Project Details

Patients with macroscopic Stage III malignant melanoma are a heterogeneous group of patients with an average overall survival of less than 30%. Previously it has not been possible to predict which patients will achieve longer term survival.We recently completed a molecular profiling study which has identified a gene signature capable of predicting those patients whose survival will be good and those whose survival will be poor.

The purpose of this project is to gain a greater understanding of the biological programs that underpin these genetic signatures and to develop the gene signature further as a diagnostic tool for routine clinical use. The project will use a combination of molecular genetic and immunohistochemical techniques to adapt the current gene profile for routine use, to validate itsa pplication in independent patient cohorts and to assess itsfeasibility in routine clinical care. The expected outcome will be that this project will generate a tool which will be clinically useful for clinicians treating this fatal form of skin cancer.

References

John T, Black MA, Toro TT, Leader D, Gedye CA, Davis ID, Guilford P J, CEBON JS. Predicting Clinical Outcome through Molecular Profiling in Stage III Melanoma. Clin Cancer Res 2008;14: 5173-80

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Project Details

Although cancer is often a genetically heterogeneous disease, it has become clear that certain tumours are driven by specific pathways that render them particularly sensitive to targeted therapies. These include somatic mutations in the c-kit gene in gastrointestinal stromal tumours (GIST) as a predictor of response to imatinib. In addition, activating epidermal growth factor receptor (EGFR) mutations are a useful predictor of benefit to small molecule tyrosine kinase inhibitors of EGFR such as erlotinib in non-small cell lung cancer (NSCLC). Recently, antibodies targeting EGFR such as cetuximab or panitumumab have shown benefit in patients with advanced colorectal cancer (CRC) who have failed chemotherapy. Importantly, the benefit associated with these treatments is restricted to those patients with k-ras gene wild type tumours, indicating that the k-ras gene is an important predictive marker of benefit of this class of agents.

Although these genetic changes allow accurate prediction of patient groups who will derive greater degrees of benefit from particular therapies, inevitably treatment resistance will evolve. In some cases, the mechanism of resistance has been defined. For example in GIST secondary activating mutations in c-kit overcome the inhibition of c-kit activity induced by imatinib. Similarly, in NSCLC, the T790M mutation overcomes EGFR inhibition induced by tyrosine kinase inhibitors. In the case of cetuximab or panitumumab, mechanisms of resistance to treatment have not been defined. We propose to undertake a project aimed at identifying mechanisms of resistance to anti-EGFR antibodies in colon cancer. We propose an approach involving both in vitro and in vivo studies.

1. We will evaluate mechanisms of resistance of tumour cells to anti-EGFR antibodies in vitro Two colon cancer cell lines, LIM1215 and Difi, which are WT for K-Ras and sensitive to anti-EGFR antibodies will be continuously cultured in the presence of panitumumab for 4-6 weeks, or until a 50% reduction in cell viability is observed. Surviving cells will be passaged and cultured in a 2-fold higher concentration of the drug for a subsequent 4-6 weeks. DNA from surviving clones will be extracted and screened for mutations in the known hotspots in the K-Ras gene. The mutational status of other putative determinants of panitumumab resistance, BRAF and PIK3CA will also be determined by direct sequencing. Changes in expression of EGFR and PTEN will be determined by western blot.

2. We will then aim to validate these findings in vivo. Whilst the gold standard method to determine resistance mechanisms would involve repeat biopsies of metastatic tissue, this is rarely practical in real life. Hence we propose to isolate and study circulating tumour cells which are likely to be representative of the changes occurring in metastatic tissue. We would aim to study circulating tumour cells before therapy and after the development of resistance to anti-EGFR antibodies. The strategy we will adopt will be to use a FACS-based approach to select out tumour cells from PBMCs using the Ep-CAM cell surface marker. DNA will be extracted from circulating tumour cells and screened for mutations in the K-Ras, BRAF and PIK3CA genes.

Other biomarker studies

Several other studies related to biomarkers relevant to the use of targeted therapies could be developed, based on the existing trial portfolio. These depend on the interests of the candidate and whether they plan to embark on a PhD or DMedSc degree. These would involve evaluation of biomarkers relevant to the targeted therapy being used in the ATTAX2 study, the Vengeance study and the Radichol study.

We would be happy to discuss possible options for projects in more detail. To contact Niall Tebbutt please call 9496 5763.

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Project Details

DNA methylation (an epigenetic modification) is an important mechanism by which expression of tumor suppressor genes is inactivated in cancer. Through utilization of genome-wide DNA methylation screening assays we have identified a number of novel gene promoters that are methylated in colon cancer. The goal of this project is to exogenously express a subset of these genes in tumor cells and determine the effect on tumor cell growth, differentiation and survival. This is an open-ended / high risk project that would be suited to a more experienced candidate.

References

HDACs and HDAC inhibitors in colon cancer. JM Mariadason. Epigenetics. 2008 Jan-Feb;3(1):28-37.

HDAC4 promotes growth of colon cancer cells via repression of p21. AJ Wilson, D-S Byun, S Nasser, LB Murray, K Ayyanar , D Arango, M Figueroa, A Melnick, G Kao, LH. Augenlicht and JM. Mariadason. Mol. Biol. Cell. 2008. 19: 4062-4075.

Class I Histone deacetylases are upregulated in human colonic tumors and are linked to reduced cell differentiation in vivo and in vitro. AJ Wilson, DS Byun, HJ Smartt, K L’Italien, Y Sowa, D Arango, LH Augenlicht and JM Mariadason. J. Biol. Chem. 2006 May 12;281(19):13548-58.

PIK3CA/PTEN mutation status predicts response of colon cancer cells to cetuximab. M Jhawer, S. Goel, YH Ling, D-S Byun, A Wilson, S Nasser, J Shin, D Arango, L Augenlicht, R Perez-Soler, JM Mariadason. Cancer Res, 2008, Mar 15;68(6):1953-61

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Project Details

The MAX study, was a randomised phase III multi-centre study conducted by the AGITG in Australia, New Zealand and the United Kingdom with a total of 471 patients randomised. The primary objective of the study was to compare progression-free survival (PFS) for patients receiving the capecitabine arm versus capecitabine plus bevacizumab or capecitabine, mitomycin C plus bevacizumab. The primary analysis of the study will be presented at ASCO 2009.

Over 80% of patients participating in the study gave consent for tissue collection for use in biomarker studies. No other studies involving bevacizumab have involved significant rates of tissue banking and thus the ability to address the role of tissue biomarkers with this targeted agent. Tissue samples are currently being collected at Austin Health. We propose to use the tissue samples to address relevant biologic questions relating to the use of capecitabine and bevacizumab in patients with mCRC.

The most valuable projects will involve assessment of novel biomarkers and their role as predictors of benefit with bevacizumab. A current project is examining the role of other VEGF family members (VEGF B-D) as predictors of resistance. However, possible other relevant biomarkers yet to be examined include angiopoietins, FGFs and HIF1-alpha and LDH. In addition to hypothesis driven research, an exploratory analysis using array technology with mRNA derived from tumour samples may also be possible.

Other biomarker studies:

Several other studies related to biomarkers relevant to the use of targeted therapies could be developed, based on the existing trial portfolio. These depend on the interests of the candidate and whether they plan to embark on a PhD or DMedSc degree. These would involve evaluation of biomarkers relevant to the targeted therapy being used in the ATTAX2 study, the Vengeance study and the Radichol study.

We would be happy to discuss possible options for projects in more detail. To contact Niall Tebbutt please call 9496 5763.

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