Abstract 1823: Identification of molecular determinants of vinorelbine resistance in BRAF(V600E) mutated chemorefractory metastatic colorectal cancer patients

Abstract

Abstract Background BRAF(V600E) colon cancers (CCs) are characterized by a distinct gene expression profile when compared to KRAS mutant and KRAS-BRAF double wild type (WT2) CCs. Most importantly, 20% of WT2 CCs are BRAF-like by gene expression profile (1,2). By using a loss of function genetic approach, we previously found that Vinorelbine (VBN) might represent a new therapeutic option for BRAF-like metastatic colorectal cancer (mCRC) patients (3). Recently, in a phase II study, Cremolini et al (4) reported no activity of VBN in BRAFV600E mutated chemorefractory mCRC patients. We hypothesize that the lack of response could be driven by the loss of the BRAF-like signature after several lines of treatment and/or the acquisition of a multidrug resistant, an EMT and/or a hypoxia phenotype. Material and methods We retrospectively collected formalin-fixed-paraffin-embedded (FFPE) tumor tissue of primary tumor or metastatic lesions of mCRC patients enrolled in the Cremolini et al study. In particular, both chemonaive tissue (before the start of any treatment) and chemorefractory tissue (before the start of VBN) were collected to perform gene expression analysis and whole genome sequencing (WGS). Agendia's full genome arrays were used for gene expression analysis and the TrueSeq Nano Dna protocol was used for WGS analysis. In parallel, two independent genome wide CRISPR screens for resistance to VBN were performed in VACO432 CRC cell line by using the Gecko half library A and the Brunello library. Results and conclusions Matched paired samples were available for six out of twenty patients from the Cremolini et al cohort (Female: 0%, Male: 100%, median age at the start of VBN: 53 (26-71), Stage IV: 100%, chemorefractory: 84%). Samples were available for both gene expression and WGS. For WGS, genomic DNA was extracted from peripheral blood mononuclear cell (pbmc) for four patients and from normal colon FFPE tissue for two patients. All samples passed the quality control steps for both gene expression analysis and WGS. Six hits were identified from the CRISPR screens. Comparative genomic and transcriptomic analysis of the patients´ data will be integrated with CRISPR screens results and presented at the meeting.