Identification of candidate genes in preclinical model systems

It is essential that common features exist in the clinical and preclinical investigations. Thus, drugs used in preclinical models will be mainly the same as in the clinical studies. Moreover, matched sets of treated and untreated preclinical specimens will be analysed by the genomics platform with the same methodologies (microarray and microRNA profiling) as for the clinical samples. Results will continuously be compared with results from the clinical samples. The main steps in the preclinical discovery phase are:

  1. Proteomic approach. These studies will focus on protein profiling of several cell lines with the aim to identify proteins of importance for sensitivity and resistance to chemotherapeutic drugs. The work will be performed using drug sensitive and resistant cell lines using mass spectrometry-based methods, as well as gel based (2DE) proteomics. The expected outcome is a defined set of peptides/proteins which are significantly altered in drug resistant cells.
  2. Animal model approach. This part will utilize mouse tumour models with defined mutations in key genes, reproducing the natural history of human cancers as accurately as possible, to interrogate the molecular mechanisms responsible for the chemoresistance of melanoma and lung cancer (both SCLC and NSCLC). The expected results include a correlation between chemoresistance/sensitivity and the underlying genetic alterations. In addition, chemoresistant and sensitive tumours will be analysed using mouse pangenomic microarrays and CGH microarrays.
  3. Stem cell approach. In this part we will focus on isolating tumour stem/progenitor cells and defining their molecular and phenotypic features in order to develop more effective therapeutic strategies. The work will address the role of cancer stem cells in the development of chemoresistance of lung cancer and melanoma. Tumour stem cells will be identified by functional and phenotypic characteristics, investigated for chemoresistance, and analysed for the underlying molecular mechanisms.
  4. Investigations of mechanisms involved in resistance to DNA damaging drugs. The aim is to identify components of DNA damage response pathways conferring chemoresistance in melanoma and lung cancer. The studies will focus on alterations of DNA repair proteins such as MGMT, APNG, PARP-1 and APE-1, in a panel of melanoma cell lines and lung cancer cell lines and also in human tumour xenografts with different sensitivities to DNA damaging drugs used in the clinical studies.
  5. Investigation of apoptosis related mechanisms of chemoresistance. A panel of melanoma, NSCLC and SCLC cell lines with different sensitivity to DNA damaging drugs (taxanes, vinorelbine and gemcitabine) will be generated, and subjected to systematic studies using genomics and proteomics platforms of apoptosis-relevant genes and a selected panel of candidate genes and signal transduction pathways, which have been identified as modifiers of chemoresistance.
  6. Integrative bioinformatics. All gene candidates and proposed pathways generated from preclinical research will be delivered to a central bioinformatics platform. A comparison will be made between the candidate genes identified in the clinical and the preclinical discovery program. This will lead to the establishment of a final list of gene candidates and pathways potentially underlying chemotherapy resistance. We aim for a list of 100 key genes and related pathways. Also, a list of approximately 100 promoter methylations of key genes will be established for the purpose of subsequent validation.
Page updated by Chemores May 28, 2007
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