Molecular and spatial dissection of endothelial cell heterogeneity in clear cell renal cell carcinoma

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Endothelial cells (ECs) line the inner wall of blood vessels fulfilling different tasks in our organs. ECs are characterized by remarkable phenotypic and functional heterogeneity. However, only the recent advances in single-cell RNA sequencing (scRNA-seq) enabled researchers to define the molecular heterogeneity of ECs in a truly comprehensive manner. Also, scRNA-seq revealed novel principles how ECs respond to stresses and injuries being relevant for many major diseases. As tumour growth is dependent on constant nutrient and oxygen supply, de novo blood vessel formation (neoangiogenesis) is a hallmark of cancer. For many cancer types, anti-angiogenic therapy that blocks vascular endothelial growth factor (VEGF) signalling was less effective than hoped for, but renal cancers proved to be quite responsive to tyrosine kinase inhibitors (TKIs) targeting the VEGF receptor (VEGFR). This is in line with the fact that renal cancers are highly vascularized and harbour mutations that drive neoangiogenesis. Clear cell renal cell carcinoma (ccRCC) represents the most frequent subtype. VEGFR TKIs are the current mainstay of ccRCC treatment (advanced stage) combined with immune checkpoint blockade, though efficacy and durability are variable. In this context, the precise role of ECs in primary or acquired resistance to VEGFR TKIs treatment is poorly understood. Thus, more profound molecular and mechanistic insights into EC heterogeneity of ccRCCs are critically needed. Proliferation and sprouting of vessels within and around tumours are typical histological features of neoangiogenesis. Most studies in the field focused either on microvasculature density or on tumour cell characteristics like mutations, but our understanding of the complex interplay between ECs and ccRCC tumour cells lacks far behind. Moreover, pathologists appreciate that ccRCCs are characterized by very different blood vessel architectures, which can be roughly classified as glomeruloid, low branching, high branching and sinusoidal-anastomosing. As a matter of fact, it is unknown whether these distinct vascular patterns actually have distinct molecular correlates of ECs or not, and whether these phenotypes are intrinsically driven by ECs, instructed by the surrounding tumour cells or both. Essentially, these are the question that we aim to address in our project. For this, we will isolate ECs and perform scRNA-seq in order to explore the phenotypic space ECs in human ccRCCs. Further, we will link novel EC phenotypes to the genomic and spatial context of ccRCCs by whole-exome sequencing and high-plex immunofluorescence. Lastly, we will employ an innovative patient-derived tumour fragment platform and EC co-culture assays to study how phenotypic diversity of ECs from ccRCCs is linked to functional diversity. We believe that we will establish novel concepts of EC heterogeneity in ccRCCs and delineate new avenues how EC phenotypes may guide the stratification for VEGFR TKI-based therapies.