Multi-scale genomic, transcriptomic and proteomic analysis of colorectal cancer cell lines to identify novel biomarkers (BeadChip)

Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. The objectives of this study were to establish which genes were differentially expressed with respect to treatment sensitivity and relate this to copy number in a panel of 15 CRC cell lines. Copy number variations of the identified genes were assessed in a cohort of colorectal cancers. IC50’s were measured for 5-fluorouracil, oxaliplatin, and BEZ-235, a PI3K/mTOR inhibitor. Cell lines were profiled using array comparative genomic hybridisation, Illumina gene expression analysis, reverse phase protein arrays, and targeted sequencing of KRAS hotspot mutations. Three sets of RNA samples were prepared for Illumina® Whole Genome Gene Expression Profiling, where 48,804 transcripts per sample were generated. The three sets consisted of two sets of biological replicates and one set of technical replicates. All the RNA samples were diluted to a concentration of 500ng/11µl. The Illumina® TotalPrepTM RNA Amplification Kit (Ambion®, cat. no. AMIL1791) was used to generate biotinylated, amplified RNA for hybridization with the Illumina® Human HT-12 v4.0 BeadChip.