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The modulation of pre‐mRNA splicing is proposed as an attractive anti‐neoplastic strategy, especially for the cancers that exhibit aberrant pre‐mRNA splicing. Here, we discovered that T‐025 functions as an orally available and potent inhibitor of Cdc2‐like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T‐025 reduced CLK‐dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression in vitro and in vivo . Further, through growth inhibitory characterization, we identified high CLK2 expression or MYC amplification as a sensitive‐associated biomarker of T‐025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T‐025 treatment. MYC activation, which altered pre‐mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated in vivo anti‐tumor efficacy of T‐025 in an allograft model of spontaneous, MYC‐driven breast cancer, at well‐tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC‐driven cancer patients. Synopsis MYC oncogene is a highly valuable target for cancer therapy. A newly discovered CLK inhibitor, T‐025, exhibited anti‐tumor efficacies against cancers with a high CLK2 expression, as well as against MYC‐driven cancers, as a result of attacking a MYC‐dependent vulnerability. A novel and potent CLK inhibitor, T‐025, was discovered and characterized as a new pre‐mRNA splicing modulating anti‐cancer agent. T‐025 exhibited in vivo anti‐tumor efficacy in both cell line xenograft tumors and mice spontaneous allograft tumors. The expression level of CLK2 in each cell line was associated with the growth‐inhibitory sensitivity and magnitude of alternative skipped exons in response to T‐025 treatment. T‐025 showed a higher growth inhibition effect on MYC‐amplified solid cancer cell lines than on non‐MYC‐amplified solid cancer cell lines and induced synergistic cell death with ectopic MYC activation. Graphical Abstract MYC oncogene is a highly valuable target for cancer therapy. A newly discovered CLK inhibitor, T‐025, exhibited anti‐tumor efficacies against cancers with a high CLK2 expression, as well as against MYC‐driven cancers, as a result of attacking a MYC‐dependent vulnerability.

Background Dysregulation of alternative splicing plays a pivotal role in tumorigenesis and metastasis in triple-negative breast cancer (TNBC). Serine/arginine-rich (SR) proteins, essential components of the spliceosome, undergo phosphorylation by Cdc2-like kinase (CLK). Here we explored the impact of pharmacological inhibition of CLK using a novel inhibitor, T-025, on the spliceosome complex and transcriptional responses in relation to cell proliferation and migration in TNBC. Methods We evaluated the anti-proliferative and anti-migratory efficacy of T-025 in a spectrum of TNBC cell lines. Fluorescent reporter cell lines and flowcytometry were used to determine the effect of T-025 on cell cycle. Deep RNA sequencing was performed to unravel the differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) upon T-025 treatment. Pulldown/MS was used to uncover the impact of T-025 on SRSF7 interactome. Live-cell imaging and photobleaching experiments were conducted to determine the subnuclear localization of SRSF7-GFP and its dynamic mobility. Results T-025 exhibited a potent anti-proliferative effect in a spectrum of TNBC cell lines, particularly in highly proliferative cell lines. Treatment with T-025 induced cell cycle arrest in the G1-S phase, resulting in an increased proportion of aneuploidy cells and cells with 4 N DNA. T-025 significantly inhibited cell migration in highly migratory TNBC cell lines. Deep RNA sequencing uncovered numerous DEGs and ASGs upon T-025 treatment, which were significantly enriched in pathways related to cell division, RNA splicing and cell migration. Pulldown/MS showed that SRSF7 interacted more with nuclear-speckle-residing proteins, while less with RNA helicases and polymerases upon T-025 treatment. Enhanced interactions between SRSF7 and other phosphorylated SR proteins localized at nuclear speckles were also observed. Live-cell imaging indicated that T-025 treatment induced the accumulation of SRSF7-GFP at nuclear speckles and nuclear speckles’ enlargement, restricting its protein dynamic mobility. Conclusions CLK inhibition using T-025 leads to the accumulation of splicing factors at nuclear speckles and stalls their release to splicing sites, resulting in the RNA splicing reprogramming of a large number of genes involved in cell division, migration and RNA splicing. Our findings provide evidence that T-025 could be a promising therapeutic drug for TNBC patients.

Platinum resistance represents a major barrier to the survival of patients with ovarian cancer (OC). Cdc2‐like kinase 2 (CLK2) is a major protein kinase associated with oncogenic phenotype and development in some solid tumors. However, the exact role and underlying mechanism of CLK2 in the progression of OC is currently unknown. Using microarray gene expression profiling and immunostaining on OC tissues, we found that CLK2 was upregulated in OC tissues and was associated with a short platinum‐free interval in patients. Functional assays showed that CLK2 protected OC cells from platinum‐induced apoptosis and allowed tumor xenografts to be more resistant to platinum. Mechanistically, CLK2 phosphorylated breast cancer gene 1 (BRCA1) at serine 1423 (Ser1423) to enhance DNA damage repair, resulting in platinum resistance in OC cells. Meanwhile, in OC cells treated with platinum, p38 stabilized CLK2 protein through phosphorylating at threonine 343 of CLK2. Consequently, the combination of CLK2 and poly ADP‐ribose polymerase inhibitors achieved synergistic lethal effect to overcome platinum resistance in patient‐derived xenografts, especially those with wild‐type BRCA1. These findings provide evidence for a potential strategy to overcome platinum resistance in OC patients by targeting CLK2. Cisplatin‐stimulated p38 phosphorylates Thr343 of CLK2 to increase CLK2 protein stability by blocking its ubiquitination and degradation. Increased CLK2 activates BRCA1 to enhance DNA damage repair and induced resistance to cisplatin. Thus, targeting the CLK2/BRCA1 axis overcomes platinum resistance in ovarian cancer.

Host cdc2-like kinase 1 (CLK1) is responsible for the alternative splicing of the influenza virus M2 gene during influenza virus infection and replication that has been recognized as a potential anti-influenza virus target. In this study, we showed that gallocatechin-7-gallate (J10688), a novel CLK1 inhibitor isolated from Pithecellobium clypearia Benth, exerted potent anti-influenza virus activity in vivo and in vitro. ICR mice were intranasally infected with a lethal dose of H1N1. Administration of J10688 (30 mg·kg − 1 ·d −1 , iv, for 5 days) significantly increased the survival rate of the H1N1-infected mice to 91.67% and prolong their mean survival time from 5.83 ± 1.74 days to 13.66 ± 1.15 days. J10688 administration also slowed down body weight loss, significantly alleviated influenza-induced acute lung injury, reduced lung virus titer, elevated the spleen and thymus indexes, and enhanced the immunological function. We further explored its anti-influenza mechanisms in the H1N1-infected A549 cells: as a novel CLK1 inhibitor, J10688 (3, 10, 30 μmol/L) dose-dependently impaired synthesis of the viral proteins NP and M2, and significantly downregulated the phosphorylation of splicing factors SF2/ASF and SC35, which regulate virus M2 gene alternative splicing. As a novel CLK1 inhibitor with potent anti-influenza activity in vitro and in vivo, J10688 could be a promising antiviral drug for the therapy of influenza A virus infection.

Recent studies have shown that there exists a family of protein kinases structurally and functionally related to the yeast cell cycle regulatory kinase cdc2 [Meyerson, M., Faha, B., Su, L.-K., Harlow, E. \\& Tsai, L.-H. (1991) Cold Spring Harbor Symp. Quant. Biol. 56, 177-186 and Meyerson, M., Enders, G. H., Wu, C.-L., Su, L.-K., Gorka, C., Nelson, C., Harlow, E. \\& Tsai, L.-H. (1992) EMBO J. 11, 2909-2917]. Two members of cdc2 family, p34cdc2(also named cdk1) and cdk2, have been identified in mammalian cells. cdk1 kinase regulates the progression from G2to M phase, and cdk2 kinase has been proposed to regulate the progression from G1to S phase. In this work, we have cloned and structurally characterized a third member of the cdc2 kinase family with 58% amino acid sequence identity to mouse cdk1 and 61% identity to human cdk2. We call this kinase neuronal cdc2-like kinase (nclk) because, in contrast to either cdk1 or cdk2, nclk is expressed at high levels in terminally differentiated neurons no longer in the cell cycle. Previous studies have shown [Hisanaga, S., Kusubata, M., Okumura, E. \\& Kishimoto, T. (1991) J. Biol. Chem. 266, 21798-21803 and Guan, R. J., Hall, F. L. \\& Cohlberg, J. A. (1992) J. Neurochem. 58, 1365-1371] that cdk1 kinase, but not other structurally defined protein kinases, could phosphorylate the repeated Lys-Ser-Pro (KSP) motifs found in mammalian high and middle molecular mass neurofilament subunits in vitro, but the precise molecular nature of the endogenous neuronal KSP kinase has remained undefined. The structural similarity of nclk to cdk1 kinase and its high level of expression in terminally differentiated neurons suggest that nclk may play a role in the phosphorylation of the neurofilament KSP repeats in vivo, a function distinct from cell cycle regulation.

Glioblastoma (GBM; grade 4 glioma) is a highly aggressive and incurable tumor. GBM has recently been characterized as highly dependent on alternative splicing, a critical driver of tumor heterogeneity and plasticity. Estrogen-related receptor beta (ERRβ, ESRRB, NR3B2) is an orphan nuclear receptor expressed in the brain, where alternative splicing of the 3' end of the pre-mRNA leads to the production of three validated ERRβ protein products: ERRβ short form (ERRβsf), ERRβ2, and ERRβ exon 10-deleted (ERRβ-Δ10). Our prior studies have shown the ERRβ2 isoform to play a role in G2/M cell cycle arrest and induction of apoptosis, in contrast to the function of the shorter ERRβsf isoform in senescence and G1 cell cycle arrest. In this study, we sought to better define the role of the pro-apoptotic ERRβ2 isoform in GBM. We show that the ERRβ2 isoform is located in the nucleus, but also the cytoplasm. ERRβ2 suppresses GBM cell migration, interacts with the actin nucleation-promoting factor cortactin, and an ERRβ agonist is able to remodel the actin cytoskeleton and similarly suppress GBM cell migration. We further show that inhibition of the splicing regulatory cdc2-like kinases (CLKs) in combination with an ERRβ agonist shifts isoform expression in favor of ERRβ2 and potentiates inhibition of growth and migration in GBM cells and intracranial tumors. Footnotes * Figures 1, 5, and 6 revised