Genetic Patterns of Relapsed AML Differ Significantly from First Manifestation and Are Dependent on Cytogenetic Risk Groups at Diagnosis: Results in 175 Patients with Paired Samples

Introduction: Genetic changes between diagnosis and relapse in AML have not been analyzed comprehensively yet. Especially in the favorable risk group (acute promyelocytic leukemia (APL) with PML-RARA, and core binding factor (CBF) leukemias with CBFB-MYH11 or RUNX1-RUNX1T1) data is scarce.

Aim: To investigate genetic patterns in AML with favorable risk cytogenetics at diagnosis and at relapse in comparison to all other AML subtypes.

Patients and Methods: We investigated 175 AML patients diagnosed by cytomorphology, immunophenotyping and cytogenetics following WHO criteria both at diagnosis and at relapse (350 samples). Cytogenetic risk stratification followed MRC as favorable, intermediate, and adverse (Grimwade, Blood 2010). 30 patients were diagnosed as APL or CBF leukemia (favorable), while 122 patients were intermediate, and 23 adverse risk. Data on molecular mutations was available for subsets of patients including ASXL1, CEBPA, DNMT3A, EZH2, FLT3-ITD, FLT3-TKD, KIT, IDH1, IDH2, MLL-PTD, NPM1, NRAS, KRAS, RUNX1, TET2, TP53, and WT1. Gene mutations were analyzed by Sanger sequencing, NGS, melting curve analysis, or gene scan. Cytogenetics was available for all 350 samples.

Results: Changes in mutational and cytogenetic patterns of APL and CBF leukemias: 28 relapse samples revealed in total 22 gene mutations in 12 genes, with a median number of 0.8 mutations per patient. 7 patients (25%) showed no mutation, 20 (71%) showed 1 mutation, and 1 (4%) had 2 mutations. Most frequently FLT3-ITD was found (n=5), followed by mutations in KIT (n=3), EZH2, FLT3-TKD, NRAS, TET2 (for each n=2), and ASXL1, DNMT3A, IDH1, KRAS, TP53, and WT1(for each n=1). In 17/20 patients with molecular mutations identified either at relapse or primary diagnosis both samples were analyzed for the specific mutation. 22 mutations were present in this subset. Of these 10 (46%) mutations were already detected at primary diagnosis and thus remained stable, while 3/22 (14%) mutations were gained and 9/22 (41%) were lost at relapse. Including patients with no mutation revealed that 13/24 (54%) patients showed an unchanged mutation pattern while 11/24 (46%) gained or lost mutations. The karyotype was stable in 16/30 (53%) cases with favorable cytogenetics, while 14/30 (47%) showed cytogenetic changes: although the main cytogenetic aberration remained unchanged in all relapse samples the latter patients showed either clonal evolution (n=11), clonal regression (n=2) or both (n=1).

Changes in mutational and cytogenetic patterns of AML with intermediate risk cytogenetics: In the intermediate risk group (97/122 patients (80%) had normal karyotype) the cytogenetic changes were slightly less frequent with 44/122 (36%). Interestingly, in this group 3 patients occurred with a totally different karyotype at relapse compared to primary diagnosis. In 2 cases, however, the molecular markers remained stable, while in 1 patient also the mutation pattern changed completely. Therefore, the latter one might be a t-AML, while the other two are most likely relapses. The molecular mutation patterns were unstable in this subgroup with 56/94 (60%) patients showing mutational gains as well as losses.

Changes in mutational and cytogenetic patterns of AML with adverse cytogenetics: 11/23 patients (48%) showed cytogenetic changes. Also in this group 1 patient might have acquired a t-AML rather than a relapse as suggested by complete changes in cytogenetics and molecular markers. Only 5/18 (26%) showed changes in the mutational pattern at all. Of notice, while in favorable AML mutation patterns changed at relapse more by losses than by gains of mutations, in the intermediate and adverse groups gains of mutations were more frequent. The latter two groups had more mutations already at primary diagnosis and acquired additional mutations mostly in FLT3-ITD but also in the whole spectrum of analyzed genes, particularly in prognostically unfavorable genes such as TP53, ASXL1, RUNX1, DNMT3A, or WT1.

Conclusions: 1) In AML with favorable cytogenetics the defining aberrations persist at relapse but changes in karyotype and mutational pattern occur in 47% and 46% of cases. 2) AML with intermediate risk cytogenetics is characterized by instability predominately on the molecular level. 3) AML with adverse cytogenetics shows only few changes in the molecular profile but high karyotype instability.