Identification and Mechanistic Characterization of CMPD1 As a Selective Sensitizer of Histone Deacetylase Inhibitors in Myeloid Malignancies

Background: Histone deacetylase inhibitors (HDIs) have shown clinical activity in myeloid malignancies, albeit insufficient to justify single-agent therapy. Thus, we have sought targets/therapies that synergistically enhance the activity of HDIs for combination therapy. We conducted RNA-interference (RNAi) drug modifier screens with the HDI SAHA, and have previously reported convergence of multiple screen hits on different points of the p38-SAPK/JNK signaling pathway. However, in subsequent pharmacological studies, well-characterized p38α/β inhibitors SB2012190 and LY2228820, and JNK inhibitor SP600125 did not modulate SAHA anti-leukemic activity. Nonetheless, a putative MK2 substrate-selective p38 inhibitor known as CMPD1 (Biochemistry 2004 Sep 21; 43(37):11658-71) was found to potently synergize with SAHA in all AML cell lines tested (N=8) in a dose-dependent manner. Further, using ex vivo cultures of primary myeloid malignancies (N=14), CMPD1 showed strong, selective synergy with SAHA in malignant CD34⁺ isolated cells, as compared to little or no synergy in CD34-depleted cells. Furthermore, CMPD1 specifically synergized with SAHA and a similar HDI panobinostat, but was found to interact antagonistically with cytarabine, and only additively with azacitidine. Herein, we present additional data from our investigation to better understand the mechanism of CMPD1 synergy with HDIs for future clinical translation.

Results: Concurrent cell cycle and apoptosis measurements by flow cytometry show that single-agent CMPD1 results in a potent G2/M arrest that is resolved over time without a significant induction of apoptosis, whereas the combination of SAHA + CMPD1 results in a similar or increased level of G2/M arrest, which conversely culminates in a significant induction of apoptosis. The synergistic dose of single-agent SAHA used in these flow cytometry studies did not cause any significant cell cycle changes, and did not induce significant apoptosis alone in the AML cell lines studied. CMPD1 is known to be a MK2 substrate-selective p38 inhibitor; however, we find that CMPD1 potently increases the phosphorylation of MK2 at doses strongly synergistic with SAHA. This is not a universal activity of p38 inhibitors in our in vitro AML models, as the p38 inhibitor SB202190 does not increase MK2 phosphorylation alone or in combination with SAHA. We further hypothesized that CMPD1 synergizes with SAHA through a transcription-based mechanism, thus we measured mRNA expression by next-generation sequencing after SAHA and CMPD1 treatment alone, and in combination, in an AML cell line TF-1. We find that SAHA + CMPD1 treatment induces a synergistic increase in transcript levels of: i) several chemokines such as IL-8, CXCL1, CXCL2, and CXCL3, ii) inhibitor of DNA binding proteins ID2 and ID3, and iii) cell cycle regulator p21. Transcript levels of the Hippo pathway transcription factor YAP1 were also found to be increased by CMPD1 treatment in TF-1. We confirm an increase of total YAP1 protein levels by western blot. We also find an increase of YAP1 phosphorylation at serine 127 in CMPD1 or CMPD1 + SAHA treated samples in several AML cell lines, yet we find that Ser-127 phosphorylated YAP1 is located in the nucleus. Consistent with YAP1 Ser-127 phosphorylation, we find that upstream signaling kinase LATS1 is activated/phosphorylated at serine 909 in AML cell lines after treatment with CMPD1 or SAHA + CMPD1. We also confirm a synergistic increase in p21 protein levels upon SAHA + CMPD1 treatment by western blot in several AML cell lines. Changes in the protein levels of ID2 and ID3 were confirmed in TF-1 by western blot; however, ID protein levels appear to be uniquely affected by CMPD1 or the combination in a cell line-dependent manner.

Conclusion: CMPD1 selectively synergizes with histone deacetylases inhibitors in myeloid malignancies. The synergistic activity of this combination highlights the potential for selectively targeting malignant CD34⁺ cells. The phosphorylation of LATS1 observed is consistent with i) the known roles for LATS1 in cell cycle regulation, ii) the G2/M arrest observed with CMPD1, and iii) the downstream phosphorylation of YAP1 observed. These findings linking CMPD1 with LATS1/YAP1 await further study and characterization. Although CMPD1 is not a clinically-relevant compound, CMPD1 may be used as a scaffold or tool compound to enable future development and research.