Genomic complexity and dynamics of clonal evolution in childhood acute myeloid leukemia studied with whole-exome sequencing

Riccardo Masetti,Ilaria Castelli,Tamara Belotti,Marco Togni,Martina Pigazzi,Annalisa Astolfi,Giuseppe Basso,Marco Zecca,Salvatore Serravalle,Andrea Pession,Salvatore Nicola Bertuccio,Giuseppe Tarantino,Valentina Indio,Franco Locatelli

doi:10.18632/oncotarget.10778

Abstract

Despite significant improvement in treatment of childhood acute myeloid leukemia (AML), 30% of patients experience disease recurrence, which is still the major cause of treatment failure and death in these patients. To investigate molecular mechanisms underlying relapse, we performed whole-exome sequencing of diagnosis-relapse pairs and matched remission samples from 4 pediatric AML patients without recurrent cytogenetic alterations. Candidate driver mutations were selected for targeted deep sequencing at high coverage, suitable to detect small subclones (0.12%). BiCEBPα mutation was found to be stable and highly penetrant, representing a separate biological and clinical entity, unlike WT1 mutations, which were extremely unstable. Among the mutational patterns underlying relapse, we detected the acquisition of proliferative advantage by signaling activation (PTPN11 and FLT3-TKD mutations) and the increased resistance to apoptosis (hyperactivation of TYK2). We also found a previously undescribed feature of AML, consisting of a hypermutator phenotype caused by SETD2 inactivation. The consequent accumulation of new mutations promotes the adaptability of the leukemia, contributing to clonal selection. We report a novel ASXL3 mutation characterizing a very small subclone (<1%) present at diagnosis and undergoing expansion (60%) at relapse. Taken together, these findings provide molecular clues for designing optimal therapeutic strategies, in terms of target selection, adequate schedule design and reliable response-monitoring techniques.

Highlights

Outcome of children with acute myeloid leukemia (AML) has improved significantly over the past 30 years [1]
A total amount of 65 single nucleotide variants (SNVs) and 17 insertion/deletion mutations (Ins/Dels) were considered somatic mutations, resulting in: 6 mutations in AML#1, 41 in AML#2, 11 in AML#3 and 7 in AML#4
These results agree with the evidence that the AML genome usually has a low number of somatic mutations [11], with the exception of AML#2 samples, which were found to carry a higher burden of mutations, despite comparable sequencing performance

Summary

Introduction

Outcome of children with acute myeloid leukemia (AML) has improved significantly over the past 30 years [1]. Given the high frequency of treatment-related deaths (5%– 10%), both with first-line treatment and with protocols for relapsed disease, further intensification of standard chemotherapy does not seem to be an option for further improvement of patientsoutcome [8] This said, better knowledge of the molecular lesions underlying AML and especially of those involved in the development of relapse is mandatory in order to devise novel patient-specific treatment strategies. Disease recurrence seems to be associated with clonal evolution from early stage to relapse, promoted at least in part by chemotherapy itself This model is supported by the seminal work of Ding et al [9] in adult AML, and has only recently been confirmed by Farrar et al [10] in childhood AML. In this group of patients, adequate molecular characterization, risk stratification and disease monitoring remain difficult tasks, this leading to a great variability in terms of response to therapy and final prognosis

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