Periodic Reporting for period 1 - EXPAND IT (EXPANDing Immune Cells and their Tumor Antigens during checkpoint immunotherapy)
Reporting period: 2023-01-01 to 2025-06-30
Cancer immunotherapy using immune checkpoint blockade (ICB) has revolutionized cancer treatment. However, durable responses occur only in some patients and cancer types. Our analysis of tumor biopsies from breast cancer patients undergoing ICB revealed that in only a subset of patients tumor-infiltrating T-cells undergo rapid expansion when exposed to ICB (Bassez et al., Nature Medicine 2021). We characterized the gene expression programs underlying this expansion at the single-cell level and defined several unanswered questions about their function. First, we lack precise knowledge of where in the heterogeneous tumor microenvironment (TME) and in which metabolic niches T-cell expansion occurs. Second, based on their T-cell receptor (TCR) sequence, we cannot predict which T-cells will expand, nor identify to which tumor antigens these expanding T-cells react. Third, it remains unclear whether tumor mutation alone or other genetic mechanisms contribute to the generation of the tumor antigens regulating T-cell expansion. Lastly, can T-cell expansion be detected in blood? Through this ERC Advanced Grant ‘EXPAND IT’, we will employ innovative (single-cell) technologies to address these critical questions. Our insights will not only enhance the understanding of ICB response mechanisms but also inform strategies to sensitize non-responding patients. Furthermore, our findings could facilitate the discovery of high-avidity anti-tumor TCRs and tumor-specific antigens, paving the way for novel engineered TCR-based therapies and personalized anti-tumor vaccination strategies.
To determine where in the tumor expanding T-cells are located, we successfully implemented spatial single-cell methods. Recently, we published a single-cell study investigating the mechanisms distinguishing anti-PD-L1+ anti-CTLA4 combination therapy from anti-PD-L1 monotherapy in head and neck squamous cell carcinoma (HNSCC) (Franken et al., Immunity, 2024). Through comprehensive single-cell and spatial analyses of the TME, as well as single-cell profiling of peripheral blood mononuclear cells (PBMCs), we identifed CD4+ T-cell activation as a hallmark of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC.
To identify the tumor antigens to which expanding T-cells react to, we developed a novel high-throughput method, Transcriptome-WIde Screening for T-cell Antigen Research (TWISTAR). TWISTAR successfully identifies tumor antigens, making it a unique platform to identify tumor antigens for the generation of individualized cancer vaccines. Key strengths of TWISTAR include: i) it was developed using on-treatment biopsies collected during ICB, thereby focusing on expanding TCRs likely to be tumor-reactive (and not bystanders), ii) it is a TCR-driven approach, based on TCRs detected in patient tumors, iii) the tumor transcriptome is presented in a tailored human cell line, closely resembles the patient’s antigen representation, and iv) TWISTAR is not limited to tumor mutations, it detects everything embedded in the transcriptome including splicing events and non-coding sequences (which we refer to as ‘dark antigens’).
To explore other tumor antigen sources beyound somatic mutations, we identified several cancer-specific alternative splicing events linked to tumor antigenicity, antitumor immune activity, and ICB response in breast and other cancers.
To enable non-invasive detection of T-cell expansion, we demonstrated that TCR sharing between tumor and blood serves as a marker for response to ICB in hepatocellular carcinoma (HCC) patients (Cappuyns et al., Nature Communications, 2023).
To identify the tumor antigens to which expanding T-cells react to, we developed a novel high-throughput method, Transcriptome-WIde Screening for T-cell Antigen Research (TWISTAR). TWISTAR successfully identifies tumor antigens, making it a unique platform to identify tumor antigens for the generation of individualized cancer vaccines. Key strengths of TWISTAR include: i) it was developed using on-treatment biopsies collected during ICB, thereby focusing on expanding TCRs likely to be tumor-reactive (and not bystanders), ii) it is a TCR-driven approach, based on TCRs detected in patient tumors, iii) the tumor transcriptome is presented in a tailored human cell line, closely resembles the patient’s antigen representation, and iv) TWISTAR is not limited to tumor mutations, it detects everything embedded in the transcriptome including splicing events and non-coding sequences (which we refer to as ‘dark antigens’).
To explore other tumor antigen sources beyound somatic mutations, we identified several cancer-specific alternative splicing events linked to tumor antigenicity, antitumor immune activity, and ICB response in breast and other cancers.
To enable non-invasive detection of T-cell expansion, we demonstrated that TCR sharing between tumor and blood serves as a marker for response to ICB in hepatocellular carcinoma (HCC) patients (Cappuyns et al., Nature Communications, 2023).
The development of TWISTAR marks a technological breakthrough in the field of tumor antigen discovery, enabling high-throughput and scalable identification of tumor antigens. The reliable identification of tumor antigens marks a significant step forward in the development of personalized cancer vaccines. This tool’s fast, easy-to-implement design and superior performance in TCR specificity identification makes it a revolutionary advancement in tumor immunology. TWISTAR's potential extends beyond oncology, with applications in virology and autoimmune disease research. TWISTAR has enormous potential as a platform-based biotech company that discovers and develops novel tumor antigens to fuel an internal pipeline for vaccine-based cancer medicines. Further research will focus on applying TWISTAR in phase I feasibility vaccination trials to assess its potential in therapeutic settings.
Additionally, our recent findings from Franken et al. (Immunity, 2024) identified CD4+ T-cell activation as a hallmark of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC. This highlights the potential efficacy of combined anti-PD-L1/anti-CTLA4 therapy, especially for patients who initially failed to mount an anti-tumor immune response. This research sheds light on the complexities of ICB therapies, offering valuable insights into their mechanisms and paving the way for informed advancements in the treatment of HNSCC and potentially other cancer types as well.
Additionally, our recent findings from Franken et al. (Immunity, 2024) identified CD4+ T-cell activation as a hallmark of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC. This highlights the potential efficacy of combined anti-PD-L1/anti-CTLA4 therapy, especially for patients who initially failed to mount an anti-tumor immune response. This research sheds light on the complexities of ICB therapies, offering valuable insights into their mechanisms and paving the way for informed advancements in the treatment of HNSCC and potentially other cancer types as well.