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

Abstract

Background: CIC is a transcriptional repressor inactivated by loss-of-function mutations in several cancer types, including gliomas, lung cancers, and gastric adenocarcinomas. CIC alterations and/or loss of CIC activity have been associated with poorer outcomes and more aggressive phenotypes across cancer types, which is consistent with the notion that CIC functions as a tumour suppressor across a wide range of contexts.Results: Using mammalian cells lacking functional CIC, we found that CIC deficiency was associated with chromosome segregation (CS) defects, resulting in chromosomal instability and aneuploidy. These CS defects were associated with transcriptional dysregulation of spindle assembly checkpoint and cell cycle regulators. We also identified novel CIC interacting proteins, including core members of the SWI/SNF complex, and showed that they cooperatively regulated the expression of genes involved in cell cycle regulation. Finally, we showed that loss of CIC and ARID1A cooperatively increased CS defects and reduced cell viability. Conclusions:Our study ascribes a novel role to CIC as an important regulator of the cell cycle and demonstrates that loss of CIC can lead to chromosomal instability and aneuploidy in human and murine cells through defects in CS, providing insight into the underlying mechanisms of CIC's increasingly apparent role as a "pan-cancer" tumour suppressor.

Making heads or tails – the emergence of capicua (CIC) as an important multifunctional tumour suppressor

“…This functional interaction with the SWI/SNF complex may be critical for the dynamic regulation of the epigenome during normal differentiation or contribute to epigenomic dysregulation in cancer. CIC interaction with several SWI/SNF complex members (ARID1A, ARID2, SMARCA2, SMARCC1) has also been observed during mitosis, colocalising around chromosomes during cytokinesis, suggesting that CIC may also play a role in maintaining chromosomal integrity during mitosis [55]. CIC interaction with other proteins involved in epigenomic gene silencing, such as L3MBTL3, MECP2 and UTP3, has also been observed, further supporting the notion of CIC's involvement in chromatin maintenance and/or architecture [55].…”

“…In ELS, activation of CCNE1 by CIC-DUX4 fusion promotes tumour survival and proliferation [76]. Context-dependent dysregulation of cyclin genes CCND1/2, CCNE1/2, CCNA1/2 and CCNB1/2 has also been observed in several cancers with CIC aberrations [32,40,55,76]. Taken together, these studies suggest that apart from the ETS factors, CIC is a regulator of an array of context-dependent cell cycle pathways and acts as a general regulator of the cell cycle.…”

“…Another hallmark of cancer that CIC has been linked to is genomic instability. Loss of CIC in normal human astrocytes has been found to dysregulate several mitotic regulators (HMGA1, PLK1/3, AURKA1), resulting in mitotic defects, chromosomal instability, and aneuploidy [55]. Interestingly, chromosomal instability and aneuploidy was recently demonstrated to induce epithelial cell invasion through downregulation of CIC in a Drosophila model [77].…”

TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L

“…Using CIC KO cell lines with stably expressing FLAG-tagged CIC-S [ 30 ], CIC interaction with 14-3-3 regulatory proteins and the nuclear pore protein TPR was observed to increase following siRNA knockdown of ATXN1L using PLA (Additional file 5 : Figure S4A, B, C). CIC was not found to interact with many previously identified proteins involved in transcriptional regulation such as SIN3A, HDAC1/2, and members of the SWI/SNF complex in our ATXN1L KO background which may contribute to the dysregulation of CIC target genes [ 30 – 32 ]. Among the most highly enriched CIC interactors was the E3-ligase TRIM25.…”

“…Cells were harvested 24–72 h post-transfection for experiments. Stable transfection of FLAG-tagged CIC-S in CIC KO cells was performed as previously described [ 30 ].…”