (nivolumab, pembrolizumab, and atezolizumab) consented to an IRB-approved biomarker profiling protocol. We collected baseline peripheral blood samples before first treatment and subsequently prior to each new treatment cycle until progression of disease or for a maximum of six cycles. Peripheral blood mononuclear cells (PBMCs) were isolated and analyzed by flow cytometry for kinetics of proliferation of PD1+CD8+ T cells. Clinical response to anti PD-1 therapy was classified according to Response Evaluation Criteria in Solid Tumors (RECIST1.1) criteria and correlated with T cell proliferation kinetics. Results: We enrolled 27 patients with baseline characteristics: median age 66, male 70%, smokers 85%, adenocarcinoma 70%; 10 (37%) patients achieved partial response (PR), 7 (26%) had stable disease (SD) and 10 (10%) had disease progression (PD) as best response. There was a > 1.5-fold increase in Ki67+CD8+ T cells expressing PD-1 within 4 weeks of treatment initiation in 80% of patients with PR compared with 30% in patients with SD and 30% in those with PD. Conclusions: Early proliferation of PD1+CD8+ T cells in peripheral blood is a potential pharmacodynamic biomarker of anti PD-1 immunotherapy that could serve as a tool to identify the NSCLC patient subset most likely to respond to PD-1 and PDL-1 inhibitors.

Viral infection duration mediates locus specific de novo DNA methylation in antigen-specific CD8 T cells (154.41)

Progressive loss of antiviral functions in antigen-specific CD8 T cell during chronic infection is caused by continuous upregulation and signaling by immunoinhibitory receptors including Programmed Death 1(PD-1). Using human and murine model systems of acute and chronic viral infections, we found that differentiation of naïve CD8 T cells into effector cells during acute infection was accompanied by a transient loss of DNA methylation of the PD-1 locus. Viral clearance and the subsequent effector to memory differentiation resulted in memory-specific DNA remethylation of the PD-1 locus. Conversely, chronic infection induced complete and sustained DNA demethylation of the PD-1 regulatory region in exhausted CD8 T cells. Surprisingly, reduction of virus levels and PD-1 expression in chronically infected animals did not result in remethylation and coincided with decreased expression of a specific de novo methyltransferase (Dnmt3a) isoform. The unmethylated PD-1 locus allowed for rapid PD-1 re-expression, potentially prematurely terminating antiviral functions. These studies provide a foundation for efforts towards reprogramming of PD-1 expression to rejuvenate exhausted T cells.

Understanding heterogeneous CTL responses to the yellow fever vaccine using mathematical models

In an acute infection, such as those caused by attenuated vaccines, we should expect the immune response to depend in some manner upon the precursor frequency as well as the magnitude of the viral load within the patient. However, we do not have a quantitative understanding of this process. In a recent study, 80 patients received the yellow fever vaccine and their viral titer and T-cell responses were tracked for several days. It was found that there were substantial differences between individuals in peak viral load, but that the difference in CTL response was relatively small. Moreover, although the CTL response was positively correlated with viral load, the response saturated for high viral loads. Using mathematical models, we investigated which rules of T-cell proliferation could give rise to this pattern. We considered three models: antigen-dependent proliferation in which the T-cells must receive continuous antigen stimulation to continue to divide, programmed proliferation in which T-cells commit to a fixed number of division upon recruitment and a hybrid model in which T-cells commit to a variable number of division based on viral load. We find that this latter model is the most plausible description of the data. We also considered whether negative feedback in the form of T-cell competition may play a role in determining CTL response, however we found no evidence for any such mechanism.