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Immunogenicity; Proteogenomics Inmunogenicidad; Proteogenómica Immunogenicitat; Proteogenòmica Purpose: Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from noncanonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. Experimental Design: Peptides presented on HLA-I were identified in 9 patient-derived tumor cell lines from melanoma, gynecologic, and head and neck cancer through proteogenomics. A total of 507 candidate tumor antigens, including nonC-TL, neoantigens, cancer-germline, or melanocyte differentiation antigens, were tested for T-cell recognition of preexisting responses in patients with cancer. Donor peripheral blood lymphocytes (PBL) were in vitro sensitized against 170 selected nonC-TL to isolate antigen-specific T-cell receptors (TCR) and evaluate their therapeutic potential. Results: We found no recognition of the 507 nonC-TL tested by autologous ex vivo expanded tumor-reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However, in vitro sensitization of donor PBL against 170 selected nonC-TL, led to the identification of TCRs specific to three nonC-TL, two of which mapped to the 5′ UTR regions of HOXC13 and ZKSCAN1, and one mapping to a noncoding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. Conclusions: Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies. We thank the patients for their participation in this study, Steven A. Rosenberg for providing valuable reagents and support for NGS studies, R. Pujol for helpful scientific discussion, J. Gonzalez for bioinformatics support, CRG/UPF Flow Cytometry Unit for assistance with cell sorting, and CRG/UPF and IRB Proteomics Units for technical support. A. Gros and this work were funded by the Comprehensive Program of Cancer Immunotherapy & Immunology II (CAIMI-II) supported by the BBVA Foundation (53/2021), Institute Carlos III (MS15/00058 and PI17/01085), AECC (IDEAS197PORT), and La Fundació La Marató de TV3 (201919–30). We thank CERCA Programme / Generalitat de Catalunya for institutional support. M. Lozano-Rabella was supported by the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) (2018FI_B 00946). A. Garcia-Garijo was supported by Generalitat PERIS award (SLT017/20/000131). A. Yuste-Estevanez was supported by the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) (2021 FI_B 00365). J. Palomero was supported by the Beatriu de Pinós programme (BP 2018), cofounded by the Agency for Management of University and Research Grants (AGAUR) and European Union's Horizon 2020.

Includes a large list of all the peptides and details of the HLA-I ligands identified at =30 ALC score

Supplementary Figure 1. Validation of HLA-I ligand tumor antigen candidates with synthetic peptides Supplementary Figure 2. Validation of selected HLA-I ligand tumor antigen candidates identified in Mel-1 and Mel-3 with isotope-labeled peptides Supplementary Figure 3. Frequency of nonC peptides detected in HLA-I. Supplementary Fig. 4. HLA-I allele binding motif of all patients included in the study. Supplementary Figure 5. A fraction of nonC-TL can be detected in publicly available immunopeptidomics datasets from human tumor biopsies Supplementary Figure 6. Evaluation of pre-existing T-cell responses to candidate tumor antigens in cancer patients Supplementary Figure 7. Enrichment of antigen-specific T cells from cancer patients by flow cytometry-based sorting. Supplementary Figure 8. Deconvolution of peptide pools containing recognized CGA or melanoma-associated antigens. Supplementary Figure 9. Functional avidity and specificity of neoantigen-specific T cells isolated from cancer patients. Supplementary Figure 10. HLA restriction element and recognition of autologous tumor cell lines by antigen-specific T cells isolated from cancer patients. SupplementaryFigure 11. Genomic location of the three immunogenic nonC-TL identified through IVS. Supplementary Figure 12. Recognition of the predicted ORFs encoding the immunogenic nonC-TL by TCR transduced cells. Supplementary Figure 13. Loss of recognition of TCL transfected with Cas9-sgRNA targeting the predicted 5’U-HOXC13 ORF. Supplementary Figure 14. Assessment of expression and translation of the immunogenic nonC-TL in human healthy cells. Supplementary Figure 15. NonC-TL are the main source of candidate tumor antigens identified by proteogenomics but tumor-reactive T cells preferentially recognize neoantigens derived from NSM.

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BackgroundDespite the growing interest in immunotherapeutic interventions for endometrial cancer (EC), the prevalence, phenotype, specificity and prognostic value of tumor infiltrating lymphocytes (TILs) in this tumor type remains unclear.MethodsTo better understand the role of TILs in EC, we analyzed the phenotypic traits of CD8+and CD4+EC-resident T cells from 47 primary tumors by high-dimensional flow cytometry. In addition, CD8+and CD4+TIL subpopulations were isolated based on the differential expression of programmed cell death protein-1 (PD-1) (negative, dim and high) and CD39 (positive or negative) by fluorescence activated cell sorting (FACS), expanded in vitro, and screened for autologous tumor recognition. We further investigated whether phenotypic markers preferentially expressed on CD8+and CD4+tumor-reactive TIL subsets were associated with the four distinct molecular subtypes of EC, tumor mutational burden and patient survival.ResultsWe found that CD8+TILs expressing high levels of PD-1 (PD-1hi) co-expressed CD39, TIM-3, HLA-DR and CXCL13, as compared with TILs lacking or displaying intermediate levels of PD-1 expression (PD-1−and PD-1dim, respectively). Autologous tumor reactivity of sorted and in vitro expanded CD8+ TILs demonstrated that the CD8+PD-1dimCD39+and PD-1hiCD39+T cell subsets both contained tumor-reactive TILs and that a higher level of PD-1 expression was associated with increased CD39 and a superior frequency of tumor reactivity. With respect to CD4+T conventional (Tconv) TILs, co-expression of inhibitory and activation markers was more apparent on PD-1hicompared with PD-1−or PD-1dimT cells, and in fact, it was the CD4+PD-1hisubpopulation that accumulated the antitumor T cells irrespective of CD39 expression. Most importantly, detection of CD8+PD-1hiCD39+ and CD4+PD-1hitumor-reactive T-cell subsets, but also markers specifically expressed by these subpopulations of TILs, that is, PD-1hi, CD39, CXCL13 and CD103 by CD8+TILs and PD-1hiand CXCL13 by CD4+Tconv TILs, correlated with prolonged survival of patients with EC.ConclusionsOur results demonstrate that EC are frequently infiltrated by tumor-reactive TILs, and that expression of PD-1hiand CD39 or PD-1hican be used to select and expand CD8+and CD4+tumor-reactive TILs, respectively. In addition, biomarkers preferentially expressed on tumor-reactive TILs, rather than the frequency of CD3+, CD8+and CD4+lymphocytes, hold prognostic value suggesting their protective role in antitumor immunity.

Despite the growing interest in immunotherapeutic interventions for endometrial cancer (EC), the prevalence, phenotype, specificity and prognostic value of tumor infiltrating lymphocytes (TILs) in this tumor type remains unclear.To better understand the role of TILs in EC, we analyzed the phenotypic traits of CD8We found that CD8Our results demonstrate that EC are frequently infiltrated by tumor-reactive TILs, and that expression of PD-1

Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from non-canonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. Using proteogenomics, we identified 517 nonC-TL from 9 patients with melanoma, gynecological, and head and neck cancer. We found no recognition of the 507 nonC-TL tested by autologousex vivoexpanded tumor reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However,in vitrosensitization of donor peripheral blood lymphocytes against 170 selected nonC-TL, led to the identification of T-cell receptors (TCRs) specific to three nonC-TL, two of which mapped to the 5’ UTR regions of HOXC13 and ZKSCAN1, and one mapping to a non-coding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies.

BackgroundDespite recent advances in exome and RNA sequencing to identify tumor-rejection antigens including neoantigens, the existing techniques fail to identify the vast majority of antigens targeted by tumor-reactive cells. A growing number of studies suggest that HLA-I peptides derived from non-canonical (nonC) open reading frames or derived from allegedly non-coding regions can contribute to tumor immunogenicity. Here we use proteogenomics to identify personalized candidate canonical and non-canonical tumor-rejection antigens and to evaluate their contribution to cancer immune surveillance in patients.MethodsWhole exome sequencing was performed to identify the non-synonymous somatic mutations (NSM) and immunopeptidomics to identify the HLA-I presented peptides (pHLA) in 9 patient-derived tumor cell lines (TCL). Peptid-PRISM proteogenomics pipeline was used to identify both canonical and non-canonical pHLA, including those derived from NSM in coding regions. All peptides containing mutations and derived from either cancer-testis (CTA) or tumor-associated antigens (TAA) were selected as candidate tumor antigens. For nonC peptides, an immunopeptidomics healthy dataset containing several tissues and HLA-allotypes was used to eliminate those derived from normal ORFs and select nonC peptides preferentially expressed in tumor cells (nonC-TE). The selected candidate peptides were synthesized, pulsed onto autologous APCs and co-cultured with tumor-reactive ex vivo expanded lymphocytes to assess immune recognition (figure 1).ResultsNonC-TE peptides were identified in all TCL studied, ranging from 0.5% to 5.4% of the total HLA-I presented peptides (n= 506). As described previoulsy, 5’UTR were the main source. Of note, the tumor type did not have an impact on the frequency of presented nonC peptides, but rather the presence of HLA-A*11:01 and HLA-A*03:01 was a major determinant. T cell responses were detected against at least 13/33 putative neoantigens, 2/24 CTA and 2/61 TAA. On the contrary, none of the 471 nonC-TE candidate peptides tested thus far, including one containing a NSM were able to elicit a recall immune response. Nevertheless, T cells recognizing at least 3 of them were detected through in vitro sensitization of non-autologous PBMCs.Abstract 912 Figure 1Workflow diagramTumor biopsies and blood samples are obtained from cancer patients (left panel). Patient-derived tumor cell lines are generated in vitro, the peptides presented on HLA molecules are further isolated and analyzed in a mass-spectrometer (top panel). Whole exome sequencing (WES) from matched tumor and healthy tissue is performed to identify the non-synonymous somatic mutations (NSM) (middle panel). Peptide-PRISM proteogenomics pipeline combines the information from the immunopeptidomics data and WES to identify pHLA sequences from both canonical and non-canonical candidate tumor antigens (top right panel). Lymphocyte populations either TILs or sorted PBMCs are expanded and further screened for pre-existing T cell responses (bottom panel) against the candidate epitopes by co-culturing the T cells with peptide-pulsed autologous APC. The recognition is assessed by measuring IFNg release by elispot and the upregulation of activation surface markers by FACS (bottom right panel).ConclusionsOur results show that although HLA-I nonC peptides were frequently presented in all TCLs studied and they can be immunogenic, neoantigens derived from mutations in canonical coding regions were preferentially recognized by tumor-reactive lymphocytes, suggesting T cells targeting the latter are primed more efficiently. The identification of mutated nonC antigens using whole genome sequencing to identify mutations in non-coding regions warrants further examination. Still, the specificity of many tumor-reactive TILs remains unknown.Ethics Approval”This study was approved by the ”Comité de Ética de Investigación con Medicamentos del Hospital Universitario Vall d’Hebron” institution’s Ethics Board; approval number PR(AG)537/2019.”

T-cell receptor β analysis can be exploited to monitor changes in the clonotypic composition of tumor-infiltrating lymphocyte (TIL) during ex vivo expansion in IL2. Oligoclonal TILs are often outgrown by infrequent clonotypes with greater proliferative capacity, and this could impact the antitumor reactivity of the expanded TILs. See related article by Poschke et al., p. 4289