Ponatinib (AP24534) inhibits MEKK3-KLF signaling and prevents formation and progression of cerebral cavernous malformations

Abstract

Cerebral cavernous malformation (CCM) is a common cerebrovascular disease that can occur sporadically or be inherited. They are major causes of stroke, cerebral hemorrhage, and neurological deficits in the younger population. Loss-of-function mutations in three genes, CCM1, CCM2, and CCM3, have been identified as the cause of human CCMs. Currently, no drug is available to treat CCM disease. Hyperactive mitogen-activated protein kinase kinase Kinase 3 (MEKK3) kinase signaling as a consequence of loss of CCM genes is an underlying cause of CCM lesion development. Using a U.S. Food and Drug Administration-approved kinase inhibitor library combined with virtual modeling and biochemical and cellular assays, we have identified a clinically approved small compound, ponatinib, that is capable of inhibiting MEKK3 activity and normalizing expression of downstream kruppel-like factor (KLF) target genes. Treatment with this compound in neonatal mouse models of CCM can prevent the formation of new CCM lesions and reduce the growth of already formed lesions. At the ultracellular level, ponatinib can normalize the flattening and disorganization of the endothelium caused by CCM deficiency. Collectively, our study demonstrates ponatinib as a novel compound that may prevent CCM initiation and progression in mouse models through inhibition of MEKK3-KLF signaling.

Fig. 1. Ponatinib directly inhibits MEKK3 kinase activity.

(A to C) Computer modeling demonstrating that ponatinib can bind with the MEKK3 kinase domain in the ATP-binding pocket with hydrogen-bonds and π-π interaction (color) as demonstrated by a ribbon plot with full-length proteins (A) and the ribbon plot (B) and surface plot (C) of the binding pocket. (D) Immunoprecipitation (IP) demonstrating robust MEKK3 and MEK5 interactions. Deletion of 66 amino acids at the N terminus (MEKK3-ΔN66) abolishes the interaction. Deletion of 11 amino acids at the N terminus (MEKK3-ΔN11) or kinase-dead MEKK3 (MEKK3-KD) do not affect MEKK3-MEK5 interaction. (E) In vitro kinase assays showing changes in MEK5 phosphorylation following treatment with ponatinib. MEKK3-K391A, a kinase-dead mutant, was included as a negative control. The quantification of p-MEK5/MEK5 density ratios was shown between the blots. Results are representative of three independent experiments.

Fig. 2. Ponatinib blocks MEKK3-induced signaling in endothelial cells.

(A to F) Gene expression analysis of ponatinib-treated HUVECs with siRNA-induced CCM1 (si-CCM1) gene knockdown. Ponatinib treatment in HUVECs normalized the increased expression of KLF2 (A), eNOS (B), and AQP1 (C), as well as ADAMTS1 (D), ADAMTS4 (E), and ADAMTS9 (F), following CCM1 knockdown. (G to H) Western blotting analysis showing that ponatinib treatment decreased KLF2, eNOS, ADAMTS1, and ADAMTS4 expression. (I) Ponatinib treatment decreased the expression levels of ERK5 and p-ERK5. Error bars shown as SEM and significance determined by one-way analysis of variance (ANOVA) for multiple comparisons (n = 4). “*” indicates P < 0.05, “**” indicates P < 0.001, and n.s. indicates P > 0.05. Western blotting images are representatives of three independent experiments. The quantification of relative density ratios is shown underneath each blot.

Fig. 3. Ponatinib inhibits CCM lesion formation and progression in the CCM1-deficient CCM model.

(A) Schematic of experimental design. Neonatal pups at P1 were induced with 4-HT and treated with ponatinib at P6. Brains were collected at P13 for micro–computed tomography (CT) analysis. (B to G) Micro-CT imaging of CCM lesions in Ccm1^iECKO with (E to G) or without (B to D) ponatinib treatment. (H to J) Quantification of micro-CT analysis shows that ponatinib treatment in the Ccm1^iECKO reduced CCM lesion burden by 72% (H) and total lesions number by 35% (I) compared with that of sham-treated controls. CCM lesions distribution analysis showing decreased number (I) and total volume (J) of medium and large lesions in ponatinib-treated Ccm1^iECKO mice, but the number and collective volume of small lesions did not change. Error bars are shown as SEM, and significance was determined by Student’s t test. “**” indicates P < 0.001. n = 10 for the sham group, n = 9 for the ponatinib treatment group.

Fig. 4. Ponatinib inhibits CCM lesion formation and progression in the CCM2-deficient CCM model.

(A) Schematic of experimental design. (B to G) Micro-CT imaging of CCM lesions in the CCM2^iECKO with (E to G) or without (B to D) ponatinib treatment. (H and I) Quantification of micro-CT analysis shows that ponatinib treatment reduced CCM lesion burden by 85% (H) and total lesions number by 36% (I) in the Ccm2^iECKO mice compared with that of sham controls. (J) CCM lesions distribution analysis showing that the decreased lesion burden was mainly due to the reduction in the number of large lesions. Error bars are shown as SEM, and significance was determined by Student’s t test. “**” indicates P < 0.001; n = 8 for both sham and ponatinib treatment groups.

Fig. 5. Ponatinib impairs the growth of established CCM lesions in mouse model.

(A) Schematic of experimental design. Neonatal pups at P1 is induced with 4-HT and treated with ponatinib at P11. Brains and eyes were collected at P22 for micro-CT analysis and retina staining. (B to G) Micro-CT imaging of CCM lesions in brain in Ccm1^iECKO with (E to G) or without (B to D) ponatinib treatment. (H to J) Quantification of micro-CT analysis shows that ponatinib treatment reduced CCM lesion volume burden by 70% (H) without changes to the total lesion number (I) in Ccm1^iECKO mice compared with that of sham controls. CCM lesion distribution analysis shows decreased number of medium and large lesions in ponatinib-treated Ccm1^iECKO mice, but the number of small lesions increased (I). Collective volume of small and medium lesions did not change, but the collective volume of large lesions is decreased (J). (K to M) Isolectin staining of retinal vasculature demonstrates smaller CCM lesions in the ponatinib-treated retina (M) compared with that of sham treatment (K and L). Error bars are shown as SEM, and significance was determined by Student’s t test. “**” indicates P < 0.001; n = 7 for the sham group, n = 9 for the ponatinib treatment group.

Fig. 6. Ponatinib normalized MEKK3-induced signaling and endothelium ultrastructure in CCM mouse models.

(A to D) Gene expression analysis of ponatinib-treated Ccm1^iECKO mice. Ponatinib treatment at P6 normalized the increased expression of Klf2, Klf4, eNos, and Id1 in the freshly isolated brain endothelial cells from Ccm1^iECKO mice as analyzed at P8. Error bars are shown as SEM, and significance was determined by one-way ANOVA, n = 6. “**” indicates P < 0.001; (E) Western blotting analysis of Klf4 protein level in freshly isolated brain endothelial cells. Band density ratios are shown underneath the Klf4 blot. (F to J) Immunocytochemistry analysis shows increased pMLC2 level in the si-CCM1 (G) and si-CCM2 (I) endothelial cells compared with control (F), while treatment with ponatinib returned pMLC2 levels to near baseline (H and J). (K) Quantification of pML2 relative fluorescence intensity. (L to Q) Scanning electron microscope images of murine brain microvessels in P30 mouse brains. In microvessels without CCM lesions (L and M), endothelium ridges are present and aligned in the direction of blood flow. In CCM lesions (N and O), endothelium is flattened and disorganized. CCM lesions treated with ponatinib (P and Q) show partially normalized ridge structures of endothelium and alignment in the direction of blood flow. Results are representative of three independent experiments.