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Mach N, Berri M, Esquerré D, Chevaleyre C, Lemonnier G, Billon Y, Lepage P, Oswald IP, Doré J, Rogel-Gaillard C, Estellé J. Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing. PLoS One 2014; 9:e88515. [PMID: 24533095 PMCID: PMC3922923 DOI: 10.1371/journal.pone.0088515] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/07/2014] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.
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Affiliation(s)
- Núria Mach
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
- * E-mail:
| | - Mustapha Berri
- UMR1282 ISP, INRA, Nouzilly, France
- UMR1282 ISP, Université de Tours, Tours, France
| | - Diane Esquerré
- UMR444 LGC-Plateforme GET, INRA, Castanet-Tolosan, France
| | - Claire Chevaleyre
- UMR1282 ISP, INRA, Nouzilly, France
- UMR1282 ISP, Université de Tours, Tours, France
| | - Gaëtan Lemonnier
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
| | | | - Patricia Lepage
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
| | - Isabelle P. Oswald
- UMR1331 TOXALIM, INRA, Toulouse, France
- UMR1331 TOXALIM-INP, Université de Toulouse III, Toulouse, France
| | - Joël Doré
- UMR1319 MICALIS, INRA, Jouy-en-Josas, France
- UMR1319 MICALIS, AgroParisTech, Jouy-en-Josas, France
| | - Claire Rogel-Gaillard
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
| | - Jordi Estellé
- UMR1313 Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Jouy-en-Josas, France
- DSV/iRCM/SREIT/LREG, CEA, Jouy-en-Josas, France
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Zhang X, Jaramillo M, Singh S, Kumta P, Banerjee I. Analysis of regulatory network involved in mechanical induction of embryonic stem cell differentiation. PLoS One 2012; 7:e35700. [PMID: 22558203 PMCID: PMC3338716 DOI: 10.1371/journal.pone.0035700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 03/20/2012] [Indexed: 01/14/2023] Open
Abstract
Embryonic stem cells are conventionally differentiated by modulating specific growth factors in the cell culture media. Recently the effect of cellular mechanical microenvironment in inducing phenotype specific differentiation has attracted considerable attention. We have shown the possibility of inducing endoderm differentiation by culturing the stem cells on fibrin substrates of specific stiffness. Here, we analyze the regulatory network involved in such mechanically induced endoderm differentiation under two different experimental configurations of 2-dimensional and 3-dimensional culture, respectively. Mouse embryonic stem cells are differentiated on an array of substrates of varying mechanical properties and analyzed for relevant endoderm markers. The experimental data set is further analyzed for identification of co-regulated transcription factors across different substrate conditions using the technique of bi-clustering. Overlapped bi-clusters are identified following an optimization formulation, which is solved using an evolutionary algorithm. While typically such analysis is performed at the mean value of expression data across experimental repeats, the variability of stem cell systems reduces the confidence on such analysis of mean data. Bootstrapping technique is thus integrated with the bi-clustering algorithm to determine sets of robust bi-clusters, which is found to differ significantly from corresponding bi-clusters at the mean data value. Analysis of robust bi-clusters reveals an overall similar network interaction as has been reported for chemically induced endoderm or endodermal organs but with differences in patterning between 2-dimensional and 3-dimensional culture. Such analysis sheds light on the pathway of stem cell differentiation indicating the prospect of the two culture configurations for further maturation.
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Affiliation(s)
- Xinan Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Maria Jaramillo
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Satish Singh
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Prashant Kumta
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Complex Engineered Multifunctional Materials, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ipsita Banerjee
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Olsen AK, Boyd M, Danielsen ET, Troelsen JT. Current and emerging approaches to define intestinal epithelium-specific transcriptional networks. Am J Physiol Gastrointest Liver Physiol 2012; 302:G277-86. [PMID: 22094602 DOI: 10.1152/ajpgi.00362.2011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Upon developmental or environmental cues, the composition of transcription factors in a transcriptional regulatory network is deeply implicated in controlling the signature of the gene expression and thereby specifies the cell or tissue type. Novel methods including ChIP-chip and ChIP-Seq have been applied to analyze known transcription factors and their interacting regulatory DNA elements in the intestine. The intestine is an example of a dynamic tissue where stem cells in the crypt proliferate and undergo a differentiation process toward the villus. During this differentiation process, specific regulatory networks of transcription factors are activated to target specific genes, which determine the intestinal cell fate. The expanding genomewide mapping of transcription factor binding sites and construction of transcriptional regulatory networks provide new insight into how intestinal differentiation occurs. This review summarizes the current overview of the transcriptional regulatory networks driving epithelial differentiation in adult intestine. The novel technologies that have been implied to study these networks are presented and their prospects for implications in future research are also addressed.
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Affiliation(s)
- Anders Krüger Olsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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Lehner F, Kulik U, Klempnauer J, Borlak J. Inhibition of the liver enriched protein FOXA2 recovers HNF6 activity in human colon carcinoma and liver hepatoma cells. PLoS One 2010; 5:e13344. [PMID: 20967225 PMCID: PMC2954183 DOI: 10.1371/journal.pone.0013344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 09/09/2010] [Indexed: 02/08/2023] Open
Abstract
Recently, we demonstrated that the transcription factors HNF6 and FOXA2 function as key regulators in human colorectal liver metastases. To better understand their proposed inhibitory crosstalk, the consequences of functional knockdown of FOXA2 on HNF6 and C/EBPα activity were investigated in the human colon Caco-2 and HepG2 carcinoma cell lines. Specifically, siRNA-mediated gene silencing of FOXA2 repressed transcript expression by >80%. This resulted in a statistically significant 6-, 3-, 4-, and 8-fold increase in mRNA expression of HNF6 and of genes targeted by this transcription factor, e.g., HSP105B, CYP51, and C/EBPα, as determined by qRT-PCR. Thus, functional knockdown of FOXA2 recovered HNF6 activity. Furthermore, with nuclear extracts of Caco-2 cells no HNF6 DNA binding was observed, but expression of HNF1α, FOXA2, FOXA3, and HNF4α protein was abundant. We therefore transfected a plasmid encoding HNF6 into Caco-2 cells but also employed a retroviral vector to transfect HNF6 into HepG2 cells. This resulted in HNF6 protein expression with DNA binding activity being recovered as determined by EMSA band shift assays. Furthermore, by flow cytometry the consequences of HNF6 expression on cell cycle regulation in transfected cells was studied. Essentially, HNF6 inhibited cell cycle progression in the G2/M and G1 phase in Caco-2 and HepG2 cell lines, respectively. Here, proliferation was reduced by 80% and 50% in Caco-2 and HepG2 cells, respectively, as determined by the BrdU labeling assay. Therefore functional knockdown of FOXA2 recovered HNF6 activity and inhibited growth of tumor-cells and may possibly represent a novel therapeutic target in primary and secondary liver malignancies.
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Affiliation(s)
- Frank Lehner
- Department of General, Visceral and Transplantation Surgery, Hannover Medical School, Hannover, Germany
| | - Ulf Kulik
- Department of General, Visceral and Transplantation Surgery, Hannover Medical School, Hannover, Germany
| | - Juergen Klempnauer
- Department of General, Visceral and Transplantation Surgery, Hannover Medical School, Hannover, Germany
| | - Juergen Borlak
- Molecular Medicine and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
- Center of Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany
- * E-mail:
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