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

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.

SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia

“…6 Other studies have reported a high frequency (;20%) of SETD2 alterations in chemotherapy-resistant, MLL-arranged ALL and AML and hepatosplenic T-cell lymphoma. 9 A lower frequency of SETD2 alterations are found in other hematological malignancies, including early T-cell precursor ALL, 10 non-MLL-rearranged AML, 11 and chronic lymphocytic leukemia (CLL) 12 ( Figure 1A; supplemental Table 1, available on the Blood Web site) and multiple solid tumors. [13][14][15][16][17] SETD2 loss has been associated with adverse clinical outcomes in clear cell renal cell carcinoma, 18,19 and CLL 12 and has been shown to accelerate disease and increase cell proliferation in some experimental models.…”

Focusing on frequent ASXL1 mutations in myeloid neoplasms, and considering rarer ASXL2 and ASXL3 mutations

“…ASXL3 mutations are present in a variety of malignancies, including 10% of melanomas and lung adenocarcinoma, but its role in hematologic malignancies is unclear 2,11 . ASXL3 is expressed in the bone marrow 11 but ASXL3 mutations are rare in myeloid neoplasms: one patient with an ASXL3 mutation was identified in the AML TCGA study 12 and one case of pediatric AML with a point mutation clone that significantly expanded from less than 1% at initial diagnosis to 30% at relapse has also been identified 13 . Unlike ASXL1/2, ASXL3 mutations are rare in AML with t (8;21), where a single case was identified in a cohort of 110 cases 14 .…”

Phosphatase Sequencing of Pediatric Acute Myeloid Leukemia Reveals a Novel Mutation in the Phosphatase Gene PTPN4

“…Recent high-throughput genome wide sequencing has shed light on the role of somatic mutations, including signal transduction molecules involved in AML [5]. These mutations generally involve protein tyrosine kinases (PTKs) that confer upon these cells a proliferative advantage.…”