Empty-loadable MHC class I tetramers for efficient detection of antigen-specific T cells

The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use for peptide-MHC multimer-based approaches to comprehensively analyze T cell immunity. We demonstrate here the generation, analysis, and use of empty-loadable (peptide-free) MHC class I tetramers made from disulfide-stabilized MHC molecules.

A disulfide bond links the α1 and α2 helices of MHC class I molecule at the extreme end of the F pocket. It allows in vitro folding of recombinant A2 with a dipeptide and subsequent removal of the dipeptide to yield stable peptide-receptive MHC monomers. Empty-loadable tetramers prepared using disulfide-stabilized MHC monomers can be loaded with peptides within minutes. These tetramers efficiently detects antigen-specific T cells. Furthermore, peptide-MHC tetramers prepared using disulfide-stabilized MHC molecules provide a better staining index for antigen-specific T cell detection compared to multimers prepared with wild-type MHC class I molecules. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition, for the identification of T cells specific to several neo- and cancer-associated antigens in melanoma. Disulfide stabilization has been achieved with several MHC class I allotypes-HLA-A* 02:01, HLA-A*01:01, HLA-A*03:01, HLA-A*11:01, HLA-A*24:02, HLA-B*07:02, and H-2Kb.

The T cell differentiation landscape is shaped by tumour mutations in lung cancer

Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.

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.

T cell recognition of novel shared breast cancer antigens is frequently observed in peripheral blood of breast cancer patients

Advances within cancer immunotherapy have fueled a paradigm shift in cancer treatment, resulting in increasing numbers of cancer types benefitting from novel treatment options. Despite originally being considered an immunologically silent malignancy, recent studies encourage the research of breast cancer immunogenicity to evaluate immunotherapy as a treatment strategy. However, the epitope landscape in breast cancer is minimally described, limiting the options for antigen-specific, targeted strategies. Aromatase, never in mitosis A-related kinase 3 (NEK3), protein inhibitor of activated STAT3 (PIAS3), and prolactin are known as upregulated proteins in breast cancer. In the present study, these four proteins are identified as novel T cell targets in breast cancer. From the four proteins, 147 peptides were determined to bind HLA-A*0201 and -B*0702 using a combined in silico/in vitro affinity screening. T cell recognition of all 147 peptide-HLA-A*0201/-B*0702 combinations was assessed through the use of a novel high-throughput method utilizing DNA barcode labeled multimers. T cell recognition of sequences within all four proteins was demonstrated in peripheral blood of patients, and significantly more T cell responses were detected in patients compared to healthy donors for both HLA-A*0201 and -B*0702. Notably, several of the identified responses were directed toward peptides, with a predicted low or intermediate binding affinity. This demonstrates the importance of including low-affinity binders in the search for epitopes within shared tumor associated antigens (TAAs), as these might be less subject to immune tolerance mechanisms. The study presents four novel TAAs containing multiple possible targets for immunotherapy of breast cancer.

Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells

The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use in peptide-MHC multimer–based approaches to comprehensively analyze T cell immunity. To overcome this challenge, we demonstrate the use of functionally empty MHC class I molecules stabilized by a disulfide bond to link the α1and α2helices close to the F pocket. Peptide-loaded disulfide-stabilized HLA-A*02:01 shows complete structural overlap with wild-type HLA-A*02:01. Peptide-MHC multimers prepared using disulfide-stabilized HLA-A*02:01, HLA-A*24:02, and H-2Kbcan be used to identify antigen-specific T cells, and they provide a better staining index for antigen-specific T cell detection compared with multimers prepared with wild-type MHC class I molecules. Disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without affecting their capacity to stain T cells. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition through their use to identify T cells specific for mutation-derived neoantigens and other cancer-associated antigens in human melanoma.

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 B049: Empty MHC class I molecules for improved detection of antigen-specific T-cells

Major histocompatibility complex (MHC) class I multimers have been widely used to identify antigen specific T-cells for immune monitoring, epitope discovery, and T-cell isolation. A bottleneck to many peptide-MHC driven applications for T-cell interrogation is the peptide ligand dependent stability of the MHC class I proteins, which thus compels high-affinity peptide dependent in-vitro folding of each MHC protein and the use of a peptide-exchange technology to investigate antigens of interest. To overcome this challenge, we demonstrate the use of empty peptide-receptive MHC class I molecule for detection of antigen specific T-cells. This strategy is based on an HLA-A*02:01 variant which is stabilized by a disulfide bond to link the alpha-1 and alpha-2 helices close to the F pocket. Determined by the crystal structure, peptide-loaded disulfide-stabilized HLA-A*02:01 show complete structural overlap to wild-type HLA-A*02:01. Following peptide loading, we used such disulfide-stabilized HLA-A*02:01 molecules to form fluorescence labeled tetramers and applied them for detections of T-cell responses against common viruses in healthy donor peripheral blood mononuclear cells. In all tested samples, disulfide-stabilized HLA-A*02:01 tetramers detected T-cell with same specificity as wild-type MHC tetramers and they consistently provide a better staining index for antigen-specific T-cell detection. Importantly, disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without impacting the T-cell staining capacity. We demonstrate the value of empty loadable tetramers, converted to antigen-specific tetramers by a single-step peptide addition, for identification of T-cells specific to several neo- and cancer-associated antigens among tumor-infiltrating lymphocytes in melanoma.To evaluate if the disulfide linkage has an impact on TCR recognition of peptide-MHC complexes, we determined and compared TCR fingerprints of T-cell clones specific to a given peptide-MHC complex using both the wild-type and the disulfide-stabilized HLA-A*02:01 multimers. No differences were observed in the TCR interaction profile between the disulfide optimized and the wild-type MHC class I. In conclusion, disulfide-stabilized empty HLA class I proteins are a potentially powerful tool for interrogating T-cell recognition—offering a fast and flexible transformation from an empty peptide receptive state to a set of personalized reagents generated to match individual tumor characteristics for T-cell monitoring or selection.

Citation Format: Tripti Tamhane, Sunil Kumar Saini, Raghavendra Anjanappa, Ankur Saikia, Sofie Ramskov, Marco Donia, Inge Marie Stenfoft Svane, Søren Nyboe Jakobsen, Maria Garcia-Alai, Martin Zacharias, Rob Meijers, Sebastian Springer, Sine Reker Hadrup. Empty MHC class I molecules for improved detection of antigen-specific T-cells [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 B049.

Abstract B036: T-cell recognition of breast cancer antigens

Breast cancer remains the leading cause of cancer death among women worldwide, rendering conventional therapies insufficient despite decades of research. Despite originally considered an immunologically silent malignancy, recent studies have shown encouraging results, from treatment of breast cancer with checkpoint inhibition to enhance the immunogenicity and tumor cell killing mediated by immune cells. The epitope landscape in breast cancer is minimally described; thus it is necessary to identify T-cell targets to develop cancer-specific immune-mediated therapies. This project investigates four proteins commonly upregulated in breast cancer and thus probable tumor-associated antigens (TAAs), namely, aromatase, prolactin, never in mitosis a related kinase 3 (NEK3), and protein inhibitor of activated STAT3 (PIAS3). Each contributes to increase growth, survival, and motility of malignant cells. To uncover novel epitopes for cytotoxic T-cells, a reverse immunology approach is applied. In silico screening via NetMHC was used to predict peptides within the full length of each of the four proteins that bind to HLA-A*0201 and HLA-B*0702. Via in silico screening 415 HLA-A*0201 or HLA-B*0702 binding peptides were predicted An MHC ELISA was applied to experimentally confirm which of the peptides are true HLA-A*0201 and HLA-B*0702 binders, reducing the library from 415 to 147. The 147 peptides were evaluated for T-cell recognition utilizing DNA barcode labeled MHC multimers to screen peripheral blood lymphocytes from 24 breast cancer patients and 18 healthy donor samples. Significantly more TAA specific T-cell responses were detected in breast cancer patients than healthy donors for both HLA-A*0201 (p=0.0039) and HLA-B*0702 (p&lt;0.001) restricted peptides. Thus, the inspected proteins aromatase, prolactin, NEK3 and PIAS3 indeed contain targets for T-cell reactivity. Importantly, several of the responses were identified towards peptides with a predicted intermediate HLA-binding affinity. This emphasizes the importance of including such weaker affinity ligands in the search for epitopes within shared TAAs.

Citation Format: Nadia Viborg Petersen, Sofie Ramskov, Rikke Sick Andersen, Özcan Met, Per thor Straten, Amalie Kai Kai Bentzen, Sine Reker Hadrup. T-cell recognition of breast cancer antigens [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 B036.

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes

Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy-induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens.