GSE174249
A systems-level analysis of bile acids effects on rat colon epithelial cells
Bile acid diarrhoea is a chronic condition caused by increased delivery of bile acids to the colon. The underlying mechanisms remain to be elucidated. To investigate genes involved in bile acid diarrhoea, systems-level analyses were employed on a rat bile acid diarrhoea model. Twelve male Wistar Munich rats, housed in metabolic cages, were fed either control or bile acid-mixed (1% w/w) diets for ten days. Food intake, water intake, urine volume, bodyweight and faecal output were monitored daily. After euthanasia, colonic epithelial cells were isolated using calcium-chelation and processed for systems-level analyses, i.e. RNA-sequencing transcriptomics and mass spectrometry proteomics. Bile acid-fed rats suffered diarrhoea, indicated by increased drinking, faeces weight and faecal water content compared with control rats. Urine output was unchanged. With bile acid-feeding, RNA-sequencing revealed 204 increased and 401 decreased mRNAs; mass spectrometry 183 increased and 111 decreased proteins. Among the altered genes were genes associated with electrolyte and water transport (including Slc12a7, Clca4 and Aqp3) and genes associated with bile acid transport (Slc2b1, Abcg2, Slc51a, Slc51b and Fabps). Correlation analysis showed a significant positive correlation (Pearson's r=0.28) between changes in mRNA-expression and changes in protein-expression. However, caution must be exercised in making a direct correlation between experimentally determined transcriptomes and proteomes. Genes associated with bile acid transport responded to bile acid-feeding, suggesting that colonic bile acid transport occur by regulated protein facilitated mechanisms rather than passive diffusion. In addition, the study provides annotated rat colonic epithelial cell transcriptome and proteome with response to bile acid-feeding. Overall design: Twelve male Wistar Munich rats were housed in single-animal metabolic cages (Techniplast) with ad libitum access to water and standard rodent chow (cat. no. 1321, Altromin). For an initial three days, the rats were acclimatized to the metabolic cages with ad libitum access to water and standard rodent chow. Subsequently, six rats were switched to standard rodent chow mixed with 1% w/w sodium cholate (Sigma Aldrich). After 10 days on the different diets rats were euthanized by cervical dislocation, their abdomens opened and the colons were dissected out and colonic epithelial cells (CECs) were processed for RNA sequencing. Purified total RNA from distal colon CECs from the five sodium cholate treated rats with highest RNA concentration in the extract and from the five controls with highest RNA concentration in the extract was selected for sequencing. Preparation of strand-specific cDNA libraries, RNA selection using polyA purification and single channel RNA sequencing was performed by Eurofins Genomics (Germany) using HiSeq SBS Kit v4 on a HiSeq 2500 (Illumina). BWA-MEM version 0.7.12-r1039 was used to map RNA reads to reference sequences (Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2[q-bio.GN]). Normalization of reads was performed using Trimmed Mean of M values (TMM) normalization method with the edgeR-package version 3.16.2 in R. Gene expression profiling was performed and differential expression analysis was performed. Inclusion criteria included a false discovery rate (FDR) of less than 1% as recommended by the company. A fold change of more than 2 was used as the cut off value.