Prognostic Impact of Kinase Mutations and Minimal Residual Disease in Core-Binding Factor Leukemia
Authors: Sanford David , Cortes Jorge E. , Ravandi Farhad , Qiao Wei , Patel Keyur P. , Hoang Thuyvan , Kadia Tapan , Kantarjian Hagop M. , Borthakur Gautam 
Published: October 2019

Abstract
Background
Core-binding factor (CBF) acute myeloid leukemia (AML) is characterized by recurrent cytogenetic abnormalities t(8;21)(q22;q22) or inv(16)(p13q22)/t(16;16)(p13;q22), amenable for minimal residual disease (MRD) monitoring by quantitative reverse transcription polymerase chain reaction (RT-PCR). Kinase mutations (KIT, RAS, FLT3) have been reported to carry adverse prognostic implication. Promising results using FLAG-based treatment (fludarabine/Ara-C/G-CSF) in CBF leukemia in phase 2 [Borthakur G, Am J Hematol, 10, 89 (2014)] and phase 3 [Burnett AK, JCO, 27, 31 (2013)] clinical trials prompted us to review the prognostic impact of MRD evaluation and mutations.
Methods
The primary aim was to assess the prognostic impact of kinase-activating mutations (KIT, FLT3-TKD, FLT3-ITD, KRAS and NRAS) and MRD in CBF leukemia treated with FLAG-based regimens. Newly diagnosed patients were treated in 2 consecutive phase 2 clinical trials (clinicaltrials.gov identifier: NCT00801489) and received FLAG during induction (1 cycle) and consolidation (up to 6 cycles) in combination with either gemtuzumab (for 3 cycles) or idarubicin (for 2 cycles). Mutation analysis was performed at baseline on bone-marrow aspirates and MRD was measured on serial bone marrow aspirates using RT-PCR to detect RUNX1-RUNX1T1 and CBFB-MYH11 fusion transcripts, normalized to ABL1 transcript. The Kaplan-Meier method was used to estimate unadjusted overall survival (OS) and relapse-free survival (RFS). The Cox-proportional hazards model was used to estimate the association of covariates with OS and RFS. Landmark survival analysis was used to determine the association between OS/RFS and MRD, to account for time-dependent nature of this covariate.
Results:
One hundred and seven patients were included [t(8;21)=54, inv(16)=53]. Forty-eight were treated with FLAG + gemtuzumab and 59 were treated with FLAG + idarubicin. The 3 year OS and RFS for the cohort was 79% (95% CI, 71-89%) and 82% (95% CI, 74 - 91%) respectively with comparable outcomes with both regimens. The incidence of mutations in KIT, FLT3-ITD, FLT3-TKD and NRAS/KRAS was 13%, 7%, 10% and 38.5% respectively. In univariate analysis, the presence of mutations in KIT, FLT3 and NRAS/KRAS individually or together were not associated with OS or RFS. A 3-log or greater reduction in RT-PCR level at 1 month and 3-4 months was associated with improved RFS. A 3-log or greater reduction in RTPCR level at 6-9 months was also significantly associated with improved OS (HR 0.19, 95% CI 0.03 -1.0, p=0.05) and there was a trend towards improved OS with 3-log reduction at 1 month (HR 0.39, 95% CI 0.14 - 1.06, p=0.06).
Conclusion:
In contrast to some reports, mutations in KIT, FLT3 and RAS were not prognostic for RFS or OS in our study. Favorable outcomes using FLAG-based therapy in CBF leukemia may abrogate adverse impact of kinase mutations and this hypothesis needs to be clinically tested. The incidence of KIT mutations was slightly lower in our cohort in comparison to most previous reports, which may relate to differences in sensitivity of detection. Significantly, quantitative detection of MRD by PCR early on appears to be a broadly applicable predictor of relapse and may be the most relevant prognostic factor for clinical management of CBF leukemia patients.
Table 1. Univariate analysis showing hazard of relapse for all patients HR 95% CI p-value Age 1.00 0.97 - 1.04 0.89 Performance status (ECOG 1,2 vs. 0) 3.59 1.3 - 9.95 0.01 Therapy related (Y vs. N) 0.38 0.05 - 2.93 0.36 CBF Type - [inv(16) vs. t(8;21)] 0.95 0.34 - 2.62 0.92 Treatment (FLAG-ida vs. FLAG-GO) 1.59 0.56 - 4.51 0.38 Mutated KIT (Y vs. N) 1.55 0.35 -6.91 0.56 FLT3-ITD (Y vs. N) 0.7 0.09 - 5.39 0.73 FLT3-TKD (Y vs. N) 2.07 0.46 - 9.32 0.34 RAS - NRAS/KRAS (Y vs. N) 0.79 0.24 - 2.63 0.7 Any mutation -KIT/FLT3/ RAS (Y vs. N) 1.17 0.42 - 3.22 0.76 MRD - 3 log reduction at 1 month (Y vs. N) 0.23 0.06 - 0.81 0.02 MRD - 3 log reduction at 3-4 months (Y vs. N) 0.18 0.05 - 0.61 <0.01 MRD - 3 log reduction at 6-9 months (Y vs. N) 0.29 0.06 - 1.41 0.12 MRD - negative at 6-9 months (Y vs. N) 0.3 0.06 - 1.47 0.13
Figure 1. Outcomes by mutation status (KIT or FLT3 or RAS). (a) Overall survival; (b) Relapse free survival. Figure 1. Outcomes by mutation status (KIT or FLT3 or RAS). (a) Overall survival; (b) Relapse free survival.

Disclosures
Cortes: Teva: Research Funding; Novartis: Consultancy, Research Funding; BerGenBio AS: Research Funding; Pfizer: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Ariad: Consultancy, Research Funding; Astellas: Consultancy, Research Funding; Ambit: Consultancy, Research Funding; Arog: Research Funding; Celator: Research Funding; Jenssen: Consultancy.