Recurrent Mutations in Cyclin D3 Confer Clinical Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia.

Abstract

Biomarkers of response and resistance to FLT3 tyrosine kinase inhibitors (TKI) are still emerging, and optimal clinical combinations remain unclear. The purpose of this study is to identify co-occurring mutations that influence clinical response to the novel FLT3 inhibitor pexidartinib (PLX3397). We performed targeted sequencing of pretreatment blasts from 29 patients with <i>FLT3</i> internal tandem duplication (ITD) mutations treated on the phase I/II trial of pexidartinib in relapsed/refractory <i>FLT3</i>-ITD+ acute myeloid leukemia (AML). We sequenced 37 samples from 29 patients with available material, including 8 responders and 21 non-responders treated at or above the recommended phase II dose of 3,000 mg. Consistent with other studies, we identified mutations in <i>NRAS, TP53, IDH2</i>, and a variety of epigenetic and transcriptional regulators only in non-responders. Among the most frequently mutated genes in non-responders was Cyclin D3 (<i>CCND3)</i>. A total of 3 individual mutations in <i>CCND3</i> (Q276*, S264R, and T283A) were identified in 2 of 21 non-responders (one patient had both Q276* and S264R). No <i>CCND3</i> mutations were found in pexidartinib responders. Expression of the Q276* and T283A mutations in <i>FLT3</i>-ITD MV4;11 cells conferred resistance to apoptosis, decreased cell-cycle arrest, and increased proliferation in the presence of pexidartinib and other FLT3 inhibitors. Inhibition of CDK4/6 activity in <i>CCND3</i> mutant MV4;11 cells restored pexidartinib-induced cell-cycle arrest but not apoptosis. Mutations in <i>CCND3</i>, a gene not commonly mutated in AML, are a novel cause of clinical primary resistance to FLT3 inhibitors in AML and may have sensitivity to CDK4/6 inhibition.