Genetic factors such as the HLA type of patients may play a role in regard to disease severity and clinical outcome of patients with COVID-19. Taking the data deposited in the GISAID database, we made predictions using the IEDB analysis resource (TepiTool) to gauge how variants in the SARS-CoV-2 genome may change peptide binding to the most frequent MHC-class I and-II alleles in Africa, Asia and Europe. We caracterized how a single mutation in the wildtype sequence of of SARS-CoV-2 could influence the peptide binding of SARS-CoV-2 variants to MHC class II, but not to MHC class I alleles. Assuming the ORF8 (L84S) mutation is biologically significant, selective pressure from MHC class II alleles may select for viral varients and subsequently shape the quality and quantity of cellular immune responses aginast SARS-CoV-2. MHC 4-digit typing along with viral sequence analysis should be considered in studies examining clinical outcomes in patients with COVID-19.

Memory formation, guided by microbial ligands, has been reported for innate immune cells. Epigenetic imprinting plays an important role herein, involving histone modification after pathogen-/danger-associated molecular patterns (PAMPs/DAMPs) recognition by pattern recognition receptors (PRRs). Such "trained immunity" affects not only the nominal target pathogen, yet also non-related targets that may be encountered later in life. The concept of trained innate immunity warrants further exploration in cancer and how these insights can be implemented in immunotherapeutic approaches. In this review, we discuss our current understanding of innate immune memory and we reference new findings in this field, highlighting the observations of trained immunity in monocytic and natural killer cells. We also provide a brief overview of trained immunity in non-immune cells, such as stromal cells and fibroblasts. Finally, we present possible strategies based on trained innate immunity that may help to devise host-directed immunotherapies focusing on cancer, with possible extension to infectious diseases.

Vaccination against COVID-19 relies on the in-depth understanding of protective immune responses to SARS-CoV-2. We characterized the polarity and specificity of memory T cells directed against SARS-CoV-2 viral lysates and peptides to determine correlates with spontaneous, virus-elicited or vaccine-induced protection against COVID-19 in disease-free and cancer bearing individuals. A disbalance between type 1 and type 2 cytokine release was associated with high susceptibility to COVID-19. Individuals susceptible to infection exhibited a specific deficit in the TH1/Tc1 peptide repertoire affecting the receptor binding domain of the spike protein (S1-RBD), a hot spot of viral mutations. Current vaccines triggered T helper 1/T cytotoxic 1 (TH1/Tc1) responses only in a fraction of all subject categories, more effectively against the original sequence of S1-RBD than that from viral variants. We speculate that the next generation of vaccines should elicit TH1/Tc1 T cell responses against the S1-RBD domain of emerging viral variants

BACKGROUNDOur understanding of the immune system stems, in great part, from studying the host response to infection, which in most individuals leads to the absence of clinical disease and establishment of highly apt immunological memory. The host immune response in relation to opportunistic pathogens as well as to the endogenous microbiota is pivotal to deter not only infectious diseases, yet also central to providing general physiological health (Manfredo Vieira et al., 2018;

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.

Immune responses to human cytomegalovirus (CMV) can be used to assess immune fitness in an individual. Further to its clinical significance in posttransplantation settings, emerging clinical and translational studies provide examples of immune correlates of protection pertaining to anti-CMV immune responses in the context of cancer or infectious diseases, e.g., tuberculosis. In this viewpoint, we provide a brief overview about CMV-directed immune reactivity and immune fitness in a clinical context and incorporate some of our own findings obtained from peripheral blood or tumour-infiltrating lymphocytes (TIL) from patients with advanced cancer. Observations in patients with solid cancers whose lesions contain both CMV and tumour antigen-specific T-cell subsets are highlighted, due to a possible CMV-associated “bystander” effect in amplifying local inflammation and subsequent tumour rejection. The role of tumour-associated antibodies recognising diverse CMV-derived epitopes is also discussed in light of anti-cancer immune responses. We discuss here the use of anti-CMV immune responses as a theranostic tool—combining immunodiagnostics with a personalised therapeutic potential—to improve treatment outcomes in oncological indications.

The SARS-CoV-2 pandemic still represents a threat for immunosuppressed and hematological malignancy (HM) bearing patients, causing increased morbidity and mortality. Given the low anti-SARSCoV-2 IgG titers post-vaccination, the COVID-19 threat prompted the prophylactic use of engineered anti-SARS-CoV-2 monoclonal antibodies. In addition, potential clinical significance of T cell responses has been overlooked during the first waves of the pandemic, calling for additional in-depth studies. We reported that the polarity and the repertoire of T cell immune responses govern the susceptibility to SARS-CoV-2 infection in health care workers and solid cancer patients. Here, we longitudinally analyzed humoral and cellular immune responses at each BNT162b2 mRNA vaccine injection in 47 HM patients under therapy. Only one-third of HM, mostly multiple myeloma (MM) bearing patients, could mount S1-RBD-specific IgG responses following BNT162b2 mRNA vaccines. This vaccine elicited a S1-RBD-specific Th1 immune response in about 20% patients, mostly in MM and Hodgkin lymphoma, while exacerbating Th2 responses in the 10% cases that presented this recognition pattern at baseline (mostly rituximab-treated patients). Performing a third booster barely improved the percentage of patients developing an S1-RBD-specific Th1 immunity and failed to seroconvert additional HM patients. Finally, 16 patients were infected with SARS-CoV-2, of whom 6 developed a severe infection. Only S1-RBD-specific Th1 responses were associated with protection against SARS-CoV2 infection, while Th2 responses or anti-S1-RBD IgG titers failed to correlate with protection. These findings herald the paramount relevance of vaccine-induced Th1 immune responses in hematological malignancies.

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.