Mutational and Cytogenetic Dynamics at Diagnosis and Relapse in Acute Myeloid Leukemia: Influence of Intensity and Type of Treatment

Introduction: Cytogenetic and molecular aberrations are common at diagnosis in patients with acute myeloid leukemia (AML) and may have significant prognostic impact. Relapse after prior response is associated with a poor outcome. The dynamics of cytogenetic and molecular abnormalities at relapse and their impact on outcome is less well studied.

Methods: This is a retrospective single center study including patients with AML diagnosed from April 2017 to October 2022 who relapsed after achieving a prior response. Mutations were detected using a targeted 81-gene NGS panel and cytogenetics were assessed using conventional karyotyping and FISH testing. To assess disappearance, maintenance or appearance of cytogenetic and molecular aberrations, they were evaluated at diagnosis and relapse and differences in incidence were evaluated with the Chi-square and Fisher test.

Results: The cohort includes 164 patients who had relapsed after achieving remission. The median age at diagnosis and relapse was 67 years (range, 20-94) and 68 years (range, 21-95). 53% were male. Patients received intensive treatment (IT; 40% of patients, 41% of whom with the addition of venetoclax) or low intensity therapy (LIT; 60% of patients, 72% with venetoclax). The median time from diagnosis to relapse was 8.9 months (range, 2.2-52). According to the ELN 2022 risk classification, 15%, 15% and 70% had favorable, intermediate and adverse risk, respectively.

At diagnosis, the most frequent mutations were DNMT3A (32%), TP53 (31%), RUNX1 (19%), TET2 (18%), SRSF2 (17%) and NPM1 (17%). At relapse, the most frequent mutations were DNMT3A (35%), TP53 (35%), TET2 (24%), RUNX1 (20%) and SRSF2 (17%). The median number of mutations per patient at diagnosis and relapse was 3 (0-12) and 3 (0-14), respectively (p=0.07). Most frequent karyotypes at diagnosis were diploid (34%), complex (32%), chromosome 5 abnormalities (29%) and chromosome 7 abnormalities (26%). At relapse, the most frequent karyotypes included complex (36%), chromosome 7 abnormalities (31%), chromosome 5 abnormalities (30%) and diploid karyotype (27%).

When analyzing each mutation individually, the rate of mutation clearance from diagnosis to relapse was higher for FLT3-ITD (58%, p=0.01), FLT3-TKD (83%, p<0.001), KIT (88%, p=0.003), NF1 (71%, p=0.004) and WT1 mutations (71%, p=0.004), compared to other remaining mutations (32%). Conversely, ASXL1 (95%, p=0.01), DNMT3A (84%, p=0.006), SRSF2 (89%, p=0.01), TET2 (84%, p=0.02) and TP53 mutations (86%, p=0.002) persisted more frequently at relapse compared to other mutations (66%). At relapse, WT1 mutations were more frequently acquired (77%, p=0.001), compared to other mutations (36%). Diploid karyotype changed more frequently than other cytogenetic abnormalities (33% vs 5%, p <0.001), whereas complex karyotype persisted at relapse (98% vs 87%, p=0.04) more frequently. Chromosome 7 abnormalities were more frequently acquired at relapse (23%), compared to other cytogenetic abnormalities acquired at relapse (11%, p=0.04).

We then compared mutational dynamics from diagnosis to relapse between patients receiving IT and LIT. NRAS mutations disappeared more frequently from diagnosis to relapse in patients treated with IT (73%), compared with patients treated with LIT (27%, p=0.01) whereas TP53 mutations were acquired more frequently in IT treated patients (67% vs 10%). Patients treated with IT acquired chromosome 7 abnormalities more frequently than patient treated with LIT (60% vs 14%, p=0.007). No significant differences were found regarding disappearance, maintenance or appearance of mutations when comparing patients treated with or without Venetoclax.

Conclusion: The number of mutations does not vary significantly from diagnosis to relapse, and most mutations persist, suggesting maintenance of leukemic clones as the cause of relapse. Overall, genes involved in signaling pathways tend to disappear more frequently at relapse whereas chromatin and histone modifiers as well as TP53 mutations tend to persist. NRAS mutations disappear more frequently at relapse with IT, whereas TP53 mutations are acquired more frequently.