Clonal and microclonal mutational heterogeneity in high hyperdiploid acute lymphoblastic leukemia.

Adam J De Smith,Stephen S Francis,Alyson A Endicott,Erica Sanders,Catherine Metayer,Amanda M Termuhlen,Helen M Hansen,Joseph L Wiemels,Juhi Ojha,Ivan Smirnov,Kyle M Walsh

doi:10.18632/oncotarget.12238

Abstract

High hyperdiploidy (HD), the most common cytogenetic subtype of B-cell acute lymphoblastic leukemia (B-ALL), is largely curable but significant treatment-related morbidity warrants investigating the biology and identifying novel drug targets. Targeted deep-sequencing of 538 cancer-relevant genes was performed in 57 HD-ALL patients lacking overt KRAS and NRAS hotspot mutations and lacking common B-ALL deletions to enrich for discovery of novel driver genes. One-third of patients harbored damaging mutations in epigenetic regulatory genes, including the putative novel driver DOT1L (n=4). Receptor tyrosine kinase (RTK)/Ras/MAPK signaling pathway mutations were found in two-thirds of patients, including novel mutations in ROS1, which mediates phosphorylation of the PTPN11-encoded protein SHP2. Mutations in FLT3 significantly co-occurred with DOT1L (p=0.04), suggesting functional cooperation in leukemogenesis. We detected an extraordinary level of tumor heterogeneity, with microclonal (mutant allele fraction <0.10) KRAS, NRAS, FLT3, and/or PTPN11 hotspot mutations evident in 31/57 (54.4%) patients. Multiple KRAS and NRAS codon 12 and 13 microclonal mutations significantly co-occurred within tumor samples (p=4.8×10−4), suggesting ongoing formation of and selection for Ras-activating mutations. Future work is required to investigate whether tumor microheterogeneity impacts clinical outcome and to elucidate the functional consequences of epigenetic dysregulation in HD-ALL, potentially leading to novel therapeutic approaches.

Highlights

High hyperdiploidy (HD), characterized by a non-random pattern of chromosomal gains (51 to 67 chromosomes), comprises the largest cytogenetic subgroup of B-cell acute lymphoblastic leukemia (B-ALL) and is one of the most common malignancies in children [1]
Genome-wide association studies (GWAS) have identified SNPs that distinguish HD-ALL from other subtypes, for example in ARID5B, CEBPE, and PIP4K2A [8,9,10,11]
Recent next-generation sequencing analyses of HD-ALL confirmed that mutations in these genes, and in the epigenetic regulatory gene CREBBP, are the most frequent somatic alterations in this leukemia subtype [16, 17]

Summary

Introduction

High hyperdiploidy (HD), characterized by a non-random pattern of chromosomal gains (51 to 67 chromosomes), comprises the largest cytogenetic subgroup of B-cell acute lymphoblastic leukemia (B-ALL) and is one of the most common malignancies in children [1]. Hyperdiploidy has been shown to arise prenatally [4, 5] and is likely initiated by a single abnormal mitotic event [6, 7], implicating it as the primary genetic lesion This is followed by additional somatic alterations, arising pre- or postnatally, and these are believed to be required for overt leukemia. We describe targeted sequencing of 538 cancerrelevant genes using a clinical sequencing platform in a set of 57 HD-ALL patients lacking the common KRAS and NRAS codon 12 and 13 hotspot mutations and common gene deletions, to enrich for discovery of novel driver genes and to assess recurrently-mutated pathways in HD-ALL tumorigenesis. This deep-sequencing enabled identification of putative novel drivers and permitted an in-depth assessment of intratumoral heterogeneity

Methods

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Discussion

Conclusion