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MicroRNA profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis.

ABSTRACT: microRNA profiling of a cellular model of colorectal cancer progression, which is based on four defined derivates of a CRC cell line that resulted from EMT/MET transitions and phenotypically recapitulate the metastatic cascade: epithelial-like primary tumor, mesenchymal-like tumor cells growing in soft agar or as colonospheres, and mouse xenografts of the latter resulting in lung-metastasis comprised of epithelial-state cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85687 | GEO | 2017/03/28

SECONDARY ACCESSION(S): PRJNA339109

REPOSITORIES: GEO

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RNA profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis.

Project description:RNA profiling of a cellular model of colorectal cancer progression, which is based on four defined derivates of a CRC cell line that resulted from EMT/MET transitions and phenotypically recapitulate the metastatic cascade: epithelial-like primary tumor, mesenchymal-like tumor cells growing in soft agar or as colonospheres, and mouse xenografts of the latter resulting in lung-metastasis comprised of epithelial-state cells.

2017-03-28 | GSE85685 | GEO

DNA methylation profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis.

Project description:DNA methylation profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs.

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Functional shifts in microbial mats recapitulate early Earth metabolic transitions.

Project description:Phototrophic microbial mats dominated terrestrial ecosystems for billions of years, largely causing, through cyanobacterial oxygenic photosynthesis, but also undergoing, the Great Oxidation Event approximately 2.5 billion years ago. Taking a space-for-time approach based on the universality of core metabolic pathways expressed at ecosystem level, we studied gene content and co-occurrence networks in high-diversity metagenomes from spatially close microbial mats along a steep redox gradient. The observed functional shifts suggest that anoxygenic photosynthesis was present but not predominant under early Precambrian conditions, being accompanied by other autotrophic processes. Our data also suggest that, in contrast to general assumptions, anoxygenic photosynthesis largely expanded in parallel with the subsequent evolution of oxygenic photosynthesis and aerobic respiration. Finally, our observations might represent space-for-time evidence that the Wood-Ljungdahl carbon fixation pathway dominated phototrophic mats in early ecosystems, whereas the Calvin cycle probably evolved from pre-existing variants before becoming the dominant contemporary form of carbon fixation.

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Evaluation of gene expression between CD44+ and CD44- cells in colonospheres

Project description:To identify genes that are differentially expressed between CD44+ and CD44- cells in colonospheres, we have employed whole genome microarray expression profiling as a discovery platform. Colonospheres from four colon cancer patients were sorted into CD44+ and CD44- cells using the FACS Aria II Cell Sorter, and total RNA extracted from the cells were labeled with Cy3 and used for microarray analyses with Agilent Whole Human Genome Oligo Microarrays. Gene expression in fluorescence-activated cell-sorted CD44+ and CD44- cells derived from four colon cancer patients was measured.

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Exposure of an immortalized human bronchial epithelial cell line, BEAS-2B, to one of four metals (arsenic, chromium, nickel or vanadium) to determine the early changes that lead to cell transformation

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Evaluation of gene expression between CD44+ and CD44- cells in colonospheres

2012-12-07 | GSE38706 | GEO

RB1 depleted pluripotent stem cell retinal organoids recapitulate state cell transitions of retinoblastoma development

Project description:Retinoblastoma (Rb) is a childhood cancer of the developing retina that begins in utero in response to bi-allelic inactivation of RB1 or MYCN amplification, accounting for up to 1% of all tumours in infancy. To gain insights into the transcriptional events of each state cell transition during Rb development, we developed two Rb models via retinal organoid differentiation of RB1 depleted human embryonic stem cell line (RB1-null hESCs) and RB1patient-specific induced pluripotent (iPSC) line harbouring RB1 biallelic mutation (c.2082delC). Both models were characterised by RB1 depletion and a significant increase in the fraction of proliferating cone precursors (RXRγ+Ki67+), which were defined as cell of origin for Rb by the single cell RNA-Seq analysis. The RB1 depleted retinal organoids displayed similar features to Rb tumours including mitochondrial cristae aberration and rosette-like structures and were able to undergo cell growth in an anchorage-independent manner, indicative of cell transformation in vitro. The patient-specific iPSC model displayed an enhanced reduction of amacrine, horizontal and retinal ganglion cells and an accelerated loss of cone photoreceptor markers during transition towards retinoma and Rb, compared to RB1-null hESC. In both models, the Rb cells of origin, intermediate retinoma and/or Rb cells expressed retinal ganglion and horizontal cell in addition to cone markers, a novel finding, which should help to better identify and eradicate these cells within the tumour mass. Application of Melphalan, Topotecan and TW-37 led to a significant reduction in the fraction of proliferating cone precursors, validating the suitability of these in vitro models for testing novel therapeutics for Rb.

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