DNA Methylation-Based Subtype Prediction for Pediatric Acute Lymphoblastic Leukemia (ALL)

We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. We used the methylation status of ~450,000 CpG sites from 546 well-characterized patients with T-ALL or B-cell precursor ALL with the cytogenetic subtypes high hyperdiploidy (HeH), t(12;21)(p13;q22)[ETV6/RUNX1], t(1;19)(q23;p13.3)[TCF3/PBX1], 11q23/MLL-rearrangements, t(9;22)(q34;q11)[BCR/ABL1], dic(9;20)(p13.2;q11.2), and intrachromosomal amplification of chromosome 21 iAMP21[RUNX1 x >3], to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived consisting of only 246 CpG sites that accurately predicted the subtype of >96% of the patients with known subtype. The mean sensitivity and specificity across the subtypes was 0.90 and 0.99, respectively. We then used the DNA methylation classifier to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations (“other” subtype). Nearly half (n=106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative PCR and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5. The CpG sites constituting the classifiers highlight relevant biological characteristics of otherwise unclassified ALL patients and provide clues to the origin and development of leukemic transformation. Together with response to induction therapy, genetic aberrations are among the most important prognostic factors in pediatric ALL. Our findings indicate that DNA methylation profiling can help clarify some of the heterogeneity in cytogenetically undefined ALL patient groups and can potentially be implemented for diagnostics of ALL and other types of hematological cancers.