A Gene Expression Profile of Non-Neoplastic Colonic Sigmoid Epithelium
WD Mojica, L Stein, J Luce, LA Hawthorn. Univ @ Buffalo, Buffalo, NY; RPCI, Buffalo, NY; Medical College of Georgia, Augusta, GA
Background: A rational approach to biomarker discovery involves the identification of differentially expressed genes between diseased and non-diseased cells of the same lineage. This is particularly true for colon cancer which demonstrates a molecular step-wise progression from normal to cancer. To date, an expression profile completely representative of non-neoplastic colonic epithelial cells (NNCEC) has not been reported. Because of an inability to maintain NNCEC in culture, expression profiles have come from various sources. These results may be biased due to several factors: tissue sections because of cellular heterogeneity; FFPE material from degradation; and colon cancer cell lines thought to be differentiating to NNCEC due to growth in an artificial environment and genotypic drift. Herein is presented the expression profile data from unfixed, enriched NNCEC with high molecular integrity run on an high density expression array.
Design: NNCEC were procured by exfoliation and enrichment from 10 separate patients undergoing segmental resection of the sigmoid for diverticular disease. Ex vivo bias was minimized by keeping the time between extirpation and placement of cells into buffer under 10 minutes. A highly enriched population of NNCEC was obtained through the dissolution of mucus, lysis of rbc's and the use of immunomagnetic beads. Extracted RNA was run on the Human Exon 1.0 ST Array to evaluate whole transcript and alternative splicing events. Principal component analysis (PCA) was performed on the NNCEC data and compared to colorectal cancer (CRC) data. Differentially expressed genes were identified through the comparison with publicly available CRC expression data.
Results: There were 4302 alternative splicing events in the exon array data. The NNCEC samples were distincly segregated from the CRC data by PCA. A total of 3828 differentially expressed genes were identified between the NNCEC and the publicly available colon cancer data with 2505 genes upregulated and 321 downregulated in the CRC data relative to the NNCEC.
Conclusions: A baseline of knowledge is needed before any comparative analysis can be performed. The absence of such a baseline may lead to errant conclusions particularly if the sample assayed possesed an inherent bias. The rapid acquisition of unfixed, enriched cells means a reproducible baseline expression profile can be established for NNCEC, the proverbial starting point from which to assess pathology in the sigmoid colon.
Category: Special Category for 2009 - Pan-genomic/Pan-proteomic approaches to Cancer
Tuesday, March 10, 2009 9:30 AM
Poster Session III # 246, Tuesday Morning