Synthetic Lethality between Cohesin and WNT Signaling Pathways in Diverse Cancer Contexts

Abstract

Cohesin is a highly conserved ring-shaped complex involved in topologically embracing chromatids, gene expression regulation, genome compartmentalization, and genome stability maintenance. Genomic analyses have detected mutations in the cohesin complex in a wide array of human tumors. These findings have led to increased interest in cohesin as a potential target in cancer therapy. Synthetic lethality has been suggested as an approach to exploit genetic differences in cancer cells to influence their selective killing. In this study, we show that mutations in ESCO1, NIPBL, PDS5B, RAD21, SMC1A, SMC3, STAG2, and WAPL genes are synthetically lethal with stimulation of WNT signaling obtained following LY2090314 treatment, a GSK3 inhibitor, in several cancer cell lines. Moreover, treatment led to the stabilization of β-catenin and affected the expression of c-MYC, probably due to the occupancy decrease in cohesin at the c-MYC promoter. Finally, LY2090314 caused gene expression dysregulation mainly involving pathways related to transcription regulation, cell proliferation, and chromatin remodeling. For the first time, our work provides the underlying molecular basis for synthetic lethality due to cohesin mutations and suggests that targeting the WNT may be a promising therapeutic approach for tumors carrying mutated cohesin.

Keywords: LY2090314; WNT; c-MYC; cancer; cohesin; synthetic lethality; β-catenin.

Figure 1

Effects of LY2090314 (LY) treatment in cancer cell lines carrying mutations in cohesin genes. (A) Western blotting showing that GSK3 levels did not change in MCF7 (1, untreated; 2, plus LY); HCT116 (3, untreated; 4, plus LY2090314); HCT15 (5, untreated; 6, plus LY), and IGROV1 (7, untreated; 8, plus LY4) cell lines. (B) LY2090314 treatment caused an increase in the expression of β-catenin in MCF7 (1, untreated; 2, plus LY); HCT116 (3, untreated; 4, plus LY); HCT15 (5, untreated; 6, plus LY), and IGROV1 (7, untreated; 8, plus LY) cell lines. (C) MTT assay shows that LY2090314 treatment caused the reduction of viability in all cell lines except for MCF7, the control cell lines without mutation in cohesin genes, and IGROV1 carrying mutation in the ESPL1 gene. (D) β-catenin was found to be co-precipitated with SMC1A, whereas no SMC1A signal was detected in the IPs using IgG-coated beads. * p < 0.05.

Figure 2

Effects of LY2090314 (LY) treatment on MYC locus. (A) MYC was downregulated in all cell lines carrying mutation in cohesin genes, apart from IGROV1 harboring ESPL1 mutation and MCF7, the control cell line. (B) LY treatment caused decreased binding of β-catenin at P1/P2 promoters of MYC locus in all cell lines carrying a single cohesin mutation, again except for IGROV1 and MCF7 cell lines. (C,D) ChIP experiments with antibodies against SMC1A or SMC3 showed decreased cohesin binding at both P0 and P1/2 promoters of the MYC gene following LY treatment in UO31 and HCT116, respectively. ** p < 0.01, * p < 0.05.

Figure 3

Effects of LY2090314 treatment on gene expression. GO term enrichment analysis of biological process that were significantly over-represented when considering differentially expressed genes following LY2090314 treatment.

Figure 4

Effects of LY2090314 treatment on gene expression. STRING network analysis of the 133 dysregulated proteins. They were grouped in two different clusters.

Figure 5

Model for the synthetic lethal interaction between LY2090314 treatment and mutated cohesin. In cancer cells with and without cohesin gene mutations, LY2090314 inhibits GSK3, which acts as an agonist of the WNT signaling pathway. In cells without cohesin mutation, this leads to an increase in both cohesin and β-catenin binding at MYC promoters, stimulating cell growth. Instead, in the presence of mutated cohesin, the recruitment of both β-catenin and cohesin at the MYC locus is decreased and MYC expression is downregulated, leading to decreased viability.