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Ab2a98d3-f893-477d-b9e5-130b90791066 - samples

ABSTRACT: Organoid cultures derived from colorectal adenomas. RNA and DNA was isolated from these cultures for genome wide profiling.

PROVIDER: EGAD00001008949 | EGA |

REPOSITORIES: EGA

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3aed91d8-8e5e-4959-8ac2-598a5c719b3a - samples

Project description:Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

| EGAD00001008411 | EGA

d752d442-a029-48b8-a23b-d72060c225b2 - samples

Project description:Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

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49a825c3-18bb-44ea-a4bc-f1afcc86c4ad - samples

Project description:Organoid cultures derived from colorectal adenomas were transduced with a miR-17-92 expressing vector. RNA from miR17-92-overexpressing organoids and respective non-transduced organoids (controls) was isolated for expression analysis.

| EGAD00001008480 | EGA

Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression

Project description:Colorectal adenomas are benign precursor lesions of colorectal cancer (CRC) that arise from normal epithelium1. The prevalence of adenomas in the large intestine is much higher than the incidence of cancer implying that the majority of adenomas will never progress to CRC4. In clinical practice, adenomas detected during colonoscopy are completely removed, and consequently the natural history of disease disrupted. Based on the prevalence of focal cancer in endoscopically removed adenomas, it is estimated that only 5% of adenomas will eventually progress to CRC. The aim of the present study was to characterize adenomas at low and high risk of progressing to cancer by extensive molecular profiling at DNA, RNA, and protein level, allowing to examine the biological processes in which they differ and to discover putative drivers of early colorectal tumor development.

2019-08-22 | PXD012254 | Pride

Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model

Project description:Patient derived organoids (PDOs) have been established as a 3D culture model which closely recapitulates the in vivo tumor biology. However, one limitation of this culture model is the lack of tumor microenvironment which has a significant role in tumor progression and drug response. To address this, we established and molecularly characterized a novel 3D co-culture model of colorectal cancer (CRC) based on PDOs and patient matched fibroblasts. Both normal and cancer associated fibroblasts, NFs and CAFs respectively, were able to support organoid growth without addition of niche factors to the media. Additionally, co-cultures showed closer resemblance to primary patient material than organoid mono-cultures as evaluated by histology. Finally, RNA gene expression signatures of tumor cells and fibroblasts isolated from mono- or co-cultures demonstrated that co-cultures support greater cell type heterogeneity. In this proteomics dataset we compared pairs of NFs and CAFs derived from five patients. Collectively, we present a newly established human derived organoid-fibroblast model which, closely recapitulates in vivo tumor heterogeneity and involves the tumor microenvironment.

2023-03-14 | PXD032047 | Pride

TGFÎ² signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids]

Project description:The aim of this study was to determine the effects of TGFÎ² at the premalignant stage of CRC development. Organoid cultures were isolated from normal colon and from tubular adenomas. One normal colon culture was genetically engineered using the CRISPR-Cas9 system to carry the BRAFV600E mutation. Organoid cultures of three different tubular adenomas and two normal colon samples, and one BRAFV600E-mutant organoid culture received TGFÎ² or control treatment after which gene expression was analyzed by microarray (Affymetrix U133+ PM Genechip Array).

2016-06-01 | E-GEOD-79461 | biostudies-arrayexpress

Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

Project description:We used Illumina Infinium 27k Human DNA Methylation BeadChip v1.2 to assess genome-wide DNA methylation profiling of normal colon epithelial, adenomas and colorectal adenocarcinomas across approximately 27,000 CpGs in fresh frozen colorectal tissue samples. We found that cancer-associated methylation changes with impact on transcription occur nearly as frequent at non-CpG island as CpG island promoters in colorectal cancer (CRC). Samples included 6 normal colon epithelial tissue samples, 6 adenomas, and 30 colorectal adenocarcinomas. Bisulfite-converted DNA from the 42 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2013-06-15 | E-GEOD-40055 | biostudies-arrayexpress

Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

2013-06-15 | GSE40055 | GEO

DNA methylation analysis of breast cancer patient-derived xenografts and organoids

Project description:To understand if the generation of xenograft and organoid models of breast cancer alters DNA methylation, we compared the genome-wide methylation profile of matching patient tumors, patient derived xenografts, and organoid cultures derived from xenografts.

2022-01-09 | GSE186747 | GEO

TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids]

Project description:The aim of this study was to determine the effects of TGFβ at the premalignant stage of CRC development. Organoid cultures were isolated from normal colon and from tubular adenomas. One normal colon culture was genetically engineered using the CRISPR-Cas9 system to carry the BRAFV600E mutation.

2016-06-01 | GSE79461 | GEO

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