Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set

CD8 T cells provide immunity to virus infection through recognition of epitopes presented by peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely recognized T cell epitopes from common viruses, we combined analysis of TCR down-regulation upon stimulation with epitope-specific enumeration based on barcode-labeled pMHC multimers. We assess CD8 T cell binding and reactivity for 929 previously reported epitopes in the context of 1 of 25 HLA alleles representing 29 viruses. The prevalence and magnitude of CD8 T cell responses were evaluated in 48 donors and reported along with 137 frequently recognized virus epitopes, many of which were underrepresented in the public domain. Eighty-four percent of epitope-specific CD8 T cell populations demonstrated reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, nonreactive T cell populations were associated primarily with naive phenotypes. Our analysis provides a reference map of epitopes for characterizing CD8 T cell responses toward common human virus infections.

IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition

Background

Mutation-derived neoantigens are critical targets for tumor rejection in cancer immunotherapy, and better tools for neoepitope identification and prediction are needed to improve neoepitope targeting strategies. Computational tools have enabled the identification of patient-specific neoantigen candidates from sequencing data, but limited data availability has hindered their capacity to predict which of the many neoepitopes will most likely give rise to T cell recognition.

Method

To address this, we make use of experimentally validated T cell recognition towards 17,500 neoepitope candidates, with 467 being T cell recognized, across 70 cancer patients undergoing immunotherapy.

Results

We evaluated 27 neoepitope characteristics, and created a random forest model, IMPROVE, to predict neoepitope immunogenicity. The presence of hydrophobic and aromatic residues in the peptide binding core were the most important features for predicting neoepitope immunogenicity.

Conclusion

Overall, IMPROVE was found to significantly advance the identification of neoepitopes compared to other current methods.

T antigen-specific CD8+ T cells associate with PD-1 blockade response in virus-positive Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a highly immunogenic skin cancer primarily induced by Merkel cell polyomavirus, which is driven by the expression of the oncogenic T antigens (T-Ags). Blockade of the programmed cell death protein-1 (PD-1) pathway has shown remarkable response rates, but evidence for therapy-associated T-Ag-specific immune response and therapeutic strategies for the nonresponding fraction are both limited. We tracked T-Ag-reactive CD8+ T cells in peripheral blood of 26 MCC patients under anti-PD1 therapy, using DNA-barcoded pMHC multimers, displaying all peptides from the predicted HLA ligandome of the oncoproteins, covering 33 class I haplotypes. We observed a broad T cell recognition of T-Ags, including identification of 20 T-Ag-derived epitopes we believe to be novel. Broadening of the T-Ag recognition profile and increased T cell frequencies during therapy were strongly associated with clinical response and prolonged progression-free survival. T-Ag-specific T cells could be further boosted and expanded directly from peripheral blood using artificial antigen-presenting scaffolds, even in patients with no detectable T-Ag-specific T cells. These T cells provided strong tumor-rejection capacity while retaining a favorable phenotype for adoptive cell transfer. These findings demonstrate that T-Ag-specific T cells are associated with the clinical outcome to PD-1 blockade and that Ag-presenting scaffolds can be used to boost such responses.

TCR-engaging scaffolds selectively expand antigen-specific T-cells with a favorable phenotype for adoptive cell therapy

BACKGROUND

Adoptive cell therapy (ACT) has shown promising results for the treatment of cancer and viral infections. Successful ACT relies on ex vivo expansion of large numbers of desired T-cells with strong cytotoxic capacity and in vivo persistence, which constitutes the greatest challenge to current ACT strategies. Here, in this study, we present a novel technology for ex vivo expansion of antigen-specific T-cells; artificial antigen-presenting scaffolds (Ag-scaffolds) consisting of a dextran-polysaccharide backbone, decorated with combinations of peptide-Major Histocompatibility Complex (pMHC), cytokines and co-stimulatory molecules, enabling coordinated stimulation of antigen-specific T-cells.

METHODS

The capacity of Ag-scaffolds to expand antigen-specific T-cells was explored in ex vivo cultures with peripheral blood mononuclear cells from healthy donors and patients with metastatic melanoma. The resulting T-cell products were assessed for phenotypic and functional characteristics.

RESULTS

We identified an optimal Ag-scaffold for expansion of T-cells for ACT, carrying pMHC and interleukin-2 (IL-2) and IL-21, with which we efficiently expanded both virus-specific and tumor-specific CD8+ T cells from peripheral blood of healthy donors and patients, respectively. The resulting T-cell products were characterized by a high frequency of antigen-specific cells with high self-renewal capacity, low exhaustion, a multifunctional cytokine profile upon antigen-challenge and superior tumor killing capacity. This demonstrates that the coordinated stimuli provided by an optimized stoichiometry of TCR engaging (pMHC) and stimulatory (cytokine) moieties is essential to obtain desired T-cell characteristics. To generate an 'off-the-shelf' multitargeting Ag-scaffold product of relevance to patients with metastatic melanoma, we identified the 30 most frequently recognized shared HLA-A0201-restricted melanoma epitopes in a cohort of 87 patients. By combining these in an Ag-scaffold product, we were able to expand tumor-specific T-cells from 60-70% of patients with melanoma, yielding a multitargeted T-cell product with up to 25% specific and phenotypically and functionally improved T cells.

CONCLUSIONS

Taken together, the Ag-scaffold represents a promising new technology for selective expansion of antigen-specific CD8+ T cells directly from blood, yielding a highly specific and functionally enhanced T-cell product for ACT.

Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations

Mutation-derived neoantigens are important targets for T cell-mediated reactivity toward tumors and, due to their unique tumor expression, an attractive target for immunotherapy. Neoepitope-specific T cells have been detected across a number of solid cancers with high mutational burden tumors, but neoepitopes have been mostly selected from single nucleotide variations (SNVs), and little focus has been given to neoepitopes derived from in-frame and frameshift indels, which might be equally important and potentially highly immunogenic. Clear cell renal cell carcinomas (ccRCCs) are medium-range mutational burden tumors with a high pan-cancer proportion of frameshift mutations. In this study, the mutational landscape of tumors from six RCC patients was analyzed by whole-exome sequencing (WES) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs), and tumor-infiltrating lymphocytes (TILs, germline reference). Neopeptides were predicted using MuPeXI, and patient-specific peptide–MHC (pMHC) libraries were created for all neopeptides with a rank score < 2 for binding to the patient's HLAs. T cell recognition toward neoepitopes in TILs was evaluated using the high-throughput technology of DNA barcode-labeled pMHC multimers. The patient-specific libraries consisted of, on average, 258 putative neopeptides (range, 103–397, n = 6). In four patients, WES was performed on two different sources (TF and TCL), whereas in two patients, WES was performed only on TF. Most of the peptides were predicted from both sources. However, a fraction was predicted from one source only. Among the total predicted neopeptides, 16% were derived from frameshift indels. T cell recognition of 52 neoepitopes was detected across all patients (range, 4–18, n = 6) and spanning two to five HLA restrictions per patient. On average, 21% of the recognized neoepitopes were derived from frameshift indels (range, 0–43%, n = 6). Thus, frameshift indels are equally represented in the pool of immunogenic neoepitopes as SNV-derived neoepitopes. This suggests the importance of a broad neopeptide prediction strategy covering multiple sources of tumor material, and including different genetic alterations. This study, for the first time, describes the T cell recognition of frameshift-derived neoepitopes in RCC and determines their immunogenic profile.

Abstract B092: Tumor infiltrating T-cells from renal cell carcinoma patients recognize neoantigens derived from point and frameshift mutations

Mutation-derived neoantigens are important targets of T-cell mediated reactivity towards tumors. Their unique tumor-restriction poses an advantage compared to shared tumor antigens in that they are in principle both foreign and tumor specific, hence presumably less impacted by T-cell tolerance and for therapeutic applications less prone to mediate immune-related destruction of noncancerous tissue. Moreover, the mutational burden and predicted number of neoantigens correlate to favorable clinical outcome and benefit from immune checkpoint therapy. Neoantigen-reactive T-cells have been detected across a number of solid cancers, ranging from immunogenic tumors such as melanoma and non-small cell lung cancer to less immunogenic tumors such as breast cancer. Renal cell carcinomas (RCCs) are among medium-range mutational burden tumors and present with the highest pan-cancer number and proportion of frameshift mutations, a mutation type considered to be highly immunogenic. However, to our knowledge, yet no reports have described neoantigen-specific T-cells in this malignancy. In this study, the mutational landscape and HLA (human leukocyte antigen) profile of tumors from six renal cell carcinoma patients were analyzed by whole-exome sequencing (WXS) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs) and tumor-infiltrating lymphocytes (TILs, germline reference). Hereafter the online MuPeXi tool was used to predict binding of mutated peptide sequences of 9-11mer length to the HLAs of each patient, using a rank score &lt; 2 for selection of peptide binding, hereby creating patient-specific libraries of putative neo-peptides. TILs extracted from the patients tumors were screened for T-cell recognition of the peptide libraries by use of a novel high-throughput platform based on DNA barcode labeled peptide-MHC multimers, and responses were verified by conventional fluorochrome labeled MHC multimers. In four of six patients WXS was performed on both TF and TCL, in two of six patients only on TF. The average mutational burden of the six patients was 271 for TF (range 146–381, n=6) and 289 for TCL (range 182-404, n=4). Prediction of HLA-restricted peptides within the mutated sequences resulted in patient specific libraries of average 269 peptides for TF and TCL combined (range 126-443, n=6). Half of the peptides were predicted from both sources (52%, range 28-74%, n=4) compared to 20% (range 8-31%, n=4) predicted solely from TF and 29% (range 18-41%, n=4) predicted solely from TCL. The proportion of predicted peptides derived from frameshift mutations out of total mutations was 16% (range 7-24%, n=6). A total of 67 neoantigen-specific T-cell responses were detected across all patients by use of a novel high-throughput DNA barcode screening platform, with the number of detected responses ranging from 4-30 and spanning 3-5 HLA restrictions per patient. Of note, we detected a number of T-cell responses towards HLA-C restricted peptides, which have previously been poorly described. For several patients, the number of HLA-C restricted T-cell responses observed was substantially higher than for both HLA-A and -B, highlighting the importance of including this HLA type for neoepitope analyses. In the four patients in whom peptides were predicted from both TF and TCL, the distribution of responses was 37% on TF (range 14-60%, n=4), 36% on TCL (range 29-43%, n=4) and 27% (range 0-43%) on TF+TCL combined. The proportion of responses towards frameshift mutations was 17% (range 0-24%, n=6) of total responses. The identification of neoantigen-specific T-cells within tumors from RCC patients is an important step towards the use of neoantigens as therapeutic targets and predictors of response to immunotherapy in this cancer subtype. Moreover, our study points toward the importance of broad peptide prediction platforms covering multiple sources for WXS and mutational analyses covering both point and frameshift mutations.

Citation Format: Sofie Ramskov, Ulla Kring Hansen, Anne-Mette Bjerregaard, Amalie Kai Bentzen, Marco Donia, Rikke Andersen, Zoltan Szallasi, Inge Marie Stentoft Svane, Aron Charles Eklund, Sine Reker Hadrup. Tumor infiltrating T-cells from renal cell carcinoma patients recognize neoantigens derived from point and frameshift mutations [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B092.

Abstract B020: T-cell recognition of large T and small T antigen in Merkel cell polyomavirus-associated cancer

Merkel cell carcinoma (MCC) is an aggressive human skin cancer mainly induced by Merkel cell polyomavirus (MCPyV). While the virus is common in humans, the unlikely event of oncogenic transformation occurs only rarely, and development of MCC is furthermore primarily seen in immunosuppressed and elderly. Indicating, that despite oncogenic potential further lack of immunosurveillance is necessary for cancer development. Two mutation events, often inflicted by UV light, allow the clonal integration of the viral genome into the host genome and the translation of the two viral oncogenes large T (LTA) and small T antigen (STA). The importance of immune recognition for clearing disease was segmented by the encouraging results using anti-PD1 for treatment of metastatic MCC. Recently, the first PD-1 checkpoint inhibitor (avelumab) became FDA approved. To further understand the mechanism of action, and to direct T-cell responsiveness specifically to MCC, there is a great interest to identify T-cell epitopes in MCPyV. To date, several T-cell epitopes derived the MCPyV-derived proteins LTA, STA and viral capsid protein1 (VP1) have been described. However, only restricted to a limited number of HLA types (HLA-A01, -A02, -A03, -A11, -A24 and B07). Here we aim to expand the knowledge about T-cell epitopes by including a broader range of HLA restrictions (HLA-B08, -B35 and -B44). Potential T-cell epitopes were selected by in-silico prediction. Given a total of 148 peptides across the nine MHC class I. Peripheral blood mononuclear cells (PBMC) from 49 patients were analyzed using a platform consisting of a magnetic-based enrichment of MHC multimer binding cells, which allowed detection of low frequency T-cell clones after 2-3 weeks of culturing. Followed by detection of T-cell reactivity against the MCPyV-derived epitopes using combinatorial color encoding of MHC multimer. Using this strategy, we identified 60 MCPyV-directed T-cell responses against 34 different peptides in PBMC from 31 of the patients. Furthermore, three patients’ tumor-infiltrating lymphocytes (TIL) were analyzed directly ex vivo for detection of T-cell reactivity against the MCPyV-derived peptides. We identified four MCPyV-directed T-cell responses against four different peptides. Importantly, epitope targets embedded in the LTA and STA proteins were solely observed in the patient samples while T-cell recognition of the capsid protein VP1 was observed in both patients and healthy donors. For selected LTA/STA-derived epitopes processing and presentation were demonstrated in MCC tumor cell lines, as well as the functional capacity of LTA/STA responsive CD8 T-cells. The identification of novel LTA/STA-derived epitopes will facilitate the use of targeted T-cell therapy to enhanced MCC recognition and clearance in combination with checkpoint inhibition. Such strategies should be tailored according to the patient’s HLA type, and hence expanding the epitope repertoire with additional HLA restrictions would benefit a larger cohort of MCC patients.

Citation Format: Ulla Kring Hansen, Rikke Lyngaa, Per Thor Straten, Jürgen C. Becker, Candice D Church, Paul Nghiem, Sine Reker Hadrup. T-cell recognition of large T and small T antigen in Merkel cell polyomavirus-associated cancer [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B020.

Epidemiology, biology and therapy of Merkel cell carcinoma: conclusions from the EU project IMMOMEC

Merkel cell carcinoma (MCC) is a highly aggressive, often lethal neuroendocrine cancer. Its carcinogenesis may be either caused by the clonal integration of the Merkel cell polyomavirus into the host genome or by UV-induced mutations. Notably, virally-encoded oncoproteins and UV-induced mutations affect comparable signaling pathways such as RB restriction of cell cycle progression or p53 inactivation. Despite its low incidence, MCC recently received much attention based on its exquisite immunogenicity and the resulting major success of immune modulating therapies. Here, we summarize current knowledge on epidemiology, biology and therapy of MCC as conclusion of the project 'Immune Modulating strategies for treatment of Merkel Cell Carcinoma', which was funded over a 5-year period by the European Commission to investigate innovative immunotherapies for MCC.