Abstract A7: Combined copy number and expression analysis of formalin fixed-paraffin embedded (FFPE) tumours

Abstract

Abstract Introduction: FFPE tissues are a valuable source of tumour material for translational research that has thus far been under-used. But progress in technology has allowed the analysis of genome wide copy number and expression changes using small amounts of degraded DNA/RNA extracted from FFPE tissues. We used two platforms: molecular inversion probes assay (MIP, Affymetrix) and c-DNA mediated Annealing Selection extension and Ligation assay (DASL, Illumina™) for analysis of RNA/DNA extracted from routine core biopsies from a clinical trial to identify molecular markers of response or resistance to chemotherapy. Method: FFPE diagnostic core biopsies of 63 patients treated with neoadjuvant adriamycin/cyclophosphamide followed by taxotere in a clinical study were used. MIP assay with 50K SNP panel was used for copy number analysis (CNA). DASL assay assessed expression of 502 genes using three probes per gene. Results: RNA and DNA of good quality were extracted from 52/63 (82%) and 46/63 (73%) core biopsy samples, respectively. Gene expression profiling was carried out using the DASL assay and there were good correlations with IHC for ER, PR and HER-2 with area under the curve of 0.95, 0.90 and 0.96 respectively, following ROC analysis for the best transcripts. Differential expression analysis between ER+ vs. ER- cancers showed that ESR1, TFF1 and LAF4 are significantly over-expressed in ER + cancers (p<0.001), while analysis of pathological complete responders vs. non responders showed over expression of CXCL9, ARHA, ARHGDIB, BCL3, ERBB2, BMYB and TGFBI among responders (p<0.2). CNA showed well described aberrations in breast cancer such as high probability of gains in 1q, 8q, 11q and 20q and loss in 4q, 12q, 13q, 18q and 22q (probability of alteration ≥0.35). Samples with pathological complete response had high probability of gains in 1q (55%), 8q (40%), 17q (40%) and losses in 8p (40%) and 13q (70%). 5/46 samples were HER-2 3+ with IHC and all showed amplification around the 17q locus. Conclusions: Reliable copy number and expression data can be generated using these assays from FFPE core biopsy samples. Role of LAF4 as an oestrogen regulated gene and roles of CXCL9, ARHA and ARHGDIB as markers of response to chemotherapy should be further investigated. Citation Information: Clin Cancer Res 2010;16(7 Suppl):A7