B16 Objectives: In this study, we proposed to use gene expression analysis of tumor biopsies obtained sequentially before and after treatment to discover new biomarkers of therapeutic benefit. This strategy was applied in a phase I study that combined sorafenib, a multikinase inhibitor, with dacarbazine, a cytotoxic agent. Methods: Patients received oral sorafenib (400 mg bid continuously) and IV dacarbazine (1000 mg/m 2 on Day 1) in repeated 21-day cycles. We sequentially obtained 2 biopsies from 17 patients with accessible advanced solid tumors. One biopsy was collected at baseline before treatment; the second was collected at Day 21 corresponding to the end of the first cycle. Among these 17 patients, 10 displayed therapeutic benefit (progression-free survival [PFS] >3 months) whereas 7 had progressive disease (PFS TM ). Direct comparison was performed on each pair of biopsies, in duplicate, with dye-swap hybridization. We selected genes differentially expressed in each biopsy pair. We then compared expression profiles between patients with or without therapeutic benefit. By using paired samples, we minimized the effect of interindividual variability. The analysis was based on a leave-one-out strategy where we generated 17 different learning sets by excluding 1 sample and using the remaining 16 to define genes associated with therapeutic benefit (gene filtering at P Results : We obtained 17 different gene sets of 21 to 81 genes. Their union generated a set of 247 genes that efficiently clustered the 17 patients according to therapeutic benefit status. The intersection of the 17 gene sets corresponded only to 4 genes (NM_172229, NM_003129, NM_006403, and AI613259). Interestingly, the expression of these 4 genes was predictive of therapeutic benefit. The gene expression of the 7 known sorafenib targets was not modified. However, the biologic pathway analysis among the 247 genes set revealed that 15 genes were related directly to sorafenib biologic activity: RAF1 pathway (8 genes); KDR pathway (4 genes), KIT pathway (2 genes), and PDGFRβ pathway (1 gene ). Conclusions: In this study, we showed the potential value of expression analysis in a phase I trial combining sorafenib and dacarbazine. Despite the high heterogeneity of tumors and the limited number of patients, we demonstrated that gene expression profiling of sequentially-obtained biopsies is a powerful approach to discover putative biomarkers in early clinical trials. The biomarkers discovered in this study still require validation. Nevertheless, it appears that they may be useful to predict therapeutic benefit at the end of the first cycle of the sorafenib and dacarbazine combination. This study also confirmed the feasibility of the genomic strategy based on sequential biopsies in terms of sample size, RNA extraction, and early detection of gene differentially expressed in response to chemotherapy.
MicroRNA is a class of noncoding RNAs able to base pair with complementary messenger RNA sequences, inhibiting their expression. These regulatory molecules play important roles in key cellular processes including cell proliferation, differentiation and response to DNA damage; changes in miRNA expression are a common feature of human cancers. To gain insights into the mechanisms involved in breast cancer progression we conducted a microRNA global expression analysis on a 21T series of cell lines obtained from the same patient during different stages of breast cancer progression. These stages are represented by cell lines derived from normal epithelial (H16N2), atypical ductal hyperplasia (21PT), primary in situ ductal carcinoma (21NT) and pleural effusion of a lung metastasis (21MT-1 and 21MT-2). In a global microRNA expression analysis, miR-205-5p was the only miRNA to display an important downregulation in the metastatic cell lines (21MT-1; 21MT-2) when compared to the non-invasive cells (21PT and 21NT). The lower amounts of miR-205-5p found also correlated with high histological grades biopsies and with higher invasion rates in a Boyden chamber assay. This work pinpoints miR-205-5p as a potential player in breast tumor invasiveness.
Eleven samples of DNA from choriocarcinomas were studied by high resolution CGH-array 244 K. They were studied after histopathological confirmation of the diagnosis, of the androgenic etiology and after a microsatellite marker analysis confirming the absence of contamination of tumor DNA from maternal DNA. Three cell lines, BeWo, JAR, JEG were also studied by this high resolution pangenomic technique. According to aCGH analysis, the de novo choriocarcinomas exhibited simple chromosomal rearrangements or normal profiles. The cell lines showed various and complex chromosomal aberrations. 23 Minimal Critical Regions were defined that allowed us to list the genes that were potentially implicated. Among them, unusually high numbers of microRNA clusters and imprinted genes were observed.
