Predictive Biomarkers

Four of ANGIOPREDICT's eight scientific work packages are dedicated to analyzing retrospective and prospective samples to identify and validate predictive biomarkers for responsiveness to combination bvz therapy in mCRC patients.

Work Package 4: Germline SNP Profiling & Target Validation

Single nucleotide polymorphisms (SNPs) will be assessed to determine if they are correlated with outcome following combination bvz therapy in mCRC. Systematic approaches will cover several hundred genetic variants using small amounts of DNA from retrospective samples (WP1) employing Illumina SNP array technology (VIB). SNPs will be classed as prognostic or predictive. The most relevant predictive SNPs will be validated in prospectively collected blood samples from the AC-ANGIOPREDICT trial (WP3). EPI will direct plans for commercialization of any findings with potential for in-licensing patented SNP germline markers for future development as a blood-based predictive test.

Work Package 5: Somatic Mutation Analysis & Validation

Somatic mutations in all known expressed genes will be assessed to determine if they are correlated with outcome following combination bvz therapy in mCRC. DNA sequence analysis of retrospective primary tumor samples from mCRC patients (WP1) treated with bvz will be carried out (UCD). Candidate mutations will be validated by Sequenome MassArray (RCSI) in both tumor and normal DNA from specific patients and in clinical samples obtained from the AC-ANGIOPREDICT trial (WP3). VIB and VUMC will also determine all somatic copy number alterations occurring in mCRC tumors treated with combination bvz therapy. Predictive and recurrent amplifications and/or deletions will be validated in prospectively collected clinical samples obtained from the AC-ANGIOPREDICT trial (WP3).

Work Package 6: DNA Methylation Based Predictive Models

Genome wide DNA methylation profiling will be performed from selected tumor endothelial cells (TEC) and isolated tumor cells (TC) populations using Differential Methylation Hybridization (DMH) array technology on retrospectively collected frozen samples (WP1) and correlated to clinical outcome. DNA will be hybridized to EPI's proprietary microarray in order to identify DNA methylation signatures that may serve as a predictive biomarker of drug response. Development of a technically reproducible DNA methylation companion diagnostic that may be used to detect predictive signatures will focus on enabling routine analysis in a standard molecular diagnostic laboratory. The initial focus will be on the development of a tissue based assay but prospective plasma samples from the AC-ANGIOPREDICT trial will facilitate feasibility studies for a blood based predictive genomic biomarker assay.

Work Package 7: Predictive Pharmacogenomic Expression Methods

Predictive pharmacogenomic gene expression signatures in patients who respond or do not respond to combination bvz treatment will be identified in this work package. Linking gene expression analysis (WP5) with results from mutation analysis methylation status (WP6), presence of SNPs (WP4) and response to bvz will help to identify signatures or single biomarkers that are predictive for response. Candidate predictive gene signatures will be verified on retrospectively collected samples (WP2) using In Situ Hybridization by ONCO. The utility of putative multi-gene signatures will be then assessed using prospectively collected materials from the AC-ANGIOPREDICT trial (WP3). In parallel, ONCO will optimize an RT-PCR based companion diagnostic assay to accelerate translation into a commercial product.