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Cancer neoantigens that arise from tumor mutations are drivers of tumor-specific T cell responses, but identification of T cell-recognized neoantigens in individual patients is challenging. Previous methods have restricted antigen discovery to selected HLA alleles, thereby limiting the breadth of neoantigen repertoires that can be uncovered. Here, we develop a genetic neoantigen screening system that allows sensitive identification of CD4+ and CD8+ T cell-recognized neoantigens across patients' complete HLA genotypes. Patient-specific tumor neoantigens are recognized by T cells. [ABSTRACT FROM AUTHOR]

Organoid models allow for the study of key pathophysiological processes such as cancer biology in vitro. They offer insights into all aspects covering tumor development, progression and response to the treatment of tissue obtained from individual patients. Tumor organoids are therefore not only a better tumor model than classical monolayer cell cultures but can be used as personalized avatars for translational studies. In this review, we discuss recent developments in using organoid models for cancer research and what kinds of advanced models, testing procedures and readouts can be considered. [ABSTRACT FROM AUTHOR]

Summary Cancer immunotherapies have shown substantial clinical activity for a subset of patients with epithelial cancers. Still, technological platforms to study cancer T-cell interactions for individual patients and understand determinants of responsiveness are presently lacking. Here, we establish and validate a platform to induce and analyze tumor-specific T cell responses to epithelial cancers in a personalized manner. We demonstrate that co-cultures of autologous tumor organoids and peripheral blood lymphocytes can be used to enrich tumor-reactive T cells from peripheral blood of patients with mismatch repair-deficient colorectal cancer and non-small-cell lung cancer. Furthermore, we demonstrate that these T cells can be used to assess the efficiency of killing of matched tumor organoids. This platform provides an unbiased strategy for the isolation of tumor-reactive T cells and provides a means by which to assess the sensitivity of tumor cells to T cell-mediated attack at the level of the individual patient. Graphical Abstract Highlights • Induction of tumor-reactive T cells by co-culture of PBMCs and tumor organoids • Induced T cell populations do not recognize healthy organoids or tissue • This platform can be used to assess the efficiency of T-cell-mediated tumor killing A modified patient-derived tumor organoids system allows the expansion of tumor-specific T cells from blood for personalized analysis of their anti-cancer properties. [ABSTRACT FROM AUTHOR]

Interferon-γ (IFN-γ) signaling mediates host responses to infection, inflammation and anti-tumor immunity. Mutations in the IFN-γ signaling pathway cause immunological disorders, hematological malignancies, and resistance to immune checkpoint blockade (ICB) in cancer; however, the function of most clinically observed variants remains unknown. Here, we systematically investigate the genetic determinants of IFN-γ response in colorectal cancer cells using CRISPR-Cas9 screens and base editing mutagenesis. Deep mutagenesis of JAK1 with cytidine and adenine base editors, combined with pathway-wide screens, reveal loss-of-function and gain-of-function mutations, including causal variants in hematological malignancies and mutations detected in patients refractory to ICB. We functionally validate variants of uncertain significance in primary tumor organoids, where engineering missense mutations in JAK1 enhanced or reduced sensitivity to autologous tumor-reactive T cells. We identify more than 300 predicted missense mutations altering IFN-γ pathway activity, generating a valuable resource for interpreting gene variant function. [Display omitted] • Systematic base editing mutagenesis of the IFN-γ pathway in colorectal cancer cells • Functional assessment of variants relevant to cancer and immune disorders • Mutagenesis highlights functional protein domains and interaction interfaces • Missense mutations in JAK1 alter sensitivity of tumor organoids to T cells Coelho et al. use functional genomics to systematically analyze the genetic determinants of IFN-γ response in colorectal cancer cells. Base editing mutagenesis of key signaling components facilitates the parallel assessment of gene variant function at scale, relevant for understanding IFN-γ signaling in cancer immune surveillance and immune disorders. [ABSTRACT FROM AUTHOR]

Patients affected by colorectal cancer (CRC) with DNA mismatch repair deficiency (MMRd), often respond to immune checkpoint blockade therapies, while those with mismatch repair-proficient (MMRp) tumors generally do not. Interestingly, a subset of MMRp CRCs contains variable fractions of MMRd cells, but it is unknown how their presence impacts immune surveillance. We asked whether modulation of the MMRd fraction in MMR heterogeneous tumors acts as an endogenous cancer vaccine by promoting immune surveillance. To test this hypothesis, we use isogenic MMRp (Mlh1 +/+ ) and MMRd (Mlh1 −/− ) mouse CRC cells. MMRp/MMRd cells mixed at different ratios are injected in immunocompetent mice and tumor rejection is observed when at least 50% of cells are MMRd. To enrich the MMRd fraction, MMRp/MMRd tumors are treated with 6-thioguanine, which leads to tumor rejection. These results suggest that genetic and pharmacological modulation of the DNA mismatch repair machinery potentiate the immunogenicity of MMR heterogeneous tumors. [Display omitted] • MMR heterogeneity affects immune surveillance in mouse CRC • In vivo 6TG treatment increases the MMRd fraction of MMR heterogeneous tumors • Pharmacological selection of MMRd cells improves immune surveillance in MMR tumors The impact of MMR heterogeneity on immune surveillance of colon cancers is largely unexplored. This proof-of-concept study by Amodio et al. suggests that MMR heterogeneity can be exploited through an endogenous vaccination approach based on pharmacological modulation of the DNA MMR, which potentiates cancer immunogenicity. [ABSTRACT FROM AUTHOR]