Transcription profiling of CaCo-2 cells differentiated to M cells - establishing and characterizing a cell culture model for M cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Martin Eisenacher
PROVIDER: E-GEOD-3054 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:M cells are special cells in the epithelium of the small intestinal bowel and play an important role during the initiation of a primary, fast immune response. On a Costar-Transwell filter cells of a colon adeno carcinoma cell line (Caco-2) are growing until differentiation. Then on the other side of the Caco cell layer lymphocytes from human venous blood are added. Pores in the filter membrane allow contact between lymphocytes and Caco cells. Therefore some cells of the Caco cell layer are differentiating to "M cell like" cells, showing the morpholgy and function of natural M cells. Keywords: cell type comparison, induction response
2006-08-04 | GSE3054 | GEO
Project description:CELL CULTURE: The human intestinal epithelial cell line Caco-2 (obtained from Dr. Stanley Falkow, Stanford University) was used to study the genome-wide expression program underlying the transition from cell proliferation to establishment of a polarized epithelial layer. Cells were first grown in sparse culture on plastic p15 dishes to generate a population of "contact naive" cells. These cells were combined and plated at confluency on Costar filter inserts. The day cells were plated on filters is designated the zero time-point. Cells were cultured for 26 days, during which time they develop structural and functional polarity. Media was changed every other day. Triplicate samples were harvested at eleven time-points over the time course for microarray analysis. The entire time course was performed twice. Three control arrays are included in this data set; (1) to determine how the gene-expression patterns in Caco-2 cells grown on a plastic dish compares to the expression profiles identified in Caco-2 cells grown on Costar filter inserts (microarray shcu182, data not shown), (2) to tested whether feeding the cells at different time-points had an effect on the Caco-2 gene-expression program. All samples taken (except at the day zero time-point) were fed with fresh media one day prior to harvesting the sample. During TC3 and TC4, we performed two test arrays analyzing the transcriptional program in Caco-2 cells that were fed with fresh cell culture media 4h prior to taking the 7D time-point (microarrays shcu177 and shcu178, indicated with * in table S1). Groups of assays that are related as part of a time series. See additional information on overall design in Series supplementary file. ABSTRACT: Although there is considerable evidence implicating post-translational mechanisms in the development of epithelial cell polarity, little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized the temporal program of gene expression during cell-cell adhesion-initiated polarization of human Caco-2 cells in tissue culture, which develop structural and functional polarity similar to that of enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell-cell contacts between neighboring cells. Expression of a cluster of genes involved in cell proliferation switched off and concomitantly the expression of genes related to functional specializations of polarized epithelial cells was induced. Induction of these latter genes correlated with formation of important structural and functional features related to enterocyte differentiation and establishment of structural and functional cell polarity. Coordinated expression of genes encoding components of functional cell structures were often observed, indicating temporal control of expression and assembly of multiprotein complexes. Changes in gene expression patterns during Caco-2 cell differentiation in vitro paralleled those in terminally differentiating enterocytes migrating up the intestinal crypt-villus axis in vivo, despite the lack of stromal cells and gradients of morphogens in this tissue culture model. Keywords: time_series_design
2007-08-17 | GSE7442 | GEO
Project description:CELL CULTURE: The human intestinal epithelial cell line Caco-2 (obtained from Dr. Stanley Falkow, Stanford University) was used to study the genome-wide expression program underlying the transition from cell proliferation to establishment of a polarized epithelial layer. Cells were first grown in sparse culture on plastic p15 dishes to generate a population of "contact naive" cells. These cells were combined and plated at confluency on Costar filter inserts. The day cells were plated on filters is designated the zero time-point. Cells were cultured for 26 days, during which time they develop structural and functional polarity. Media was changed every other day. Triplicate samples were harvested at eleven time-points over the time course for microarray analysis. The entire time course was performed twice. Three control arrays are included in this data set; (1) to determine how the gene-expression patterns in Caco-2 cells grown on a plastic dish compares to the expression profiles identified in Caco-2 cells grown on Costar filter inserts (microarray shcu182, data not shown), (2) to tested whether feeding the cells at different time-points had an effect on the Caco-2 gene-expression program. All samples taken (except at the day zero time-point) were fed with fresh media one day prior to harvesting the sample. During TC3 and TC4, we performed two test arrays analyzing the transcriptional program in Caco-2 cells that were fed with fresh cell culture media 4h prior to taking the 7D time-point (microarrays shcu177 and shcu178, indicated with * in table S1). Groups of assays that are related as part of a time series. See additional information on overall design in Series supplementary file. ABSTRACT: Although there is considerable evidence implicating post-translational mechanisms in the development of epithelial cell polarity, little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized the temporal program of gene expression during cell-cell adhesion-initiated polarization of human Caco-2 cells in tissue culture, which develop structural and functional polarity similar to that of enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell-cell contacts between neighboring cells. Expression of a cluster of genes involved in cell proliferation switched off and concomitantly the expression of genes related to functional specializations of polarized epithelial cells was induced. Induction of these latter genes correlated with formation of important structural and functional features related to enterocyte differentiation and establishment of structural and functional cell polarity. Coordinated expression of genes encoding components of functional cell structures were often observed, indicating temporal control of expression and assembly of multiprotein complexes. Changes in gene expression patterns during Caco-2 cell differentiation in vitro paralleled those in terminally differentiating enterocytes migrating up the intestinal crypt-villus axis in vivo, despite the lack of stromal cells and gradients of morphogens in this tissue culture model. Keywords: time_series_design Computed
2007-08-16 | E-GEOD-7442 | biostudies-arrayexpress
Project description:We quantified the distribution of cellular mRNAs between protrusions and cell-body of MDA-MB-231 breast carcinoma cells by RNA-seq, using a filter based fractionation method. In this method, cells are seeded on top of 3micrometer transwell filters to enable protrusions to form but to prevent the cell-bodies passing through due to the small size of the pores, thus resulting in separation of protrusions and cell-bodies on opposite sides of the filter, from which RNA can be prepared separately. RNA samples for Illumina sequencing were generated in duplicates from two biological replicate experiments (two protrusions and two cell-body).
2015-11-08 | E-MTAB-2546 | biostudies-arrayexpress
Project description:Transcriptomic analysis of the cells grown on biphenyl on a filter placed on a minimal agar medium and those grown on biphenyl to mid-exponential phase in a liquid medium
2010-06-10 | GSE22239 | GEO
Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.
2017-02-10 | GSE64017 | GEO
Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.
2017-02-10 | GSE63950 | GEO
Project description:To assess the impact of protrusion induction on the proteome of mesenchymal-like migratory cells, MDA-MB231 breast cancer cells were seeded on top of collagen-I coated 3 micron transwell filters (corning). No media was added to the bottom chamber and cells were allowed to adhere to filter overnight. The next day, the media on top of cells was refreshed, and the filters were either left with no media in the bottom chamber (closed pores), or with media also added to the bottom chamber (open pores) in order to allow formation of protrusions. Cells were allowed to form protrusions for 2 or 24 hrs, before being lysed and analysed by mass spectrometry, using TMT mediated quantitative proteomics.
2020-10-20 | PXD021206 | Pride
Project description:This upload concerns 2 independent but related experiments that were searched together: a) To reveal proteins that consistently localise to actin-rich protrusions across different human migratory cell-lines, we profiled the distribution of cellular proteins between protrusions and cell-bodies in a panel of 5 established human cell-lines (see experimental design). Cell lines were seeded on top of collagen-I coated 3 micron transwell filters (corning). No media was added to the bottom chamber and cells were allowed to adhere to the filter overnight. The next day, the media on top of the cells was refreshed, and media was also added to the bottom chamber in order to open the pores and allow formation of protrusions. Cells were allowed to form protrusions for 2 hrs before being fixed with ice-cold methanol. Cells were then rehydrated in PBS, followed by independent lysis of protrusions and cell-bodies on opposite sides of the filters in 2% SDS, 100mM Tris pH 7.5 b) To analyse the temporal dynamics of protein localisation to cell protrusions, we carried out a time-course spatial proteomics analysis of protrusions and cell-bodies in MDA-MB231 cells. Cells were seeded on top of collagen-I coated 3 micron transwell filters (corning). No media was added to the bottom chamber and cells were allowed to adhere to filter overnight. The next day, the media on top of cells was refreshed, and the filters were either left with no media in the bottom chamber (closed pores), or media added to the bottom chamber (open pores) for different lengths of times (1, 2, 4 , & 8 hrs) to induce protrusion formation. Cells were then fixed with ice-cold methanol, rehydrated in PBS, followed by independent lysis of protrusions and cell-bodies on opposite sides of each filter by 2% SDS, 100mM Tris pH 7.5.
2020-10-20 | PXD021239 | Pride
Project description:In mesenchymal-like cell migration, cells need to polarise into a protrusive front and a retracting cell body. To understand this process better, we set out to quantify the distribution of cellular proteins between protrusions and cell-body by proteomics, using MDA-MB-231 cells, a highly invasive breast cancer cell-line. We utilised a transwell filter based fractionation method in conjugation with SILAC proteomics. In this method, cells are seeded on top of 3μm transwell filters to enable protrusions to form through the pores of the filters but to prevent the cell-bodies passing through due to the small size of the pores, thus resulting in separation of protrusions and cell-bodies on opposite sides of the filter, which can then be lysed and prepared separately. Prepration of protrusion and cell-body fractions from heavy and light SILAC labelled cells then allows for reciprocal mixing and quantification of proteins between protrusions and cell-body. In this study, we determined the relative distribution of 3240 proteins between protrusions and cell-body from two SILAC mixes. Associated ArrayExpress data: E-MTAB-2546.
2015-10-09 | PXD000914 | Pride