E-GEOD-8019 - Transcription profiling of mouse small intestine reveals fasting induces a biphasic adaptive metabolic response

Status
Submitted on 5 June 2007, released on 13 May 2009, last updated on 2 May 2014
Organism
Mus musculus
Samples (24)
Array (1)
Protocols (10)
Description
Background; The gut is a major energy consumer, but a comprehensive overview of the adaptive response to fasting is lacking. Gene-expression profiling, pathway analysis, and immunohistochemistry were therefore carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting. Results; Intestinal weight declined to 50% of control, but this loss of tissue mass was distributed proportionally among the gut’s structural components, so that the microarrays’ tissue base remained unaffected. Unsupervised hierarchical clustering of the microarrays revealed that the successive time points separated into distinct branches. Pathway analysis depicted a pronounced, but transient early response that peaked at 12 hours, and a late response that became progressively more pronounced with continued fasting. Early changes in gene expression were compatible with a cellular deficiency in glutamine and metabolic adaptations directed at glutamine conservation, inhibition of pyruvate oxidation, stimulation of glutamate catabolism via aspartate and phosphoenolpyruvate to lactate, and enhanced fatty-acid oxidation and ketone-body synthesis. In addition, the expression of key genes involved in cell cycling and apoptosis was suppressed. At 24 hours of fasting, many of the early adaptive changes abated. Major changes upon continued fasting implied the production of glucose rather than lactate from carbohydrate backbones, a downregulation of fatty-acid oxidation and a very strong downregulation of the electron-transport chain. Cell cycling and apoptosis remained suppressed. Conclusion; The changes in gene expression indicate that the small intestine rapidly looses mass during fasting to generate lactate or glucose and ketone bodies. Meanwhile, intestinal architecture is maintained by downregulation of cell turnover. Experiment Overall Design: Male FVB mice (Charles River, Maastricht, The Netherlands) were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). The animals were kept in metabolic cages to prevent the consumption of beddings and were kept warm with an infrared lamp starting at 24h. Experiment Overall Design: All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The small intestine was removed quickly in such a way that adherent tissue remained behind. It was opened longitudinally, rinsed in phosphate-buffered saline, blotted, weighed, snap-frozen in liquid N2, and stored at -80°C. We opted to use extracts of full-thickness intestine for gene-expression profiling, because the epithelial component of the murine small intestine comprises over 70% of its volume The suitability of this strategy is underscored by a recent microarray study of transporters in the mouse intestine [Anderle P et al., BMC Genomics 2005, 6: 69.]. In addition, isolation of enterocytes is time-consuming and, hence, entails a risk of mRNA degradation, while mucosal scraping harvests villi more efficiently than crypts , whereas many mRNAs are most abundant in the crypts. Experiment Overall Design: Total intestinal RNA was extracted from frozen tissue with guanidiniumthiocyanate [Chomczynski P, Sacchi N: Analytical Biochemistry 1987, 162: 156-159.], followed by cesium-chloride centrifugation [Glisin V, Crkvenjakov R BC: Biochemistry 1974, 13: 2633-2637.] to avoid contamination with mucus. The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA). Microarray-based quantification of 8 mRNAs with a 1.3-9.2-fold change in expression was validated by qPCR, as described [58]. mRNA concentration was calculated using the LinReg program [59]. In the absence of reverse transcriptase, the signal was < 0.1% of that in its presence for each primer pair (not shown). Experiment Overall Design: Microarrays. The 60-mer Mouse Development (22K) Oligo Microarray G4120A (Agilent) was used. Three arrays per experimental condition were used. Per microarray, 20 μg mRNA, pooled from 2 intestines, was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit. Cy5-labeled cDNA produced from RNA pooled from 6 fed animals served as the common reference across all arrays (Figure 1A). Hybridized cDNAs were detected with Agilent’s dual-laser microarray slide scanner. The data were retrieved with Agilent’s Feature Extraction software 6.1.1.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Fasting induces a biphasic adaptive metabolic response in murine small intestine. Milka Sokolović, Diederik Wehkamp, Aleksandar Sokolović, Jacqueline Vermeulen, Lisa A Gilhuijs-Pederson, Rachel I M van Haaften, Yuri Nikolsky, Chris T A Evelo, Antoine H C van Kampen, Theodorus B M Hakvoort, Wouter H Lamers.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-8019.idf.txt
Sample and data relationshipE-GEOD-8019.sdrf.txt
Processed data (1)E-GEOD-8019.processed.1.zip
Array designA-MEXP-1183.adf.txt
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