Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq of the ecDNA-positive colon cancer cell line COLO 320DM with and without hydroxyurea treatment

ABSTRACT: Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA oncogene transcription after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days. RNA was extracted and subjected to mRNA library preparation and single-end sequencing.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Robin Xu

PROVIDER: E-MTAB-16933 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:N-nitroso compounds (NOCs) can be formed through endogenous nitrosation in the human body and are known to induce micronuclei (MN) formation in vitro. Since lymphocytic MN represent a well-validated biomarker of effect with regard to carcinogenic risk in multiple target organs, establishing a link between NOCs and MN in humans could provide evidence for a carcinogenic risk. Investigating gene expression modulations in relation to NOC exposure could provide further crucial information on underlying molecular mechanisms-of-action. The purpose of this study is therefore to establish the relationship between human NOC exposure under daily life conditions and MN formation in relation to associated transcriptomic changes, using lymphocytes as a surrogate tissue for analyzing carcinogenic events in target organs. We analyzed gene expression levels and MN frequency in lymphocytes from adults participating in a European cohort from the multidisciplinary research project NewGeneris. For assessing exposure to NOCs, urinary samples were analyzed for marker nitrosamines by GC-MS. NOC exposure was subsequently linked to peripheral blood transcriptomics. We found an association between MN frequency and urinary NOCs, indicating that NOC exposure under daily life circumstances may play an important role in human cancer development. Furthermore, we have identified modifications in pathways which indicate a molecular response to NOC-induced genotoxicity. From this, we derived a small group of genes which could be suitable as mechanistic-based transcriptomic biomarkers of NOC exposure-related cancer risk. The modified genetic processes and genes found in this study may be of interest for future investigations into NOC-associated carcinogenicity in humans. The study investigated transcription levels in human whole blood from 30 pregnant mothers in a Danish NewGeneris cohort. For each subject, cRNA copies of isolated mRNA were labeled with one dye (Cy3) and each sample was hybridized on separate arrays. One replicate per subject (so 30 arrays in total).

Dataset Information

RNAseq of the ecDNA-positive colon cancer cell line COLO 320DM with and without hydroxyurea treatment

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