An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors
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PROVIDER: PRJNA590538 | ENA |
REPOSITORIES: ENA
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Project description:Intestinal epithelial organoids established from resected gut tissue have become a widely used research tool. However, it remains unclear how environmental cues and other sources of variation before, during and after establishment impact on organoid properties. Divergent microbiota composition in separately held mouse lines has been identified as a confounding factor in murine in vivo studies. To probe the effect of donor microbiota on organoids, we analyzed the proteomes and transcriptomes of primary organoid cultures established from colonized and germ-free mice, and further compared them to their tissue of origin and to commonly used cell lines. The long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts. This signature, which closely mimicked expression patterns in the gut epithelium, included high levels of the inflammasome scaffold protein ASC in organoids which was lacking in commonly used cell lines. Mining of the transcriptome dataset uncovered similar high expression of also other inflammasome components, including Naip1-6, Nlrc4, and Caspase-1 in all organoids compared to the reference cell lines. Taken together, these results reveal a robust global expression pattern in organoids established from colonized and germ-free animals and suggest that organoids represent a more suitable culture model than immortalized cell lines for studies of intestinal epithelial inflammasomes.
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Project description:The surface proteins of the probiotic Propionibacterium freudenreichii were inventoried by an integrative approach that combines in silico protein localization prediction, surface protein extraction, shaving and fluorescent CyDye labeling. Proteins that were extracted and/or shaved and/or labeled were identified by nano-LC-MS/MS following trypsinolysis. This method's combination allowed to confirm detection of true surface proteins involved in host/probiotic interactions. The data, supplied in this article, are related to the research article entitled "Surface proteins of P. freudenreichii are involved in its anti-inflammatory properties" (Le Maréchal et al., 2014 [6]).
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Project description:Saliva aids in the predigestion of food and perception of taste. It helps to maintain the integrity of the mineralized tooth and epithelial surfaces in the mouth, and shields the oro-digestive tract from environmental hazards and invading pathogens. Although salivary glands and saliva fluid are biologically and functionally inseparable, they have thus far been investigated as separate entities. To bridge this gap, we performed an integrative analysis of the transcriptome of 27 samples collected from the major human adult and fetal major salivary glands - submandibular, sublingual, and parotid - along with mass-spectrometry-based saliva proteome data and immunohistochemical localization in glandular tissue. Our results suggest that functional maturation at the transcriptome level occurs late in gland development, and is driven mainly by the transcription of genes that code for secreted saliva proteins. We further provide evidence that protein dosage of the most abundant salivary proteins secreted by the salivary glands is predominantly regulated at the transcriptome level. Finally, we demonstrate distinct transcriptomic profiles of each major salivary gland type that reveal functional specialization and will aid in future clinical analyses. Our study provides the hitherto most comprehensive RNAseq dataset of healthy salivary glands in humans, thus establishing a robust framework for deeper studies of saliva and salivary gland biology, development, and evolution, ultimately paving the way for better understanding the importance of these craniofacial secretory organs in health and their malfunctions in disease.
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2012-07-05 | E-GEOD-31368 | biostudies-arrayexpress
Project description:Background<br>Vitellogenin is a well established biomarker for estrogenic exposure in fish. However, effects on gonadal differentiation at concentrations of estrogen not sufficient to give rise to a measurable vitellogenin response suggest that more sensitive biomarkers would be useful. Induction of zona pellucida genes may be more sensitive but their specificities are not as clear. The objective of this study was to find additional sensitive and robust candidate biomarkers of estrogenic exposure.<br>Results<br>Hepatic mRNA expression profiles were characterized in juvenile rainbow trout exposed to a measured concentration of 0.87 and 10ng ethinylestradiol/L using a salmonid cDNA microarray. The higher concentration was used to guide the subsequent identification of generally more subtle responses at the low concentration not sufficient to induce vitellogenin. A meta-analysis was performed with data from the present study and three similar microarray studies using different fish species and platforms. Within the generated list of presumably robust responses, several well-known estrogen-regulated genes were identified. Two genes, confirmed by quantitative RT-PCR (qPCR), fulfilled both the criteria of high sensitivity and robustness; the induction of the genes encoding zona pellucida protein 3 and a nucleoside diphosphate kinase (nm23).<br>Conclusions<br>The cross-species, cross-platform meta-analysis correctly identified several robust responses. This adds confidence to our approach used for identifying candidate biomarkers. Specifically, we propose that analyses of nm23 together with zona pellucida genes may increase the possibilities to detect an exposure to low levels of estrogenic compounds in fish.<br>
2007-07-24 | E-MEXP-1149 | biostudies-arrayexpress
Project description:To elucidate the molecular basis of early gastric cancer (EGC), the genome-wide expression pattern of cancer and normal tissues from 27 patients were analyzed by a microarray-based method. Using an integrative systematic bioinformatics approach, we classified the differentially expressed genes in EGC. Interestingly, the more highly expressed genes in EGC exhibited the most significant correlation with cell migration and metastasis. This implies that, even at the early stage of gastric cancer, the molecular properties usually observed in late-stage cancer are already present. Furthermore, we have found a novel association between the expression pattern and molecular pathways of EGC and estrogen receptor α (ERα)-negative breast cancer through cross-experimental analysis. These results provide new insights into the biological properties of EGC, as well as yielding useful basic data for the study of molecular mechanisms of EGC carcinogenesis.
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Project description:Intestinal epithelial organoids established from gut tissue have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation before, during and after establishment confound organoid properties, and how these properties relate to the original tissue. While environmental influences cannot be easily addressed in human organoids, mice offer a controlled assay-system. Here, we probed the effect of donor microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analysed the proteomes and transcriptomes of primary organoid cultures established from two colonised and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, the long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4 and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-ICc12 or mouse embryonic fibroblasts. Taken together, these results reveal that the donor microbiota has little effect on the organoid phenotype and suggest that organoids represent a more suitable culture model than immortalised cell lines, in particular for studies of intestinal epithelial inflammasomes.
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