Identification of a Novel Function of CX-4945 as a Splicing Regulator

<div><p>Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks) <i>in vitro</i> and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR) proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC₅₀ = 3–90 nM) was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.</p></div

CX-4945 affects alternative splicing in a CK2-independent manner.

<p>(A) Two other inhibitors of CK2, TBB and TBCA, were also tested to determine whether splicing regulation by CX-4945 is related to CK2 activity. 293T cells were treated with 10 µM CX-4945 or 100 µM TBB or and TBCA for 12 hours. Inhibitory activities of CX-4945, TBB, and TBCA on CK2 were assessed by examination of phosphorylation of AKT(S129), the major substrate of CK2. Total levels of AKT were also monitored as a control. hnRNP A1 was used as a loading control. (B) Alternatively spliced CK2 α′, ELL2, CPEB1, PRPSAP2, and QRSL1 mRNAs were examined by RT-PCR. PCR products of normal and alternatively spliced isoforms are denoted by black arrowheads. An extra PCR product of the QRSL1 gene appeared in TBB-treated samples and is denoted by an asterisk. All experiments were performed twice, and representative data for each are presented.</p

CX-4945 modulates SR protein phosphorylation via direct inhibition of Clks.

<p>(A) Total protein extracts from 293T cells treated with CX-4945 (1 and 10 µM) or TG-003 (10 and 50 µM) for 1 hour were separated by SDS-PAGE, and phosphorylated SR proteins were monitored by western blotting using the phosphoSR monoclonal antibody (1H4). SRSF1, SRSF4, SRSF9, and hnRNP A1 proteins were also monitored as controls. Western blotting was performed twice, and representative data are presented. (B) The phosphorylated SR proteins in (A) were quantified, and amounts of each protein relative to those of DMSO-treated samples are shown. The average and SD values were determined from two independent experiments. (C) The potent inhibition of Clks by CX-4945 was observed in <i>in vitro</i> kinase assays conducted by Life Technologies using recombinant human Clk1, Clk2, Clk3, SRPK1, SRPK2, and Ck2 α proteins. The average and SD values were determined from two independent assays. The IC₅₀ values were determined using PRISM software. Detailed experimental procedures are described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094978#s2" target="_blank">Materials and Methods</a>.</p

Effect of CX-4945 on pre-mRNA splicing.

<p>(A) CX-4945 induces expression of an unexpected CK2 α′ transcript, CK2 α′△. RT-PCR corresponding to exons 5–6–7 was performed with total RNA from DMSO- or CX-4945-treated 293T cells. (B) CX-4945 rapidly induces the expression of CK2 α′△. 293T cells were treated with CX-4945 for the times indicated prior to RNA preparation and RT-PCR analysis. GAPDH mRNA was analyzed as a control. (C) Analysis of the DNA sequence of CK2 α′△ revealed that it represents the exon6-skipped product (CK2 α′△exon6) of CK2 α′ pre-mRNA. The normally spliced (CK2 α′) and alternatively spliced (CK2 α′△exon6) products are illustrated schematically.</p

ATP-competitive inhibition of Clks by CX-4945.

<p>(A) Diagram of the chemical structure of CX-4945 (B) Competition of CX-4945 with ATP for inhibition of Clk2 (C) Structural model of the Clk2 in complex with CX-4945. CX-4945 was predicted to bind to the ATP-binding site of Clk2. (D) The predicted binding mode between CX-4945 and Clk2. Amino acids in the active site are denoted by yellow sticks, and CX-4945 is indicated by green sticks. Hydrogen bonds are denoted as dotted black lines, and oxygen and nitrogen atoms are indicated as red and blue sticks, respectively.</p

Inactivation of human DGAT2 by oxidative stress on cysteine residues

<div><p>Diacylglycerol acyltransferases (DGATs) have a crucial role in the biosynthesis of triacylglycerol (TG), the major storage form of metabolic energy in eukaryotic organisms. Even though DGAT2, one of two distinct DGATs, has a vital role in TG biosynthesis, little is known about the regulation of DGAT2 activity. In this study, we examined the role of cysteine and its oxidation in the enzymatic activity of human DGAT2 <i>in vitro</i>. Human DGAT2 activity was considerably inhibited not only by thiol-modifying reagents (NEM and IA) but also by ROS-related chemicals (H₂O₂ and β-lapachone), while human DGAT1 and GPAT1 were little affected. Particularly, ROS-related chemicals concomitantly induced intermolecular disulfide crosslinking of human DGAT2. Both the oxidative inactivation and disulfide crosslinking were almost completely reversed by the treatment with DTT, a disulfide-reducing agent. These results clearly demonstrated the significant role of ROS-induced intermolecular crosslinking in the inactivation of human DGAT2 and also suggested DGAT2 as a redox-sensitive regulator in TG biosynthesis.</p></div

Susceptibility of human DGAT2 activity to cysteine-specific modifying reagents.

<p>(A) Membrane extracts from human DGAT2-overexpressing Sf9 insect cells were treated with indicated concentrations of NEM or IA. Human DGAT2 activity was measured by using the conventional extraction-based <i>in vitro</i> DGAT assay. The relative DGAT2 activity in percentage was calculated by setting the value from DMSO-treated sample to 100%. (B) Selective inhibitory effect of NEM on human DGAT2 activity compared to that on human DGAT1 and GPAT1. Membrane extracts from human DGAT2-, DGAT1-, or GPAT1-overexpressing Sf9 insect cells were treated with indicated concentrations of NEM or DMSO. Human DGAT1, DGAT2, and GPAT1 activity was measured by using the conventional extraction-based <i>in vitro</i> assays which are described in detail in the Materials and Methods section. The relative enzyme activity in percentage was calculated by setting the value from DMSO-treated sample to 100%. The mean values and standard deviations were determined from four independent assays.</p

Multimeric complex of human DGAT2 formed by ROS-induced intermolecular disulfide crosslinking <i>in vitro</i>.

<p>Membrane extracts from human DGAT2-overexpressing Sf9 insect cells were treated with H₂O₂ (A) or β-lapachone (B) in the presence or absence of 20 mM DTT and subjected to Western blot analysis using anti-DGAT2 antibody. The amount of monomeric human DGAT2 proteins presented as redDGAT2 in (A) and (B) was quantified and the amount of relative redDGAT2 protein was calculated by setting the values from samples treated with PBS (C) or DMSO (D) to 100%. Asterisk indicates a non-specific band.</p

Inhibitory effect of ROS and ROS generator on human DGAT2 catalytic activity.

<p>Membrane extracts from human DGAT2-overexpressing Sf9 insect cells were treated with indicated concentrations of H₂O₂ (A) or β-lapachone (B) in the presence or absence of 20 mM DTT. Human DGAT2 activity was measured by using the conventional extraction-based <i>in vitro</i> assays which are described in detail in the Materials and Methods section. The activities of membrane extracts treated with PBS (instead of H₂O₂) or DMSO (instead of β-lapachone) in the absence of DTT were defined as 100%. The mean values and standard deviations were determined from four independent experiments.</p

Multimeric complex of human DGAT2 formed by H₂O₂-induced disulfide crosslinking in human cells.

<p>Huh-7 cells were transfected with plasmid overexpressing human DGAT2 for 47 hours and further incubated with indicated concentrations of H₂O₂ for 1 hour. Cell extracts were harvested in a way described in Materials and Methods section and subjected to Western blot analysis using anti-DGAT2 antibody (A). The amount of monomeric human DGAT2 proteins presented as redDGAT2 in (A) was quantified and the amount of relative redDGAT2 protein was calculated by setting the values from samples treated with PBS to 100% (B). The mean values and standard deviations were determined from three independent experiments. Asterisks indicate non-specific bands.</p