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Title: Investigation of association between natural variants in sub-cellular pathways and breast cancer chemotherapy response
Author: Ballal, H.
ISNI:       0000 0004 7428 5475
Awarding Body: University of Liverpool
Current Institution: University of Liverpool
Date of Award: 2018
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Invasive breast cancer is the commonest cancer in the UK and adjuvant chemotherapy is often used to reduce the risk of local and distant recurrence in early stage disease. However, it is estimated that 70-80% of women receive no benefit from chemotherapy. In the current climate of personalised medicine the aim of the treating physician is to maximise individual benefit of treatment whilst minimising exposure to harmful side effects. Here we discuss the current tools available to stratify patients’ treatment including clinicopathological and molecular features, clinical guidelines, computer based risk calculators, gene expression profiles and minimal invasive disease markers. We also review the major chemotherapy drugs in breast cancer, both historically and current regimes. This leads us to the notion that hypothesis generated biomarkers are required to help determine chemo-responsiveness of cancers. We describe why single nucleotide polymorphisms (SNPs) are the ideal candidate for a biomarker given that they are constant between cancers, easy to detect and reproducibility is reliable. Although many pathways have been implicated in cancer and response to treatment we have focused on predictive SNPs for hypothesis testing of specific candidate examples; apoptosis, cell cycle, metastor genes, drug metabolism and. We discuss the pathways in detail including their known relevance to breast cancer and current chemotherapy agents. It was our hypothesis that specific variants would be enriched in chemo responsive groups of breast cancers and we aimed to test such associations by creating a panel of candidate SNPs for a range of subcellular processes. Methods Full ethical approval was obtained to use breast cancer samples stored in the Liverpool Candis Cancer Research Tissue Bank and obtain clinical information from patient case notes held in both Royal Liverpool and Broadgreen hospital and Clatterbridge Centre for Oncology. Patients who had undergone primary breast cancer surgery and received chemotherapy between 1993 and 2005 were identified. SNP assays were developed using 96 well DNA panels from healthy volunteers using commercially Taq man real time polymerase chain reactions (PCR) and custom gel based assays as required. Tumour DNA was either available as a macromolecule from the tissue bank or extracted from frozen or paraffin embedded tissue using commercially available kits. Once probes had been optimised they were used in duplicate on DNA samples with a number of positive and negative controls. Overall survival and disease free survival were used as end points Results A cohort of 303 patients was analysed a number calculated to achieve statistical significance. All patients received chemotherapy but the regimes changed over the study period with anthracyclines and taxanes becoming more prevalent as time progressed. The presence of adverse clinical features was still associated with poorer outcome despite chemotherapy being given. Two of our apoptotic pathway SNPs (Rs 1042522, Rs 2279225) had some association with survival and sensitivity to taxanes. While our drug metabolism pathway variants weren’t expected to be associated with clinical features we found some trends linking variation with possible cause. A polymorphism associated with alternative splicing of cyclin D1 appears to be associated with response to anthracycline based chemotherapy. We hypothesise that if this SNP is associated with increased expression of the alterative cyclin D1b protein in our population, as suggested by other published studies, then the associated difference in proliferation and subsequent effects on the DNA damage response pathways can explain our findings. We have also found a possible link between SPP1 variants and overall survival (p=0.02) and chemotherapy agent sensitivity. Discussion. This work supports the hypothesis that pathway associated genetic variants can be associated with outcome in a chemotherapy treated cohort of early breast cancers and that the nature of chemotherapy is important in specific instances. It has provided a foundation for further work to be performed both on validation of these results and for testing in larger cohorts from previous clinical trials. It provides continued support for the use of SNPs in point of care testing towards truly personalised cancer treatment.
Supervisor: Sibson, Ross Sponsor: Not available
Qualification Name: Thesis (M.D.) Qualification Level: Doctoral