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GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on an FFPE cell pellet array of mixed HEK293T and CCRF-CEM cell lines.

ABSTRACT: GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on an FFPE cell pellet array of mixed HEK293T and CCRF-CEM cell lines.

PROVIDER: PRJNA731456 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14601900_1.fastq.gz	Fastqsanger.gz
	SRR14601900_2.fastq.gz	Fastqsanger.gz
	SRR14602000_1.fastq.gz	Fastqsanger.gz
	SRR14602000_2.fastq.gz	Fastqsanger.gz
	SRR14601901_1.fastq.gz	Fastqsanger.gz

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Project description:It has been shown previously that glucocorticoids exert a dual mechanism of action, entailing cytotoxic, mitogenic as well as cell proliferative and anti-apoptotic responses, in a dose-dependent manner on CCRF-CEM cells at 72 h. Early gene expression response implies a dose-dependent dual mechanism of action of prednisolone too, something reflected on cell state upon 72 h of treatment. In this work, a generic, computational microarray data analysis framework is proposed, in order to examine the hypothesis whether CCRF-CEM cells exhibit an intrinsic or acquired mechanism of resistance and to investigate the molecular imprint of this, upon prednisolone treatment. The experimental design enables the examination of both the dose (0 nM, 10 nM, 22 uΜ, 700 uΜ) effect of glucocorticoid exposure and the dynamics (early and late, namely 4 h, 72 h) of the molecular response of the cells at the transcriptomic layer. In this work we demonstrated that CCRF-CEM cells may attain a mixed mechanism of response to glucocorticoids, however, there is clear evidence predicating towards an intrinsic mechanism of resistance. More specifically, at 4 h prednisolone appeared not to perform its expected function by down-regulating apoptotic genes, which is re-enforced by mechanisms, which down-regulate other sets of apoptotic genes. Also, low and high prednisolone concentrations up-regulates metabolic and signal-transduction related genes in both time points, thus grounding for a cell proliferation machinery. In addition, regulation of NF-κB-related genes implies an inherent mechanism of resistance through the established link of NF-κB inflammatory role and GC-induced resistance. The analysis framework applied here allows derivation of regulatory mechanisms activated by prednisolone through identification of early responding sets of genes. On the other hand, study of the prolonged exposure to glucocorticoids (72 h exposure) highlights the effect of homeostatic feedback mechanisms of the treated cells. Overall, it appears that CCRF-CEM cells in this study exhibit a diversified, combined pattern of intrinsic and acquired resistance to prednisolone, yet with a tendency towards inherent resistant characteristics, through activation of different molecular courses of action.

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GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on an FFPE cell pellet array of mixed HEK293T and CCRF-CEM cell lines.

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