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Proteomics analysis of bile acids modulation on rat colonic expression of water, electrolyte and drug transporters

ABSTRACT: Bile acid diarrhoea is a chronic condition with increased delivery of bile acids to the colon causing diarrhoea. In this study we used a rodent model of bile acid malabsorption to investigate the general impact on increased levels of bile acids on mRNA- and protein-expression in colon epithelial cells. Twelve male Wistar Munich rats were housed in metabolic cages and fed control or bile acid-mixed (1% w/w) diets for ten days. After euthanasia, colonic epithelial cells were isolated using Ca2+ chelation and processed for mass spectrometry-based proteomics to quantify changes in protein expressions.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Epithelial Cell

SUBMITTER: Qi Wu

LAB HEAD: Hanne B. Møller

PROVIDER: PXD025915 | Pride | 2021-11-03

REPOSITORIES: Pride

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Publications

A systems-level analysis of bile acids effects on rat colon epithelial cells.

Yde Jonathan J Wu Qi Q Borg Johan F JF Fenton Robert A RA Moeller Hanne B HB

American journal of physiology. Gastrointestinal and liver physiology 20211013 1

Bile acid diarrhea 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 diarrhea, systems-level analyses were used on a rat bile acid diarrhea model. Twelve male Wistar Munich rats, housed in metabolic cages, were fed either control or bile acid-mixed (1% wt/wt) diets for 10 days. Food intake, water intake, urine volume, body weight, and fecal output were monitored daily. Afte ...[more]

PMID: 34643455

Similar Datasets

A systems-level analysis of bile acids effects on rat colon epithelial cells

Project description: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.

2024-05-10 | GSE174249 | GEO

The Pathogenesis of Chronic Diarrhoea After Treatment for Cancer in Cecum and the Ascending Colon

Project description:Many patients suffer from chronic diarrhoea after surgical treatment for cancer in the right side of the colon. The investigators’ main hypothesis is that colon cancer patients with chronic diarrhoea have a higher risk of bile acid malabsorption compared with colon cancer patients without diarrhoea. The investigators also expect that a part of the cases of bile acid malabsorption is caused by underlying bacterial overgrowth in the small bowel. The investigators assume that patients with severe bile acid malabsorption have a lower value of FGF19 in the blood compared to patients with moderate or none bile acid malabsorption. Furthermore, it is assumed that patients with chronic diarrhoea and documented bile acid malabsorption after surgical treatment for right-sided colon cancer will get improved bowel function when treated with a bile acid binder, or antibiotics in case of bacterial overgrowth.

| 2309640 | ecrin-mdr-crc

Project description:Gut microbiota in Bile acid Diarrhoea

| PRJNA941862 | ENA

Effects of Lin28a overexpression on gene expression changes during culturing neural stem cells (NSCs) derived from mouse embryonic ventral midbrain (VM)

Project description:Purpose: we want to see gene expression changes during in vitro expansion of VM-derived NSCs (VM-NSCs) with cell passges in the absence or presence of Lin28a overexpression. changes upon Lin28 overexpression in P1 and P3 stages of Neural stem cells. RNA-seq, sRNA-seq, and Polysome-seq with/without Lin28 overexpression in P1 and P3 stages of Neural stem cells.

2016-08-11 | E-GEOD-77851 | biostudies-arrayexpress

Quantitative label-based canine faecal proteomics

Project description:In small animals, diarrhoea is a regular presentation, the aetiology of which can be varied, from an isolated self-limiting event to more serious episodes requiring symptomatic and supportive treatment. Chronic diarrhoea, defined as diarrhoea lasting longer than 3 weeks, is a relatively common problem often prompting referral for more detailed investigation. Although the potential cause of chronic diarrhoea includes chronic intestinal parasitism and alimentary neoplasia (specifically lymphoma), the majority of these dogs will be diagnosed with idiopathic canine chronic enteropathy (CCE), previously referred to as idiopathic inflammatory bowel disease (IBD). Of those cases diagnosed with CCE, further subdivision based on response to treatment trials leads to a final diagnosis of antibiotic responsive diarrhoea (ARD), food responsive diarrhoea (FRD) or idiopathic inflammatory bowl disease (IBD). The aim of this study was to compare the proteomes of faeces of dogs with chronic enteropathies and a population of healthy dogs, and furthermore to identifying proteins that might be useful in distinguishing FRD from ARD from IBD.

2022-08-29 | PXD017454 | Pride

Proteomics defines plasma biomarkers for the early diagnosis of biliary atresia

Project description:Early diagnosis of biliary atresia (BA) is crucial for improving the chances of survival and preserving the liver function of children with BA. To explore potential biomarkers for early diagnosis of BA with other non-BA jaundice cases, we performed proteomic analysis with data-independent acquisition (DIA) and parallel reaction monitoring (PRM). With this approach we were able to detect and validate differential protein expression in plasma of patients. Bioinformatics analysis revealed the enrichment biological processes, characteristic of BA by identifying differential expression of specific proteins of which with 10 were up- and 23 down-regulated. Signaling pathway analysis demonstrated changes in protein expression associated with an alteration in immunoglobins levels, which is indicative immune dysfunction in BA. When polymeric immunoglobulin receptor (pIgR) expression was combined with an immunoglobulin lambda variable chain (IGL c2225_light_IGLV1-47_IGLJ2), revealed by machine learning, they provided a useful early diagnostic model for BA, which had a sensitivity of 0.8, specificity of 1, accuracy of 0.89, and AUC value of 0.944. Our study not only identified a possible effective plasma biomarker for the early diagnosis of BA but may also help to further elucidate the underlying mechanisms of BA.

2024-06-22 | PXD048938 | Pride

Comprehensive expression analysis of primary hepatocytes under four different culture conditions

Project description:Primary hepatocytes have been widely explored as cell sources for the study of in vitro drug metabolism and pharmacokinetics (DMPK). Aiming toward establishing an in vitro drug screening method, the current study illustrated a comprehensive increase in the DMPK-related gene expression of nanopillar (NP)-cultured 3D-spheroid. To examine the expressional changes in DMPK-related genes under four different conditions, namely, NP-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes, genome-wide gene-expression analysis using a DNA microarray was performed. Among the DMPK-related genes, cytochrome P450, UDP-glucuronosyltransferase, and transporter genes were focused on. Principal component analysis showed that the global gene expression profile in sample from NP culture is closer to that from freshly isolated hepatocytes than that from SW culture. The expressions of almost all Cyp 1 to 3 and Ugt genes of NP-cultured 3-D spheroid were higher than those of ML and SW. The expression of Abcc2 gene whose translation product has a critical role in excretion of metabolized bile acids in hepatocyte to bile canaliculi was three times higher in NP than in ML. From these results, 3-D spheroid formed by the NP culture was suggested to possess higher ability of metabolism and excretion than conventional 2-D monolayer culture. The NP culture has a potential as an alternative culturing technique for evaluating metabolism and toxicity toward the development of new drugs. Gene expression in rat hepatocyte was measured under four different conditions, namely, Nanopillar (NP)-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes. Three independent experiments were performed at 95 hours of post-seeding.

2015-06-25 | E-GEOD-38950 | biostudies-arrayexpress

IGR_PBI_SOCS1_GE_JP

Project description:Suppressor of cytokine signaling (SOCS1) is an inducible negative regulator of cytokine signaling. SOCS1 is expressed in normal colonic epithelium and colon adenocarcinomas. However, the levels of SOCS1 decreased during progression of colon adenocarcinomas, the lowest level being found in the more aggressive stage and least differentiated carcinomas. The restoration of SOCS1 in a colon cancer cell line induced expression of E-cadherin associated with disappearance of the mesenchymal form of the p120ctn. SOCS1 expression is sufficient to revert many characteristics of EMT. This reversion is dependent on the regulation of expression of the transcription factor ZEB1, both at transcriptional and translational levels. Furthermore, miRNA profiling indicates that SOCS1 also upregulates the expression of the mir-200 family of microRNAs, which can promote the mesenchymal-epithelial transition and reduce tumor cell migration. Expression of SOCS1 within the colon carcinoma cell lines dramatically reduced the invasive properties of the cells in vitro. This property was also observed in mice inoculated intracardially with SW620 cells where SOCS1 expression not only reduced the number of animals bearing metastases. Thus, SOCS1 up-regulates expression of E-cadherin to reduce colon cancer cells invasive properties. This pathway could be associated with colorectal cancer survival by reducing the capacity of generating metastases.This project concern 2 replicates in dye-swap of SW620 cells with and without transfected SOCS1 on a 244K custom human genomic expression microarray.

2014-05-01 | E-MTAB-1742 | biostudies-arrayexpress

The Microbial Metabolite Deoxycholic Acid Modulates Cholesterol Metabolism in the Germ-Free Mouse

Project description:Deoxycholic acid (DCA) is a secondary bile acid produced by a small number of commensal species of bacteria present in the mammalian gut. Elevated DCA concentration correlates with disease states including colon cancer and cholesterol gallstones, but the associated mechanisms are not fully understood. Both primary and secondary bile acids are also capable of affecting gene expression through nuclear receptors such as FXR. To better understand the impact of a commensal-derived secondary bile acid on host metabolism we fed DCA to germ-free (GF) mice, which normally lack DCA, and compared the hepatic transcriptomes of bile acid fed GF mice to GF mice receiving a control diet, as well as to those of conventionally housed control animals. Interestingly, the feeding of DCA to GF mice, but not the feeding of cholic acid (CA) from which DCA is derived, results in an up-regulation of genes of cholesterol biosynthetic pathways. GF mice normally have elevated hepatic cholesterol compared to conventionally housed mice. Despite increase in the expression of cholesterol biosynthetic genes, the DCA fed GF mice showed a markedly decreased level of hepatic cholesterol equivalent to the hepatic cholesterol concentration of conventionally colonized animals. Total cholesterol in the serum was unaffected by DCA, but there was a decrease in the HDL lipoprotein fraction as well as an increase in the non-HDL lipoprotein fraction of the serum cholesterol. DCA, but not CA, is sufficient to modulate host lipoprotein metabolism. Taken together, these results suggests that a minor component of the gut microbiome has a significant impact on cholesterol homeostasis through secondary metabolism of bile acids and suggests a possible therapeutic intervention route through the microbial metabolic pathways. two mouse strains, three diets, one time point

2015-01-08 | E-GEOD-34730 | biostudies-arrayexpress

Clariom S human microarray HCT116 tumour suppressor overexpression

Project description:overexpression of tumour suppressor ZAR1 in HCT116 (HCT116 wt and HCT116 delp53) colon carcinoma cell line (EYFPemtpy and ZAR1EYFP), sorted by Aria for fluorescent cells, RNA isolation

2020-08-27 | E-MTAB-8292 | biostudies-arrayexpress

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