Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms

Haijiao Zhang,Anna Reister Schultz,Vinay Jain,Richard Sweat,Jorge Cortes,Hoang Ho,Brian J Druker,Yee Ling Lam,Christopher A Eide,Richard N Henson ,Evan F Lind ,Tamilla Nechiporuk,Hagop M Kantarjian,Erik Segerdell,Amy S Carlos ,Samantha L Savage ,Sharyn D Baker,Chenwei Lin,Daniel Bottomly,Daelynn R Buelow,Courtney A Follit ,Shannon K Mcweeney,Farhad Ravandi,Guillermo Garcia‐Manero ,Libbey White,Robert H Collins ,Beth Wilmot,Gautam Borthakur,Robert P Searles ,Jeffrey W Tyner

doi:10.1038/s41467-018-08263-x

Abstract

FLT3 mutations are prevalent in AML patients and confer poor prognosis. Crenolanib, a potent type I pan-FLT3 inhibitor, is effective against both internal tandem duplications and resistance-conferring tyrosine kinase domain mutations. While crenolanib monotherapy has demonstrated clinical benefit in heavily pretreated relapsed/refractory AML patients, responses are transient and relapse eventually occurs. Here, to investigate the mechanisms of crenolanib resistance, we perform whole exome sequencing of AML patient samples before and after crenolanib treatment. Unlike other FLT3 inhibitors, crenolanib does not induce FLT3 secondary mutations, and mutations of the FLT3 gatekeeper residue are infrequent. Instead, mutations of NRAS and IDH2 arise, mostly as FLT3-independent subclones, while TET2 and IDH1 predominantly co-occur with FLT3-mutant clones and are enriched in crenolanib poor-responders. The remaining patients exhibit post-crenolanib expansion of mutations associated with epigenetic regulators, transcription factors, and cohesion factors, suggesting diverse genetic/epigenetic mechanisms of crenolanib resistance. Drug combinations in experimental models restore crenolanib sensitivity.

Highlights

FMS-like tyrosine kinase 3 (FLT3) mutations are prevalent in Acute myeloid leukemia (AML) patients and confer poor prognosis
We first determined whether secondary FLT3 mutations were acquired during treatment by sequencing available patient samples obtained after at least 28 days of crenolanib treatment as well as baseline samples obtained before crenolanib treatment initiation
Consistent with previous reports, no de novo activation loop mutations were detected in FLT3-internal tandem duplications (ITD) patients after crenolanib treatment as determined from 18 FLT3-ITD patients sequenced by exome sequencing (mean ± standard error of the mean (SEM) coverage is 177 ± 24) and 6 FLT3-ITD patients sequenced by Miseq[31]

Summary

Introduction

FLT3 mutations are prevalent in AML patients and confer poor prognosis. Crenolanib, a potent type I pan-FLT3 inhibitor, is effective against both internal tandem duplications and resistance-conferring tyrosine kinase domain mutations. Similar to other FLT3 TKIs observed in early clinical trials, despite initial response, subsequent drug resistance and disease relapse occurred in the majority of patients[8,9,14,25,26]. We were initially interested in investigating whether crenolanib resistance followed similar mechanisms as other FLT3 TKIs (quizartinib, gilteritinib and sorafenib)[27,28,29,30], where secondary FLT3 mutations in the activation loop and/or gatekeeper residue play a major role. Given the nature of heterogeneous genetic alterations and selective pressure of chemotherapy and prior TKI treatment in relapsed/refractory AML patients on these trials, we aimed to characterize the impact of co-occurring clones or subclones with other somatic mutations on crenolanib response and disease recurrence

Methods

Results

Conclusion