Genome-wide transcriptomic profiling of oxaliplatin response

Oxaliplatin (OXA) is a member of the family of Pt-containing chemotherapeutic agents that also include cisplatin (CDDP) and carboplatin. OXA is distinguished from these two older drugs by its different spectrum of activity both in preclinical models and in clinical trials. It is the only platinum analogue to have activity in colon cancer, a disease for which this drug has now become a mainstay of therapy. It mainly forms intrastrand adducts between two adjacent guanine residues or guanine and adenine, disrupting DNA replication and transcription. OXA has been reported to be involved in the Nucleotide Excision Repair Pathway (NER), p38 kinase activation, PI3K/AKT pathway and caspase cascade activation through the apoptotic intrinsic pathway. However, not all colon cancer cells show the same sensitivity to OXA. In this study we have compared the changes in RNA expression profiles of colon cancer cell lines with different sensitivity to OXA, determined by IC50. The goal of our experiment was to identify genes that are differentially activated or inhibited commparing OXA sensitive and OXA resistent colon cancer cell lines upon OXA treatment. We treated 6 OXA-sensitive colorectal cancer cell lines: LoVo, LS513, SW1116, SW1417, SW48 and LS174TT and 8 resistant cell lines: LS411NN, HCT116, HCT15, SW480, SW948, CACO2, DLD1 and HT29, to identify genes and pathways that could play a role in OXA sensitivity. The experimental design used was “RNA-Reference” and “Dye-Swap”. Each cell line was analyzed in duplicate with RNA reference (Stratagene) as reference sample and labeled each biological condition once by Cy3 and once by Cy5. We took the average of the dye-swapped arrays to cancel the dye effect on any particular gene. In total we used 56 slides.