Investigating the mehcanisms of drug resistance in gastro-intestinal cancers

Abstract

Despite many effective therapies for gastro-intestinal (GI) cancers, both primary and acquired mechanisms of resistance commonly occur. The subclonal complexity of intra-tumoural heterogeneity in these cancers further complicates our understanding of drivers of resistance. Using DNA and RNA sequencing data from patients, this thesis functionally validates putative novel drivers of resistance in GI cancers and tests potential new therapeutic regimens that may overcome the complex heterogeneous resistance landscape. In gastro-oesophageal adenocarcinoma, the novel use of the pan-RAF inhibitor CCT196969 in this cancer type has shown successful growth inhibition of cell lines with a wide range of Mitogen Activated Protein Kinase (MAPK) pathway activating aberrations that are seen in patients. Pan-RAF inhibition successfully constrained growth better than current in-use downstream MEK or ERK inhibitors, thus indicating pan-RAF as a putative novel therapeutic option for gastric cancer patients. In colorectal cancer (CRC) cell lines, non-canonical BRAF and KRAS mutations and loss-of-function NF1 have been successfully modelled and validated as drivers of MAPK reactivation in response to the anti-EGFR therapy, cetuximab. Furthermore the use of cancer-associated fibroblast conditioned medium has been shown to induce resistance to cetuximab therapy in CRC cell lines as well as elucidation of the individual growth factors contributing to the resistance phenotype. Using biopsies from metastatic colorectal cancer patients, a living biobank of chemotherapy naive and resistant patient derived organoids (PDOs) has been established. Drug sensitivity assays have been developed to investigate the resistance of the spheroid lines to chemotherapeutics and RNA sequencing of PDOs treated with 5FU has begun to elucidate pathways involved in 5FU chemoresistance.