Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease

BMC Genomics

Research Article

Wilfrido Mojica¹  Lesleyann Hawthorn² 

[1] Department of Pathology, University at Buffalo, SUNY, Buffalo, NY, USA;Molecular Oncology Program, Medical College of Georgia Cancer Center, Augusta, GA, USA;

关键词: Alternative Splice;    Ingenuity Pathway Analysis;    Canonical Pathway;    Colonic Epithelial Cell;    Alternative Splice Event;   

DOI  :  10.1186/1471-2164-11-5

 received in 2009-06-10, accepted in 2010-01-04,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundStudies using microarray analysis of colorectal cancer have been generally beleaguered by the lack of a normal cell population of the same lineage as the tumor cell. One of the main objectives of this study was to generate a reference gene expression data set for normal colonic epithelium which can be used in comparisons with diseased tissues, as well as to provide a dataset that could be used as a baseline for studies in alternative splicing.ResultsWe present a dependable expression reference data set for non-neoplastic colonic epithelial cells. An enriched population of fresh colon epithelial cells were obtained from non-neoplastic, colectomy specimens and analyzed using Affymetrix GeneChip EXON 1.0 ST arrays. For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and matched normal colon data. This analysis allowed an assessment of global gene expression alterations and demonstrated that adjacent normal tissues, with a high degree of cellular heterogeneity, are not always representative of normal cells for comparison to tumors which arise from the colon epithelium. We also examined alternative splicing events in tumors compared to normal colon epithelial cells.ConclusionsThe findings from this study represent the first comprehensive expression profile for non-neoplastic colonic epithelial cells reported. Our analysis of splice variants illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data. It is projected that the contribution of this set of data derived from pure colonic epithelial cells will enhance studies in colon-related disease and offer a vital baseline for studies aimed at elucidating the mechanisms of alternative splicing.

【 授权许可】

CC BY   
© Mojica and Hawthorn; licensee BioMed Central Ltd. 2010