Successful outcome of immune checkpoint blockade in patients with solid cancers is in part associated with a high tumor mutational burden (TMB) and the recognition of private neoantigens by T-cells. The quality and quantity of target recognition is determined by the repertoire of ‘neoepitope’-specific T-cell receptors (TCRs) in tumor-infiltrating lymphocytes (TIL), or peripheral T-cells. Interferon gamma (IFN-γ), produced by T-cells and other immune cells, is essential for controlling proliferation of transformed cells, induction of apoptosis and enhancing human leukocyte antigen (HLA) expression, thereby increasing immunogenicity of cancer cells. TCR αβ-dependent therapies should account for tumor heterogeneity and availability of the TCR repertoire capable of reacting to neoepitopes and functional HLA pathways. Immunogenic epitopes in the tumor-stroma may also be targeted to achieve tumor-containment by changing the immune-contexture in the tumor microenvironment (TME). Non protein-coding regions of the tumor-cell genome may also contain many aberrantly expressed, non-mutated tumor-associated antigens (TAAs) capable of eliciting productive anti-tumor immune responses. Whole-exome sequencing (WES) and/or RNA sequencing (RNA-Seq) of cancer tissue, combined with several layers of bioinformatic analysis is commonly used to predict possible neoepitopes present in clinical samples. At the ImmunoSurgery Unit of the Champalimaud Centre for the Unknown (CCU), a pipeline combining several tools is used for predicting private mutations from WES and RNA-Seq data followed by the construction of synthetic peptides tailored for immunological response assessment reflecting the patient’s tumor mutations, guided by MHC typing. Subsequent immunoassays allow the detection of differential IFN-γ production patterns associated with (intra-tumoral) spatiotemporal differences in TIL or peripheral T-cells versus TIL. These bioinformatics tools, in addition to histopathological assessment, immunological readouts from functional bioassays and deep T-cell ‘adaptome’ analyses, are expected to advance discovery and development of next-generation personalized precision medicine strategies to improve clinical outcomes in cancer in the context of i) anti-tumor vaccination strategies, ii) gauging mutation-reactive T-cell responses in biological therapies and iii) expansion of tumor-reactive T-cells for the cellular treatment of patients with cancer.

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BackgroundSARS-CoV-2 primarily infects the upper and lower airway system, yet also endothelial cells and multiple tissues/organ systems. Anti-SARS-CoV-2 directed cellular immune responses may be deleterious or may confer immune protection – more research is needed in order to link epitope-specific T-cell responses with clinically relevant endpoints.1 Analysis of epitope reactivity in blood from healthy individuals showed pre-existing (CD4+) reactivity most likely due to previous exposure to the common old coronavirus species HCoV-OC43, HCoV-229E, - NL63 or HKU1, or – not mutually exclusive - cross-reactive T-cell responses that would recognize SARS-CoV-2, yet also other non-SARS-CoV-2 targets.2,3 Detailed single cell analysis in PBMCs from patients with COVID-19 showed strong T-cell activation and expansion of TCR gamma – delta T-cells in patients with fast recovery or mild clinical symptoms.4 Previous studies examining antigen-specific T-cell responses in tumor-infiltrating T-cells (TIL) showed that EBV or CMV-specific cellular immune responses in TIL from patients with melanoma or pancreatic cancer. Such virus -specific T-cells may represent ‘bystander’ T-cell activation, yet they may also impact on the quality and quantity of anti-tumor directed immune responses. We tested therefore TIL expanded from 5 patients with gastrointestinal cancer, who underwent elective tumor surgery during the COVID-19 pandemic for recognition of a comprehensive panel of SARS-CoV-2 T-cell epitopes and compared the reactivity, defined by IFN-gamma production to TIL reactivity in TIL harvested from patients in 2018, prior to the pandemic.MethodsA set of 187 individual T-cell epitopes were tested for TIL recognition using 100IU IL-2 and 100 IU IL-15. Different peptide epitopes were selected: i) all epitopes were not shared with the 4 common old coronavirus species, ii) some peptides were unique for SARS-CoV-2, and iii) others were shared with SARS-CoV-1. Antigen targets were either 15 mers or 9mers for MHC class II or class I epitopes, respectively, derived from the nucleocapsid, membrane, spike protein, ORF8 or the ORF3a. The amount of IFN-gamma production was reported as pg/10e4 cells/epitope/5 days. Controls included CMV and EBV peptides.ResultsWe detected strong IFN-gamma production directed against antigenic ‘hotspots’ including the ORF3a, epitopes from the SARS-CoV-2 nucleocapsid and spike protein with a range of 12 up to 30 targets being recognized/TIL.ConclusionsSARS-CoV-2 epitope recognition, defined by IFN production, can be readily detected in TIL from patients who underwent surgery during the pandemic, which is not the case for TIL harvested prior to the circulating SARS-CoV-2. This suggests a broader exposure of individuals to SARS-CoV-2 and shows that SARS-CoV-2 responses may shape the quality and quantity of anti-cancer directed cellular immune responses in patients with solid epithelial malignancies.AcknowledgementsWe thank the Surgery, Pathology and Vivarium Units of Champalimaud Clinical Center (N. Figueiredo, A. Brandl, A. Beltran, M. Castillo, C. Silva ).Ethics ApprovalThis study was approved by the Champalimaud Foundation Ethics Committee.ConsentAll donors provided written consent and the study was approved by the local ethics committee. The study is in compliance with the Declaration of Helsinki.ReferencesGrifoni, A., Weiskopf, D., Ramirez, S. I., Mateus, J., Dan, J. M., Moderbacher, C. R., Rawlings, S. A., Sutherland, A., Premkumar, L., Jadi, R. S., Marrama, D., de Silva, A. M., Frazier, A., Carlin, A. F., Greenbaum, J. A., Peters, B., Krammer, F., Smith, D. M., Crotty, S., & Sette, A. ( 2020). Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell, 181(7), 1489–1501.e15. https://doi.org/10.1016/j.cell.2020.05.015Mateus, J., Grifoni, A., Tarke, A., Sidney, J., Ramirez, S. I., Dan, J. M., Burger, Z. C., Rawlings, S. A., Smith, D. M., Phillips, E., Mallal, S., Lammers, M., Rubiro, P., Quiambao, L., Sutherland, A., Yu, E. D., da Silva Antunes, R., Greenbaum, J., Frazier, A., … Weiskopf, D. ( 2020). Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science, eabd3871. https://doi.org/10.1126/science.abd3871Le Bert, N., Tan, A. T., Kunasegaran, K., Tham, C. Y. L., Hafezi, M., Chia, A., Chng, M. H. Y., Lin, M., Tan, N., Linster, M., Chia, W. N., Chen, M. I.-C., Wang, L.-F., Ooi, E. E., Kalimuddin, S., Tambyah, P. A., Low, J. G.-H., Tan, Y.-J., & Bertoletti, A. ( 2020). SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584(7821), 457–462. https://doi.org/10.1038/s41586-020-2550-zZhang, J., Wang, X., Xing, X. et al. Single-cell landscape of immunological responses in patients with COVID-19. Nat Immunol 2020;21:1107–1118. https://doi.org/10.1038/s41590-020-0762-x

BackgroundImmunotherapy has changed the standard of care for multiple cancers; however, its efficacy is limited. Chemotherapy and radiation had little effect in pancreatic ductal adenocarcinoma (PDAC) outcome1 in patients with metastatic disease, hence the urgency for new effective courses of treatment. Increasing evidence suggests mucosal-associated invariant T-cells (MAIT) play a role in anti-cancer T-cell responses, by recognizing transformed cells or bacterial products. MAIT respond towards microbial antigens and vitamin derivatives, produce pro-inflammatory cytokines2 3 and have been found present in primary and metastatic cancer lesions.3 4 Long-term survival PDAC patients present a unique microbiome pattern. In contrast, some microbial species may promote oncogenesis.5 6The focus of this project is the characterization of MAIT as immune effector cells in PDAC specimens.MethodsWe performed a retrospective analysis of long-term survivors (LTS) and short-term survivors (STS) patients with pancreatic cancer associating clinical endpoints with the presence of MAIT infiltration in the tumor tissue using immunofluorescence staining for MR1 (MHC class I-related gene, a MAIT ligand receptor), CD3 and TCR Vα7.2 (frequently reported chain in MAIT). Tumor infiltrating lymphocytes (TILs) were expanded and tested for recognition of microbial products presented to TILs or to PBMCs defined by cytokine production (ELISA), cytotoxicity (CD107a induction assay), CD69 or 4-1BB upregulation (flow cytometry). Reactive MAIT will be molecularly defined by deep TCR (T-cell receptor) sequencing which allows to ‘back-trace’ MR1 reactive TIL in the tumor specimen. The complex interaction of microbial antigen presentation from freshly harvested tumor specimens to TILs is being optimized for Nanolive technology that allows to follow live cell interactions for several days.ResultsTIL reactivity directed against microbial products from different bacterial species was detected by IFN-γ production and CD69 upregulation in responder TILs. A broader panel of TILs is currently being tested against bacterial species. TCRs will undergo laser microdissection for subsequent TCR repertoire sequencing. A more pronounced MAIT infiltration in close vicinity to tumor cells in LTS compared to STS is being studied, further supporting the anti-tumor role of MAIT.ConclusionsMAIT cells may exhibit anti-tumor properties, based on cytokine production and cellular marker activation. TCRs directed against cancer cells can serve as viable blueprints to engage with MR1 on PDAC recognizing tumor-associated targets or microbial products that elicit IFN-γ production. This allows to explore MAIT TCRs for adoptive therapies or distinct microbial species that drive clinically relevant responses.AcknowledgementsThe authors would like to thank to Champalimaud Foundation Biobank and Vivarium Facility at Champalimaud Foundation.Ethics ApprovalThis study was approved by the Champalimaud Foundation Ethics Committee and by Ethics Research Committee of NOVA Medical School of NOVA University of Lisbon.ConsentFor each patient, written informed consent and approval by the Ethical Committee of the Champalimaud Foundation will be obtained. The study will be in compliance with the Declaration of Helsinki.ReferencesSideras, K. et al. Role of the immune system in pancreatic cancer progression and immune modulating treatment strategies. Cancer Treat. Rev 2014;40: 513–522.Toubal A, Nel I, Lotersztajn S & Lehuen A. Mucosal-associated invariant T cells and disease. Nat Rev. Immunol 2019;19:643–657.Lukasik Z, Elewaut D & Venken K. Mait cells come to the rescue in cancer immunotherapy?Cancers (Basel). 12, 1–19 ( 2020).Vacchini A, Chancellor A., Spagnuolo J., Mori L. & De Libero G. MR1-restricted t cells are unprecedented cancer fighters. Front Immunol 2020;11:1–8.Aykut B, et al. The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature 2019:574;264–267.Pushalkar S, et al. The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression. Cancer Discov 2018;8:403–416.