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Non-invasive detection of molecular biomarkers in subjects with a history of insulin resistance and colorectal adenomas

ABSTRACT: We have developed novel molecular methodology utilizing a stool sample, which contains intact sloughed colon cells, in order to quantify colonic gene expression profiles. In this study, our goal was to identify diagnostic gene sets (combinations) for the noninvasive classification of different phenotypes. For this purpose, the effects of a legume enriched, low glycemic index, high fermentable fiber diet was evaluated in subjects with four possible combinations of risk factors, including insulin resistance (IR) and a history of adenomatous polyps. In a randomized crossover design controlled feeding study each participant (a total of 23, 5-12/group) consumed the experimental diet (1.5 cups of cooked dry beans) and a control diet (isocaloric average American diet) for 4 wk with a 3 wk washout period between diets. Using prior biological knowledge, the complexity of feature selection was reduced in order to perform an exhaustive search on all allowable feature (gene) sets of size 3, and among these, 27 had (unbiased) error estimates of 0.15 or less. Linear discriminant analysis (LDA) was successfully used to identify the best single genes and two- to three-gene combinations for distinguishing subjects with IR, a history of polyps or exposure to a chemoprotective legume-rich diet. These results support our premise that gene products (RNA) isolated from stool have diagnostic value in terms of assessing colon cancer risk. Keywords: Exfoliated cells, legumes, insulin resistance, polyps

ORGANISM(S): Homo sapiens

PROVIDER: GSE14797 | GEO | 2010/02/11

SECONDARY ACCESSION(S): PRJNA112083

REPOSITORIES: GEO

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