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RNA-seq profiling of gene expression in Ezh2-deficient and control murine lung epithelial and stromal cell populations at day E16.5

ABSTRACT: Epithelial (CD31-CD45-EpCAM+) and stromal (CD31-CD45-EpCAM-) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (3 biological replicates per genotype-tissue combination). Total RNA extracted from the samples was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina). Completed libraries from different samples were sequenced on HiSeq 2000 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility. RNA-seq gene expression profiles from Ezh2 deficient and control lung epithelial and stromal cell populations at day E16.5 (3 replicates per genotype-tissue combination).

ORGANISM(S): Mus musculus

SUBMITTER: Marie-Liesse Asselin-Labat

PROVIDER: E-GEOD-57391 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung.

Galvis Laura A LA Holik Aliaksei Z AZ Short Kieran M KM Pasquet Julie J Lun Aaron T L AT Blewitt Marnie E ME Smyth Ian M IM Ritchie Matthew E ME Asselin-Labat Marie-Liesse ML

Development (Cambridge, England) 20150319 8

Epigenetic mechanisms involved in the establishment of lung epithelial cell lineage identities during development are largely unknown. Here, we explored the role of the histone methyltransferase Ezh2 during lung lineage determination. Loss of Ezh2 in the lung epithelium leads to defective lung formation and perinatal mortality. We show that Ezh2 is crucial for airway lineage specification and alveolarization. Using optical projection tomography imaging, we found that branching morphogenesis is a ...[more]

PMID: 25790853

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ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility. ChIP-seq profiles of H3K27 tri-methylation from Ezh2 deficient and control lung epithelium (2 replicates per genotype).

2015-05-11 | E-GEOD-57392 | biostudies-arrayexpress

RNA-seq profiling of gene expression in Ezh2-deficient and control murine lung epithelial and stromal cell populations at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) and stromal (CD31-CD45-EpCAM-) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (3 biological replicates per genotype-tissue combination). Total RNA extracted from the samples was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina). Completed libraries from different samples were sequenced on HiSeq 2000 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

2015-05-11 | GSE57391 | GEO

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

2015-05-11 | GSE57392 | GEO

Microarray of Mst1/2 deleted epithelial cells from E18.5 mouse lungs

Project description:ShhCre;Mst1/2flx/flx (Mst1/2 D/D) mice were generated to conditionally delete Mst1 and Mst2 from epithelial progenitors during lung morphogenesis. Lungs from E18.5 control and Mst1/2 D/D mice were mechanically and enzymatically dissociated to generate single cell suspension. Epcam(+) cells were isolated using magnetic microbeads. Microarray analysis of mRNAs isolated from Epcam(+) epithelial cells from E18.5 control and Mst1/2 D/D mice was performed to identify transcriptional changes following deletion of the mammalian Hippo kinases (Mst1 and Mst2) from the embryonic lung. The mammalian Hippo kinases, Mst1 and Mst2, were conditionally deleted in epithelial progenitors of the developing lung using ShhCre. Epcam(+) epithelial cells were isolated from the lungs of E18.5 control and Mst1/2 deleted mice. mRNA isolated from Epcam(+) epithelial cells was analyzed by microarray.

2015-01-01 | E-GEOD-61582 | biostudies-arrayexpress

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

Project description:Gene expression (RNA-seq) and H3K27me3 binding (ChIP-seq) profiling of wild type and Ezh2-deficient mouse lung epithelium. Lungs from wild type and Ezh2-deficient mice (Ezh2 deletion is specific to lung epithelium) were collected at day e16.5. Lung cells were separated into epithelial and stromal populations based on EpCAM expression. Epithelial cells were profiled for both gene expression (Total RNA-seq) and H3K27me3 binding (ChIP-seq). Additionally, stromal cells were also profiled for gene expression.

2015-05-11 | E-GEOD-57393 | biostudies-arrayexpress

Ezh2 maintains proliferation, transcriptional integrity, and the timing of late differentiation during mouse retina development

Project description:We investigated the gene expression profile changes after Ezh2 conditional knockout in the mouse retina at E16.5. Loss of Ezh2 leads to up-regulation of PRC2 targeted genes including cell cycle regulators and multiple genes which are not normally expressed in the retina, including many Hox genes. Loss of Ezh2 resulted in a dramatic decline in progenitor proliferation by postnatal day 3, such that there is an early end to neurogenesis, and disruption of laminar organization. Although there are only minor effects on embryonic retinal development, there is accelerated differentiation of several late born cell types postnatally, including photoreceptors and Mueller glia, which become reactive by postnatal day 14. Peripheral retina was dissected at E16.5 from Pax6alpha-Cre:Ezh2fl/+ and Pax6alpha-Cre:Ezh2fl/null mouse embryos. Total RNA was purified and RNA deep sequencing was done using 4 controls and 4 conditional knockout samples.

2015-07-14 | E-GEOD-65082 | biostudies-arrayexpress

Single-cell RNA seq of mouse proximal small intestine at E16.5

Project description:Epcam-positive cells from fetal intestinal epithelium were FACS sorted and processed using 10X genomics to characterise the differentiation of fetal intestinal cells at E16.5.

2019-05-15 | E-MTAB-7660 | biostudies-arrayexpress

The sequence-specific peptide-binding activity of the protein sulfide isomerase AGR2 directs its’ stable binding to the oncogenic receptor EpCAM

Project description:AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a peptide motif (TTIYY). A synthetic TTIYY-containing peptide column can be used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131-135 (VDPSL). A peptide binding site consensus of Tx[IL][YF][YF] was developed for AGR2 by measuring its activity against a alanine mutagenized synthetic peptide library. Screening the human proteome for proteins harboring this consensus motif revealed an enrichment in transmembrane proteins and we focus on validating EpCAM as one such oncogenic protein. Recombinant AGR2 and EpCAM proteins formed a dose-dependent protein-protein interaction in vitro. Proximity ligation assays demonstrated that endogenous AGR2 and EpCAM protein associate in cells. Introducing a single alanine mutation in EpCAM at Tyr251 attenuated its binding to AGR2 in vitro and in cells. Hydrogen-deuterium exchange mass spectrometry was used to identify a stable binding site for AGR2 on EpCAM, adjacent to the TILYY motif and surrounding EpCAM’s detergent binding site. Together, these data define a dominant peptide-binding site on AGR2 that mediates its specific peptide-binding function. A model client protein, EpCAM, is proposed for AGR2 to study how an ER-resident chaperone can dock specifically and regulate assembly of a protein destined for the secretory pathway.

2018-01-22 | PXD005782 | Pride

A Pooled RNAi Screening Strategy Reveals Novel Regulators for EpCAM

Project description:The cell surface receptor, Epithelial Cell Adhesion Molecule (EpCAM), is overexpressed in a variety of cancers and has been carefully examined for its functional role in carcinogenesis and its potential as a therapeutic target. However, little is known about the upstream molecular pathways that regulate EpCAM expression. To elucidate the mechanisms by which EpCAM expression is controlled, we designed a combinatorial screening strategy that utilized pooled shRNA gene knockdown with magnetically-activated cell separation for selection of cells with reduced EpCAM protein expression on the cell surface. The pooled RNAi screen was analyzed by comparing EpCAM-enriched and EpCAM-depleted cell populations for shRNA abundance using competitive hybridization to microarrays. Our RNAi screen and further validation efforts revealed that at least four genes (GRM1, SLITRK5, EFNA5, and IL23A) are important for EpCAM expression in the ovarian cancer cell line OVCAR8. Further investigations into the ephrin ligand, EFNA5, suggest that its activation by the Eph receptor, EPHA4, contributes to the regulation of EpCAM expression via a reverse signaling mechanism. Our screening strategy revealed novel mechanisms for the regulation of EpCAM expression and provides insight into the biology of this cancer-associated gene. Importantly, this study also demonstrates the utility of pooled RNAi screening in the identification of genes required for the regulation of cell surface protein expression. Two condition experiment; EpCAM-Bound or EpCAM-Unbound OVCAR8 cells vs Reference population of transduced cells without phenotypic selection; biological triplicate

2011-12-01 | E-GEOD-32985 | biostudies-arrayexpress

Preclinical targeted therapy for retinoblastoma using EpCAM Aptamer siRNA chimeras

Project description:siRNAs have played a major role in cancer drug discovery, but their potential is hampered due to off-target effects. Thus, delivery systems like RNA aptamers have been used to enhance the specific delivery of these siRNAs to cancer stem cells. We report the efficacy of three different EpCAM aptamer siRNA chimeras, which were investigated both in vitro and in vivo for their ability to reduce cancer cell progression. Using these chimeras, we demonstrated specific gene knockdown in EpCAM positive cells which ultimately led to the apoptosis. To study the efficacy of these aptamer chimeras in vivo, retinoblastoma xenografts bearing NCC Rb C 51 cells were created for the first time. Systemic administration of these aptamer chimeras reduced tumour growth to about 50%. We further investigated the central Role of PLK1 in Cancer Progression and demonstrated the anti-cancer effects of targeted EpCAM siPLK1 approach. Using SILAC-Mass spectrometry analysis, we showed that silencing PLK 1 gene can lead to p53 mediated cell cycle arrest. Thus, we establish EpCAM-siRNA chimeras as potential markers for targeted anti-cancer applications, which paves a platform for efficient second line of therapies in addition to existing chemotherapy options.

2022-03-02 | PXD008221 | Pride

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