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Genomic landscape and clonal evolution of acute myeloid leukemia with t(8;21): an international study on 331 patients

Friederike Christen, Kaja Hoyer, Kenichi Yoshida, Hsin-An Hou, Nils Waldhueter, Michael Heuser, Robert K. Hills, Willy Chan, Raphael Hablesreiter, Olga Blau, Yotaro Ochi, Piroska Klement, Wen-Chien Chou, Igor-Wolfgang Blau, Jih-Luh Tang, Tomasz Zemojtel, Yuichi Shiraishi, Yusuke Shiozawa, Felicitas Thol, Arnold Ganser, Bob Löwenberg, David C. Linch, Lars Bullinger, Peter J.M. Valk, Hwei-Fang Tien, Rosemary E. Gale, Seishi Ogawa and Frederik Damm

Key points

  • RAS/RTK mutations occur in 63% of patients with t(8;21) AML and confer poor prognosis.

  • One third of patients with t(8;21) AML who relapse are genetically distinct from diagnostic findings.

Abstract

Acute myeloid leukemia (AML) with t(8;21)(q22;q22) is characterized by considerable clinical and biological heterogeneity leading to relapse in up to 40%. We sequenced coding regions or hotspot areas of 66 recurrently mutated genes in a cohort of 331 t(8;21) patients. At least one mutation in addition to t(8;21) was identified in 95% with a mean of 2.2 driver mutations per patient. Recurrent mutations occurred in genes related to RAS/RTK signaling (63.4%), epigenetic regulators (45%), cohesin complex (13.6%), MYC signaling (10.3%), and the spliceosome (7.9%). Our study identified mutations in previously unappreciated genes GIGY2F, DHX15, and G2E3. Based on high mutant levels, pairwise precedence, and stability at relapse, epigenetic regulator mutations were likely to occur before signaling mutations. In 34% of RAS/RTKmutated patients, we identified multiple mutations in the same pathway. Deep sequencing (≈42,000x) of 126 mutations in 62 CR samples from 56 patients identified 16 persisting mutations in 12 patients, of whom five lacked RUNX1-RUNX1T1 in qPCR analysis. KIThigh mutations defined by a mutant level ≥25% were associated with inferior relapse-free survival (HR=1.96; 95%-CI 1.22-3.15; P=.005). Together with age and white blood cell counts, JAK2, FLT3-ITDhigh, and KIThigh mutations were identified as significant prognostic factors for overall survival in multivariate analysis. Whole-exome sequencing was performed on 19 paired diagnosis, remission, and relapse trios. Exome-wide analysis showed an average of 16 mutations with signs of substantial clonal evolution. Based on the resemblance of diagnosis and relapse pairs, genetically stable (n=13) and unstable (n=6) subgroups could be identified.

  • Submitted May 25, 2018.
  • Accepted December 31, 2018.