Stéphanie Tissot

Tumor microenvironments (TMEs) influence cancer progression but are complex and often differ between patients. Considering that microenvironment variations may reveal rules governing intratumoral cellular programs and disease outcome, we focused on tumor-to-tumor variation to examine 52 head and neck squamous cell carcinomas. We found that macrophage polarity—defined by CXCL9 and SPP1 (CS) expression but not by conventional M1 and M2 markers—had a noticeably strong prognostic association. CS macrophage polarity also identified a highly coordinated network of either pro- or antitumor variables, which involved each tumor-associated cell type and was spatially organized. We extended these findings to other cancer indications. Overall, these results suggest that, despite their complexity, TMEs coordinate coherent responses that control human cancers and for which CS macrophage polarity is a relevant yet simple variable.

Adoptive cell therapy (ACT) using ex vivo–expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell–intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8 + TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor–reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network–based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

The accurate identification and prioritization of antigenic peptides is crucial for the development of personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration of mass spectrometry immunopeptidomics data, which can uncover antigenic peptides derived from various canonical and noncanonical sources. To address this, we present an end-to-end clinical proteogenomic pipeline, called NeoDisc, that combines state-of-the-art publicly available and in-house software for immunopeptidomics, genomics and transcriptomics with in silico tools for the identification, prediction and prioritization of tumor-specific and immunogenic antigens from multiple sources, including neoantigens, viral antigens, high-confidence tumor-specific antigens and tumor-specific noncanonical antigens. We demonstrate the superiority of NeoDisc in accurately prioritizing immunogenic neoantigens over recent prioritization pipelines. We showcase the various features offered by NeoDisc that enable both rule-based and machine-learning approaches for personalized antigen discovery and neoantigen cancer vaccine design. Additionally, we demonstrate how NeoDisc's multiomics integration identifies defects in the cellular antigen presentation machinery, which influence the heterogeneous tumor antigenic landscape.

The great success of chimeric antigen receptor (CAR) T-cell therapy in the treatment of patients with B-cell malignancies has prompted its translation to solid tumors. In the case of glioblastoma (GBM), clinical trials have shown modest efficacy, but efforts to develop more effective anti-GBM CAR T cells are ongoing. In this study, we selected protein tyrosine phosphatase receptor type Z (PTPRZ1) as a target for GBM treatment. We isolated six anti-human PTPRZ1 single-chain variable fragments from a human phage display library and produced second-generation CAR T cells in an RNA format. Patient-derived GBM PTPRZ1-knockin cell lines were used to select the CAR construct that showed high cytotoxicity while consistently displaying high CAR expression (471_28z). CAR T cells incorporating 471_28z were able to release IFNγ, IL2, TNFα, granzyme B, IL17A, IL6, and soluble FasL and displayed low tonic signaling. Additionally, they maintained an effector memory phenotype after in vitro killing. In addition, 471_28z CAR T cells displayed strong bystander killing against PTPRZ1-negative cell lines after preactivation by PTPRZ1-positive tumor cells but did not kill antigen-negative nontumor cells. In an orthotopic xenograft tumor model using NOD/SCIDγ mice, a single dose of anti-PTPRZ1 CAR T cells significantly delayed tumor growth. Taken together, these results validate PTPRZ1 as a GBM target and prompt the clinical translation of anti-PTPRZ1 CAR T cells.

BACKGROUND: Glioblastoma (GBM) is an aggressive brain tumor associated with poor outcome and limited treatment options. Chimeric antigen receptor (CAR) T cells targeting cell surface antigens were shown to induce tumor regression in patients with GBM, although efficacy was transient. To broaden the range of tumor-restricted antigens, we developed CAR T cells targeting Tenascin-C (TNC), a secreted extracellular matrix protein that is overexpressed in GBM and plays a critical role in tumor progression. METHODS: Second-generation CAR T cells were engineered to target the alternatively spliced fibronectin type III (FNIII)-D domain of TNC using a single-chain variable fragment isolated from the R6N antibody and coupled to a CD28 costimulatory domain. TNC-CAR T cells were evaluated in vitro for antigen specificity, activation, and cell proliferation using TNC-expressing patient-derived GBM cell lines cultured as adherent cells or as neurospheres. Reactivity toward purified TNC protein, tumor supernatant, and ex vivo patient tumor samples was also assessed. Cytotoxic CAR T-cell activity was tested against TNC-positive and TNC-negative GBM cell lines, including bystander effects mediated by secreted TNC. In vivo efficacy and safety were determined in NOD scid gamma mice bearing patient-derived GBM tumors. RESULTS: TNC-CAR T cells demonstrated activation when exposed to TNC-positive GBM cells, cell-derived supernatants, or purified TNC protein. They exhibited potent cytotoxicity against TNC-expressing, GBM-derived adherent cells and neurospheres, and induced bystander killing of TNC-negative cells in the presence of either TNC-secreting cells or purified TNC. In vivo, TNC-CAR T cells efficiently infiltrated tumors, triggered cancer cell apoptosis, and significantly extended survival of mice bearing patient-derived GBM, with no evidence of off-tumor toxicity. Notably, TNC-CAR T cells were activated exclusively in the presence of tumor samples and showed no reactivity toward patient-derived non-tumor tissues. CONCLUSIONS: Targeting the alternatively spliced FNIII-D domain of TNC with CAR T cells offers a promising therapeutic approach for GBM. TNC-CAR T cells demonstrated specific tumor recognition, robust antitumor activity and the ability to induce bystander effects mediated by secreted TNC. Their efficacy in preclinical models, combined with a favorable safety profile, underscores their potential for clinical translation.