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Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq]

ABSTRACT: Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq]

PROVIDER: PRJNA498073 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8096930_1.fastq.gz	Fastqsanger.gz
	SRR8096930_2.fastq.gz	Fastqsanger.gz
	SRR8096931_1.fastq.gz	Fastqsanger.gz
	SRR8096931_2.fastq.gz	Fastqsanger.gz
	SRR8096932_1.fastq.gz	Fastqsanger.gz

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Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation

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Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq]

Project description:Abnormal promoter DNA hypermethylation arises early during tumorigenesis and yet its role in cancer initiation has remained underexplored. An important scenario for examining this is, BRAFV600E-mutant colon adenocarcinomas (COAD) which most often arise in the proximal colon and harbor extensive, abnormal gene promoter CpG-island methylation or the methylator phenotype (CIMP). How CIMP and BRAF-mutations specifically interact for COAD initiation has remained unclear. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in wild type cells mimicking “aging like” phenotype. The silenced genes sufficiently activate the Wnt pathway, causing a stem–like state and profound differentiation block. This phenotype renders long-term cultured organoids to be rapidly susceptible to transformation by BRAFV600E with features of typical right-sided COAD. Our studies tightly link epigenetic abnormalities, suggested to arise with aging, to intestinal cell fate changes and define an “epi-driver” role for multiple abnormally silenced genes that predispose to BRAFV600E-driven colon tumorigenesis.

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Analysis of the transcriptomic changes in murine small and large intestinal organoids after the sudden expression of BRAFV600E and/or p53R172H

Project description:BRAFV600E confers poor prognosis and a distinct molecular type of colorectal cancer, which is often associated with TP53 alterations. In order to understand how BRAFV600E and p53R172H promote tumorigenesis in the intestinal epithelium, we generated murine organoids harboring conditional BraffloxV600E and/or Trp53LSL-R172H alleles and conducted RNA sequencing analysis after sudden oncogene induction. As expected from their phenotypes, organoids expressing BRAFV600E, either singly or in combination with p53R172H, displayed strong changes in their transcriptome, while induction of mutant p53 alone had only little impact on gene expression. Our transcriptome analyses revealed there are profound differences in the transcriptomes of SI and COL organoids, in their oncogene naïve ground state and upon BRAFV600E expression. We observed many transcripts positively associated with proliferation, invasion and metastasis to be upregulated in both organoid types expressing BRAFV600E or BRAFV600E together with p53R172H. However, several of them were only differentially regulated in COL organoids, or displayed a more pronounced fold change in COL than in SI organoids. Interestingly, COL organoids more closely recapitulate human CRC patterns and p53R172H cooperates with mutant BRAFV600E in the regulation of several transcripts.

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Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-01 | GSE114801 | GEO