Regulation of Oncogenic Transcription and Tumor Growth in Pediatric Cancers by the CDK9 Inhibitor Kb-0742

Authors D. Saffran, E. Poon, G. Ibanez, J. Nakashima, S. Naffar-Abu Amara, C. Noe, T. Hood, P. Kumar, J. DiMartino, F. Dela Cruz, L. Chesler, C.Y. Lin

Background: Disruption of transcriptional regulatory networks that drive normal cellular differentiation and development can result in oncogenic transformation and transcriptional addiction. Many pediatric sarcomas are defined by/harbor oncogenic fusion proteins, resulting from chromosomal translocations such as the EWSR1 gene fused to an ETS family transcription factor (TF) gene (FLI1 or ERG) in Ewing sarcoma (ES), or PAX3/PAX7 and FOXO1 translocations in alveolar rhabdomyosarcoma (ARMS). In neuroblastoma, MYCN, a member of the MYC family of TFs, is often amplified and localizes to super enhancer regions, where it rewires lineage-specific transcriptional programs driving oncogenesis. Oncogenic TFs have proven difficult to target directly; we and others have proposed targeting associated transcriptional co-regulators to inhibit their activity. CDK9 interacts with many oncogenic TFs and is essential for TFmediated transcription elongation through phosphorylation of the C-terminal domain of RNA pol II. KB-0742 is a potent, selective, and orally bioavailable inhibitor of CDK9 currently in clinical development that shows antitumor activity in preclinical models of sarcoma and neuroblastoma.

Materials and Methods: Cell lines and low passage patient-derived cells (PDCs) were tested for antiproliferative effects of KB-0742, using either Cell Titer Glo (Promega) or Alamar Blue cell viability reagent (Bio-Rad). Pharmacodynamic (PD) markers of KB-0742 treatment, including phospho-SER2 (pSER2) on RNA pol II, MYCN, MYC, and cleaved poly ADP ribose polymerase (PARP), were measured by Western blot. The antitumor activity of KB-0742 was evaluated using patient-derived xenograft (PDX) models of ES and ARMS in vivo. Tumor samples and plasma were collected to determine PD effects and drug concentrations, respectively. The transgenic TH-MYCN model of neuroblastoma was used to study antitumor effects of KB-0742. All in vivo models were performed according to IACUC guidelines.

Results: KB-0742 decreased the viability of immortalized and low passage PDCs from ES, ARMS, and neuroblastoma. In neuroblastoma, cell lines with MYCN amplification were more sensitive to KB-0742 treatment. KB-0742–treated neuroblastoma cells had decreased pSER2, loss of expression of MYCN and MYC, and an induction of cleaved PARP. KB0742 treatment of a TH-MYCN transgenic mouse model resulted in regression of established tumors. In PDX models of ES and ARMS, KB0742 treatment inhibited tumor growth. Analysis of tumor samples revealed decreases in pSER2 and expression and function of the oncogenic TFs.

Conclusions: CDK9 targeting by KB-0742 inhibits growth of multiple pediatric tumor types by modulating the expression and activity of key oncogenic TFs. KB-0742 is being evaluated in a phase I dose-escalation trial in patients with relapsed or refractory solid tumors or NHL (NCT04718675).