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Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

ABSTRACT: Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

PROVIDER: PRJNA834965 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19078400_1.fastq.gz	Fastqsanger.gz
	SRR19078400_2.fastq.gz	Fastqsanger.gz
	SRR19078401_1.fastq.gz	Fastqsanger.gz
	SRR19078401_2.fastq.gz	Fastqsanger.gz
	SRR19078402_1.fastq.gz	Fastqsanger.gz

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Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

Project description:To investigate transcriptomic profiles of of two dysplastic stem cell (DSC) subpopulations, CD44v6neg/CD133+/CD166+ (DP-DSC) and CD44v6+/CD133+/CD166+ (TP-DSC), in dysplastic organoids (Meta4 organoids) established from active-Kras induced mouse stomachs

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Project description:Despite malignant cutaneous melanoma is relatively rare compared to other skin cancers, it is still responsible for 80% of all skin cancer-related deaths. To identify molecular signatures of melanoma progression, excisional biopsies from 18 common melanocytic nevi (CMN), 8 primary radial growth phase melanomas (RGPM), 15 primary vertical growth phase melanomas (VGPM) and 5 melanoma metastases (MTS) were profiled using whole genome oligo-microarrays. Differentially expressed genes for each progression step were identified, and validation of selected transcripts by qRT-PCR was performed on an independent cohort of fixed samples. The comparison between CMN and RGPM showed an enrichment of Gene Ontology (GO) terms related to inter and intra-cellular junctions, whereas the transition from RGPM to VGPM was characterized by the deregulation of WNT3, MAPK and AKT pathways. In this step, enrichment analysis underlined the alteration of biological processes linked to apoptosis. Upregulation of genes involved into DNA double-strand breaks repair and downregulation of cellular adhesion genes were observed in MTS respect to VGPM. Futhermore, the gene expression profiles of 11 dysplastic nevi (DN) were compared to all the others. Some genes controlling proliferation were found more expressed than in CMN. Overall, DN displayed an heterogeneous behaviour, with relevant oncogenes, such as MYC and BCL6, less expressed than in RGPM, and a modulation pattern similar to VGPM for a subset of gene families, such as mismatch repair. This suggests that DN is not an intermediate step within melanoma progression, but a separate entity with an independent risk of progression to melanoma Keywords: Melanoma progression, gene expression profiling, qPCR

2009-09-30 | GSE12391 | GEO

Comparison of expression data from DLD-1 subpopulations I

Project description:Comparison of expression data from DLD-1 subpopulations I

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Comparison of expression data from DLD-1 subpopulations III

Project description:Comparison of expression data from DLD-1 subpopulations III

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Comparison of expression data from DLD-1 subpopulations II

Project description:Comparison of expression data from DLD-1 subpopulations II

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Differentially expressed genes between the bone metastatic subpopulations and lung metastatic subpopulations of lung adenocarcinoma

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Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use

Project description:Background: The risk of developing Barrett’s esophagus (BE) and/or esophageal adenocarcinoma (EAC) is associated with specific demographic and behavioral factors, including gender, obesity/elevated body-mass index (BMI), and tobacco use. Alterations in DNA methylation, an epigenetic modification that can affect gene expression and that can be influenced by environmental factors, is frequently present in both BE and EAC and is believed to play a role in the formation of BE and its progression to EAC. It is currently unknown whether obesity or tobacco smoking influence the risk of developing BE/EAC via the induction of alterations in DNA methylation. To investigate this possibility, we assessed the genome-wide methylation status of 81 esophageal tissues, including BE, dysplastic BE, and EAC epithelia using HumanMethylation450 BeadChips (Illumina). Results: We found numerous differentially methylated loci in the esophagus tissues when comparing males to females, obese to lean individuals, and smokers to nonsmokers. Differences in DNA methylation between these groups were seen in a variety of functional genomic regions, and both within and outside of CpG islands. Several cancer-related pathways were found to have differentially methylated genes between these comparison groups. Conclusions: Our findings suggest obesity and tobacco smoking may influence DNA methylation in the esophagus and raise the possibility that these risk factors affect the development of BE, dysplastic BE, and EAC through influencing the epigenetic status of specific loci that have a biologically plausible role in cancer formation.

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