title: The effect of food intake on gene expression in human peripheral blood.
abstract: Human gene expression traits have been shown to be dependent on gender, age and time of day in blood and other tissues. However, other factors that may impact gene expression have not been systematically explored. For example, in studies linking blood gene expression to obesity related traits, whether the fasted or fed state will be the most informative is an open question. Here, we employed a two-arm cross-over design to perform a genome-wide survey of gene expression in human peripheral blood to address explicitly this type of question. We were able to distinguish expression changes due to individual and time-specific effects from those due to food intake. We demonstrate that the transcriptional response to food intake is robust by constructing a classifier from the gene expression traits with >90% accuracy classifying individuals as being in the fasted or fed state. Gene expression traits that were best able to discriminate the fasted and fed states were more heritable and achieved greater coherence with respect to pathways associated with metabolic traits. The connectivity structure among gene expression traits was explored in the context of coexpression networks. Changes in the connectivity structure were observed between the fasted and fed states. We demonstrate that differential expression and differential connectivity are two complementary ways to characterize changes between fasted and fed states. Both gene sets were significantly enriched for genes associated with obesity related traits. Our results suggest that the pair of fasted/fed blood expression profiles provide more comprehensive information about an individual's metabolic states.
authors.affiliation: Rosetta Inpharmatics, LLC, Merck & Co., Inc., Seattle, WA 98109, USA.
authors.forename: Amy S
authors.initials: AS
authors.lastname: Leonardson
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Chen
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: John R
authors.initials: JR
authors.lastname: Lamb
authors.forename: Marc
authors.initials: M
authors.lastname: Reitman
authors.forename: Valur
authors.initials: V
authors.lastname: Emilsson
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
mesh_terms: D016000:Cluster Analysis; D005215:Fasting / Q000097:blood*; D005247:Feeding Behavior / Q000502:physiology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics; D006801:Humans; D019655:Quantitative Trait, Heritable; D012372:ROC Curve; D013997:Time Factors