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

Abstract

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 from TCGA for type I LGGs and STADs. We identified 39 candidate targets of CIC transcriptional regulation, and confirmed seven of these as direct targets. We showed that, although many CIC targets appear to be context‐specific, the effects of CIC loss converge on the dysregulation of similar biological processes in different cancer types. For example, we found that CIC deficiency was associated with disruptions in the expression of genes involved in cell–cell adhesion, and in the development of several cell and tissue types. We also showed that loss of CIC leads to overexpression of downstream members of the mitogen‐activated protein kinase (MAPK) signalling cascade, indicating that CIC deficiency may present a novel mechanism for activation of this oncogenic pathway. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity

“…As shown in Figure 1a, CIC was found throughout the nucleus during interphase, but appeared to be excluded from condensed chromosomes at metaphase and telophase. During early cytokinesis, CIC foci appeared at decondensing chromosomes during initiation of nuclear envelope reassembly, and increasingly accumulated until completion of cytokinesis (Figures 1a and Supplementary Figure 1 We confirmed this observation using an N-terminal-FLAG-tagged CIC-S construct (F-CIC-S) introduced into an isogenic CIC knockout (CIC KO ) cell line derived from HEK293A 27 (hereafter referred to as HEK F-CIC-S ). Ectopically expressed F-CIC-S displayed similar localization dynamics as endogenous CIC ( Supplementary Figure 1), indicating that both CIC isoforms were dynamically re-localized during mitotic phases, thus raising the possibility that some CIC functions may be related to the cell cycle.…”

“…Motivated by the apparent dynamic association of CIC with chromosomes, and to explore the relationship between CIC function and the cell cycle, we performed IF assays on synchronized NHA-derived CIC KO cell lines 27 . We synchronized the parental NHA cell line and two of its derivative CIC KO cell lines (A2 and H9) at G2/M phase using the reversible cyclindependent kinase 1 (CDK1) inhibitor RO-3306 28 .…”

Capicua suppresses hepatocellular carcinoma progression by controlling the ETV4–MMP1 axis

“…Knockdown of CIC did not increase levels of PEA3 group genes in HepG2 cells (Fig. C), suggesting that CIC differentially regulates its target gene expression in a cell type–dependent manner, which is consistent with previous findings . Furthermore, the up‐regulation of ETV4 expression in CIC knockdown HCC cells was confirmed at the protein level (Fig.…”

A double‐edged sword: The world according to Capicua in cancer

“…Many CIC target genes upregulated in CDS are also found upregulated following CRISPR/Cas9mediated KO in isogenic cell lines. (64) The RTK/RAS/MAPK pathway is a common target of molecular targeted therapy, and acquired resistance for these therapies has been frequently observed. (1) Therefore, downstream modifiers such as CIC are good alternative targets for the therapy.…”