Targeting Vasculogenic Mimicry in Cancer

Like any tissue, tumours depend on a constant blood supply to deliver oxygen and nutrients. Tumour neovascularization is achieved most frequently through the process of angiogenesis, in which tumour cells secrete extracellular factors to recruit host endothelium to grow into the neoplastic tissue. A tumour’s dependency on a blood supply made angiogenesis an attractive target for cancer therapy, but disappointingly, anti-angiogenic drugs often times show limited efficacy in the context of cancer, with benefits only being transient followed by relapse and resistance. In retrospect, this is not surprising because it is now well-appreciated that some aggressive cancers are able to supply themselves with blood via an alternate mechanism to angiogenesis known as vascular mimicry (VM). In VM capable tumours, pseudo blood vessels are formed by tumour cells that have acquired endothelial-like properties independently of host endothelium. VM is a marker of poor prognosis and metastasis in patients, however it is still poorly understood at the molecular level. Recent advances have empirically demonstrated that VM drives resistance to anti-angiogenic therapy (AAT), which informs a motivation to identify VM-related targets that can be exploited therapeutically in combination with existing AATs as a rational approach to target both routes of tumour neovascularization to effectively starve tumours of the blood supply needed for survival. To this end, this thesis aims to identify drivers of VM across a range of cell types, with the goal of uncovering common mechanisms that VM- capable cancer cells use to maintain their pseudo endothelial phenotype, to identify nodes that can be exploited therapeutically to improve patient response to AAT. To achieve this, first we explored what triggers VM formation, through the manipulation of oxygen levels and a previously identified master regulator of VM, FOXC2. Next, we established a high-throughput method to sort cells for VM propensity using acetylated LDL uptake and leveraged this to conduct a genome-wide CRISPR screen using a bespoke dual gRNA-tRNA expression system. Through these approaches, we identified a shortlist of candidate genes to functionally investigate for VM capabilities to validate already known and uncover previously unknown VM-related targets, which can be leveraged as a promising therapeutic route towards sensitizing tumours to AATs

FOXC2 promotes vasculogenic mimicry and resistance to anti-angiogenic therapy.

Vasculogenic mimicry (VM) describes the formation of pseudo blood vessels constructed of tumor cells that have acquired endothelial-like properties. VM channels endow the tumor with a tumor-derived vascular system that directly connects to host blood vessels, and their presence is generally associated with poor patient prognosis. Here we show that the transcription factor, Foxc2, promotes VM in diverse solid tumor types by driving ectopic expression of endothelial genes in tumor cells, a process that is stimulated by hypoxia. VM-proficient tumors are resistant to anti-angiogenic therapy, and suppression of Foxc2 augments response. This work establishes co-option of an embryonic endothelial transcription factor by tumor cells as a key mechanism driving VM proclivity and motivates the search for VM-inhibitory agents that could form the basis of combination therapies with anti-angiogenics

Clonal fitness inferred from time-series modelling of single-cell cancer genomes

Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours