Anti-cancer drug resistance: understanding the mechanisms through the use of integrative genomics and functional RNA interference.

Primary or acquired drug resistance remains a fundamental cause of therapeutic failure in cancer therapy. Post-hoc analyses of clinical trials have revealed the importance of selecting patients with the appropriate molecular phenotype for maximal therapeutic benefit, as well as the requirement to avoid exposure and potential harm for those who have drug resistant disease, particularly with respect to targeted agents. Unravelling drug resistance mechanisms not only facilitates rational treatment strategies to overcome existing limitations in therapeutic efficacy, but will enhance biomarker discovery and the development of companion diagnostics. Advances in genomics coupled with state-of-the-art biomarker platforms such as multi-parametric functional imaging and molecular characterisation of circulating tumour cells are expanding the scope of clinical trials - providing unprecedented opportunities for translational objectives that inform on both treatment response and disease biology. In this review, we propose a shift towards innovative trial designs, which are prospectively set up to answer key biological hypotheses in parallel with the RNA interference elucidation of drug resistance pathways in monotherapy pre-operative or 'window of opportunity' early phase trials. Systematic collection of paired clinical samples before and after treatment amenable to genomics analysis in such studies is mandated. With concurrent functional RNA interference analysis of drug response pathways, the identification of robust predictive biomarkers of response and clinically relevant resistance mechanisms may become feasible. This represents a rational approach to accelerate biomarker discovery, maximising the potential for therapeutic benefit and minimising the health economic cost of ineffective therapy.