Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia

Abstract

Acute lymphoblastic leukemia (ALL) is the commonest childhood malignancy and is characterized by recurring structural genetic alterations. Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. We also identified an epigenetic signature common to all cases, with correlation to gene expression in 65% of these genes, suggesting that a core set of epigenetically deregulated genes is central to the initiation or maintenance of lymphoid transformation. Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. Together, these results demonstrate subtype-and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis. IntroductionAcute lymphoblastic leukemia (ALL) is the commonest childhood malignancy (1); despite impressive advances in the success of therapy for ALL, it remains the leading cause of cancer-related death in young people. A detailed understanding of the genetic and epigenetic events contributing to leukemogenesis and treatment responsiveness is important in order to identify potential new avenues for therapy in this condition.Pediatric ALL is characterized by a range of recurring numeric and structural chromosomal alterations. These include B-precursor ALL (B-ALL) with (a) high hyperdiploidy (>50 chromosomes), (b) hypodiploidy (<44 chromosomes), (c) t(12;21)(p13;q22) encoding ETV6-RUNX1 (also known as TEL-AML1), (d) t(1;19)(q23;p13.3) encoding TCF3-PBX1 (also known as E2A-PBX1), (e) t(9;22)(q34;q11) encoding BCR-ABL1, (f) cytokine receptor-like factor 2 (CRLF2) rearrangement (CRLF2r), and (g) MLL rearrangement at 11q23 (MLLr); MYC rearrangement in mature B cell leukemia/lymphoma; and TLX1 (also known as HOX11), TLX3 (also known as HOX11L2), LYL1, TAL1, and MLL rearrangement in T-lineage ALL (T-ALL) (2). These alterations are important events in leukemogenesis and are associated with responsiveness to therapy, treatment outcome, and distinct gene expression profiles (3). However, several of these translocations may be acquired years before development of overt leukemia (4), and mouse models have shown that these alterations are frequently insufficient to cause leukemia, which suggests that cooperating genetic events are required. Furthermore, recurring chr...

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