Genomics

Dataset Information

39

Expression data from CIC wild type and knockout cell lines


ABSTRACT: Type I low-grade gliomas (LGGs), characterized by 1p/19q co-deletions and IDH1/2 mutations, show superior overall survival compared to other gliomas. Approximately 70% of cases harbour mutations in the Capicua (CIC) gene, whose product is a transcriptional repressor whose transcriptional network has yet to be extensively studied in human cells. To address this, we developed CIC knockout cell lines and used transcriptome analyses to study the consequences of CIC loss. Results were further compared to data for Type I LGGs and stomach adenocarcinomas from The Cancer Genome Atlas (TCGA). We find that CIC appears to regulate the expression of genes involved in cell-cell adhesion and nervous system development. CIC deficiency is also found to be associated with a MEK activation transcriptional signature and to act as an effector of MEK signalling. Loss of CIC may thus present a novel mechanism for the dysregulation of this and other oncogenic pathways. Overall design: Two CIC knockout cell lines (D10 and A9) were obtained using the CRIPSR/Cas9 system and a third (D1) was obtained using the ZFN system. The parental (HEK) cell line is included, along with two CIC wild type cell lines that were submitted to the CRISPR/Cas9 process.

INSTRUMENT(S): [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]

SUBMITTER: Veronique LeBlanc  

PROVIDER: GSE80359 | GEO | 2017-04-15

SECONDARY ACCESSION(S): PRJNA318740

REPOSITORIES: GEO

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Publications

Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade.

LeBlanc Veronique G VG   Firme Marlo M   Song Jungeun J   Chan Susanna Y SY   Lee Min Hye MH   Yip Stephen S   Chittaranjan Suganthi S   Marra Marco A MA  

The Journal of pathology 20170426 2


CIC encodes a transcriptional repressor, capicua (CIC), whose disrupted activity appears to be involved in several cancer types, including type I low-grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems, and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results with analyses of transcriptome data fro  ...[more]

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