Predictieve biomerkers bij het gemetastaseerde heldercellige niercarcinoom behandeld met bloedvatremmers en/of immuun checkpoint inhibitoren

Kidney cancer ranks as the 14th most frequent cancer type worldwide. The clear-cell renal cell carcinoma (ccRCC) subtype accounts for the majority of cases and cancer-related mortality. ccRCC exhibits remarkable variability in terms of disease aggressiveness, but also in terms of response to systemic therapy. Despite major outcome improvements over the past decades with the introduction of immune checkpoint inhibitors and VEGFR-TKIs, which are the current cornerstones of systemic treatment of ccRCC, clinically-usable biomarkers for predicting treatment response are still lacking. Throughout this PhD project, we have aimed to further study such potential new biomarkers. For ICBs in particular, we have also aimed to provide deeper understanding of the mechanisms of response, and hypothesize potential promising immunotherapy combinations based on this. In chapter three, we therefore performed a comprehensive multi-omic analysis of ccRCC tumors in an ICB-treated context, which was initiated at bulk transcriptome level and further validated at single-cell and spatial resolutions across internal as well as external cohorts. Our analyses revealed a distinct tumor-immune community at the core of ICB response, which consisted of crosstalk between proinflammatory tumor-associated macrophages and (pre-)exhausted CD8+ T cells in an antigenic context. This context was patient specific and was distinguished by a germline HLA repertoire with a greater preference for tumoral (neo)antigens. A cross-omics machine learning pipeline facilitated design of a new tumor transcriptomic footprint of neoantigen-favoring human leukocyte antigen alleles. This novel gene signature, tLHP, was associated with prolonged survival after ICB treatment in our cohort, as well as across multiple independent external validation cohorts. Finally, in a reverse translational effort, the RENCA RCC model was selected based on tLHP expression across mouse model transcriptomes commonly used for immune-oncology research. We tested several immunotherapeutic combinations, inspired by our single-cell analyses, and observed that only a combination which stimulated both CD8+ T cells (through PD1-blockade) and macrophages (through CD40 agonist) achieved maximal anti-tumor control. Thus, we presented a novel multiomics and spatial map of the immune-community architecture that drives ICB response in patients with advanced RCC. In this PhD project, we additionally investigated another germline trait which can impact response to ICBs, namely germline alterations of DDR genes. In chapter seven, we described a multi-tumor case series of patients harboring such germline alterations, which had superior responses to ICBs. As similar evidence is found in literature, this highlights the importance of taking germline DDR alterations into consideration when making treatment choices for this rare patient population, for whom prospective randomized trials face many challenges. For angiogenesis inhibitors, the drivers of response and resistance remain poorly understood. Current most promising biomarkers reflect upregulation of angiogenesis pathways, either through signatures or via angiogenesis-enriched molecular subtypes. In chapter 4, we developed an easy-to-used classifier to allow determination of the ccrcc1-4 molecular subtypes. In particular, the angiogenesis-enriched ccrcc2 subtype showed improved outcomes on angiogenesis inhibitors when not treated with ICBs before death. In surgical settings, this subtype also had favorable DFS and OS, in particular when patients did not access ICB's in metastatic setting before death. In chapter 5, we focused further on bone metastases, a site of metastases that is linked to resistance to VEGFR-TKIs. We identified several microRNA's expressed in the primary tumor which were specifically correlated with earlier or later occurrence of bone metastases. These hold promise as biomarkers or potential therapeutic targets. In chapter 6, we studied microRNA's which might target the drug targets of current-day angiogenesis inhibitors and possibly hamper the expression of the protein receptors. We identified several microRNA's possibly targeting VEGFR1/2 and/or HIF-2α, whose expression also correlated with worse outcomes on angiogenesis inhibitors. These microRNA's may function as biomarkers or as potential therapeutical targets. In conclusion, this thesis project has advanced insights into the mechanisms of response of current systemic treatments, as well as strategies for patient stratification in ccRCC.