Azadeh Fahim Golestaneh, PhD

Engineering Tumor Resistance via in-vivo Functional Genomic Screen

There is a long path a cell needs to traverse to become malignant, which requires several transformations resulting in capabilities known as hallmarks of cancer. The cells acquire distinctive and complementary skills which enable them to proliferate rapidly and disseminate to new micro-environments. For tumors to meet their high demands for nutrients and oxygen, they need to expand the tumor vasculature. Without new vessels, cancer cells can survive only if the tumor is not bigger than about 1 mm3. Furthermore, vessels act as “highways” inside tumors, facilitating the exit of metastatic disseminating cells. Tumors foster new vessels from pre-existing capillaries during a process called angiogenesis. Therefore, more than 30 years ago, Dr. Folkman postulated that angiogenesis is a prerequisite for tumor growth.

Among different pro-angiogenic factors, VEGFa has received attention due to its predominant role in angiogenesis. Loss of VEGFa has been shown to be lethal in mouse embryos. In addition, the non-redundant role and the high specificity for endothelial cells have made VEGFa a promising target for anti-angiogenic therapy.

Classical cancer therapies comprised of chemical agents affecting dividing cells together with radiotherapy and surgery. With emergence of targeted cancer therapies, clinical trials are more focused on monoclonal antibodies and small tyrosine kinases, affecting tumor cells as well as stromal cells. Meanwhile, drug resistance remains a key obstacle in clinic. In addition to intrinsic resistance, acquired resistance will emerge as therapy continues, affecting the treatment outcome and patient survival.

We are trying to tackle a very important quest in current translational cancer biology, namely the mechanism of tumor therapy refractoriness governed by intratumoral heterogeneity. we mimicked cancer genetic instability by employing a genome-wide shRNA library targeting ~30K mouse genes. In this model, global loss of gene function on the top of the instable genetic background of Lewis lung cancer cells was utilized to generate intratumoral heterogeneity under controlled conditions. Using a microarray based DNA-barcode readout strategy we could then longitudinally trace the fate of each single tumor cell clone (harbouring shRNA against a single gene) towards treatment with an antiangiogenic agent sunitinib, a potent receptor-tyrosine kinase inhibitor (RTKi) of the VEGF/PDGF signalling pathways. Clonal evolution tracing of tumor cells, each bearing a unique shRNA construct, indicated that the complexity of the library was affected under treatment pressure, leading to high enrichment of clones harbouring shRNA for specific genes. Using high-tech methods, such as CrispR-Cas, Chip-seq, time lapsed microscopy and proteome profiling, our group aimed to functionally decipher the role of candidate genes in anti-angiogenic drugs. To translate the findings into clinic, we verify the results in available patient clinical data cohorts, aiming to prognosticate patients at risk for therapy refractoriness to RTKi.

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