Meta-analysis of temporal intestinal gene expression data to generate reference profiles: VDI-10

Research output: Book/ReportReportProfessional

Abstract

Gene expression is measured because it reflects the status of a certain tissue in the host. Here, wetargeted the jejunum, the second part of the small intestine, because of the importance of the smallintestine for nutrient uptake and immune surveillance. Immediately after birth, the intestine rapidlydevelops morphologically, functionally, and immunologically. We acquired different transcriptomic datasetsfrom literature measuring gene expression at different time-points (age) to perform a metaanalysis.In this meta-analysis, genes were grouped into 16 clusters according to their gene expressionprofiles over time, using data from the control animals of all studies. Within these reference profiles(clusters), we investigated to what extent genes contribute to similar biological processes. From thisfunctional analysis we observed that the different temporal profiles (clusters) had different dominantprocesses, such as immune related processes, or barrier function. Subsequently, we superimposed transcriptomicsdata of piglets of the ‘dietary intervention groups’ of four of the used studies, in which thepiglets themselves, or the sow that farrowed them, had been administered either zinc-oxide, amoxicillin,or medium chain fatty acids). In this way we could investigate which temporal profiles (and which biologicalprocesses) were modulated by the interventions. Interestingly, not all 16 temporal profiles weremodulated. In conclusion, we showed that it is possible to re-use (publicly available) transcriptomicsdata and produce temporal reference gene expression profiles with overexpression of genes representingspecific biological processes. Subsequently, by superimposing gene expression data from (dietary)intervention studies we observed deviations from some of these reference profile(s). The latter suggeststhat it may be possible to modulate intestinal processes in a beneficial way.
Original languageEnglish
Place of PublicationWageningen
PublisherWageningen Livestock Research
Number of pages20
DOIs
Publication statusPublished - 2017

Publication series

NameWageningen Livestock Research rapport
No.1058

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