Despite significant advances in the understanding of the biology of adult acute myelogenous leukemia (AML), overall survival remains poor due chiefly to the high rate of relapse after achieving complete remission as well as primary failure of induction chemotherapy. Efforts to further unravel the mechanisms leading to relapse and primary refractory disease are critical in order to guide the development of effective and durable treatment strategies for AML. To that end, this study seeks to elucidate the clonal relationship of AML in various disease phases.
We employed SNP 6.0 array-based genomic profiling of acquired copy number aberrations (aCNA) and copy neutral LOH (cnLOH) together with sequence analysis of recurrently mutated genes to characterize paired AML genomes. We analyzed 28 AML sample pairs from patients that achieved complete remission with chemotherapy and subsequently relapsed (median remission duration 272 days [range 25 – 1249 days]) and 11 sample pairs from patients with persistent disease following induction chemotherapy. AML cell samples were isolated with a Ficoll gradient, negatively selected using Miltenyi microbead columns, and then further purified with flow cytometric cell sorting. Processed DNA isolated from highly purified AML blasts and paired buccal DNA was hybridized to Affymetrix SNP 6.0 arrays. aCNA were visually identified using the dChip program in paired data displays and corroborated by algorithmic lesion scoring, and cnLOH was detected using internally developed software. In addition, 11 genes known to be recurrently mutated in AML (CEBPA, DNMT3A, IDH1, IDH2, RUNX1, BCORL1, NPM1, NRAS, KRAS, FLT3 and TP53) were resequenced in all 39 presentation samples to identify somatically acquired mutations. Genes found mutated in individual AML cases were subsequently tested for the persistence of the mutation in paired samples.
For the 28 paired specimens in the relapsed cohort, comparison of aCNA and cnLOH occurrences, gene mutation patterns and karyotypes revealed 6 cases that carried no aCNA/cnLOH at either presentation or relapse, but at presentation carried at least 1 gene mutation, all of which but one were stable in relapse (1 case lost a RUNX1 mutation but carried a t(8;21) in both disease stages); 11 cases that were characterized by the presence of aCNA/cnLOH at presentation, of which 55% (6 of 11) gained additional aCNA/cnLOH at relapse; 6 cases without aCNA/cnLOH at presentation that gained aCNA/cnLOH at relapse, of which 2 concurrently lost a FLT3-ITD or CEPBA mutation; and 5 cases that carried no informative genomic events. For the 11 paired specimens in the persistent AML cohort, the same comparison revealed 2 cases without aCNA/cnLOH before or after chemotherapy and stable gene mutations; 5 cases with aCNA/cnLOH at presentation that carried the same genomic lesions and gene mutations before and after chemotherapy; 3 cases with aCNA/cnLOH present at enrollment that lost some but not all of these aCNA/cnLOH and gained none after initial induction therapy; and 1 additional case that lost a FLT3-ITD.
Comparative analysis of these patterns demonstrates that relapsed AML invariably represents reemergence or evolution of an antecedent clone. Furthermore, all individual aCNA or cnLOH detected at presentation persisted at relapse indicating that this lesion type is proximally involved in AML evolution. Analysis of informative paired persistent AML disease samples uncovered at least two coexisting dominant clones of which at least one was chemotherapy sensitive and one resistant.
This detailed genomic analysis supports the conclusion that incomplete eradication of AML founder clones rather than stochastic emergence of fully unrelated novel clones underlies AML relapse and persistence with direct implications for clinical AML research.
No relevant conflicts of interest to declare.
Asterisk with author names denotes non-ASH members.