Specific Promoter CpG Island Methylation Patterns Identify Different Subgroups of MLL - Rearranged Infant Acute Lymphoblastic Leukemia, and Define Clinical Outcome
Authors: Stumpel Dominique Jpm , Schneider Pauline , van Roon Eddy HJ , Boer Judith M , Menezes Renee X , Pieters Rob , Stam Ronald W. 
Published: April 2020

Abstract
At present, long-term survival rates in childhood acute lymphoblastic leukemia (ALL) easily exceed 80%. However, the prognosis for infants (&lt;1 year) with ALL barely reaches 50%. Infant ALL is characterized by chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene that occur in about 80% of the cases. The most frequent MLL translocations in infant ALL include t(4;11), t(11;19) and t(9;11). In about 20% of the infant ALL cases no MLL rearrangements are observed. Recent gene-expression profiling characterized MLL-rearranged ALL as a unique type of leukemia, that is genetically clearly separable from other ALL subtypes. As epigenetic modifications affect gene-expression, we hypothesized that the specific gene-expression profiles associated with MLL-rearranged ALL may well be driven by epigenetic changes. The best-studied epigenetic event in hematological malignancies constitutes the transcriptional silencing of (tumor suppressor) genes by promoter CpG island hypermethylation. To explore the DNA methylation patterns underlying MLL-rearranged infant ALL, we applied Differential Methylation Hybridization (DMH) using both 9k (Huang, 2002) and 244k CpG island microarrays (Agilent) on primary infant ALL samples carrying t(4;11) (n=21), t(11;19) (n=17), t(9;11) (n=6) or wild-type MLL genes (n=13). The resulting DNA methylation patterns were compared with the patterns found in healthy pediatric bone marrow samples (n=8). In addition, relapse material from three infants with MLL-rearranged ALL was included and compared with the corresponding patient sample obtained at diagnosis. Both CpG island microarray platforms demonstrate that t(4;11) and t(11;19) characterize extensively hypermethylated leukemias, whereas t(9;11)-positive and translocation-negative infant ALL epigenetically resemble normal bone marrow. When the CpG array data (Agilent) were compared with available gene expression profiles (Affymetrix), we found that 95% of the genes from the top 100 of genes most significantly hypermethylated in t(4;11)- or t(11;19)-positive infant ALL were indeed down-regulated. Using the t(4;11)-positive cell line models SEMK2 and RS4;11, we demonstrate that the majority of these hypermethylated genes could be demethylated by the demethylating agent zebularine. Among t(4;11)- and t(11;19)-positive infant ALL samples, two subgroups could be identified displaying either more or less pronounced methylation patterns. Heavy methylation appeared to be associated with a significantly reduced relapse-free survival (p=0.03). Encouraged by these data, we analyzed relapse samples from t(4;11)- and t(11;19)-positive infant ALL patients, and found that these samples were even more extensively hypermethylated than the corresponding initial infant ALL samples. We here present, for the first time to our knowledge, a global view of the methylome in infant patients with MLL-rearranged ALL. We demonstrate that severe promoter CpG hypermethylation is present in t(4;11)- and t(11;19)-positive infant ALL. Of main therapeutic interest is our finding that the degree of DNA methylation among t(4;11)- and t(11;19)-positive infant ALL patients is related to relapse-free survival. Therefore, MLL-rearranged infant ALL patients with heavily methylated leukemias in particular should be considered candidates for therapies including inhibitors of DNA methylation in order to reverse the malignant phenotypes of these leukemias, and improve prognosis. Since MLL-rearranged infant ALL patients are even more hypermethylated at relapse, inhibition of aberrant DNA methylation might also be of vital importance at this stage of disease. Based on these data, we propose to initiate clinical trials using demethylating agents for patients with relapsed MLL- rearranged infant ALL. Meanwhile, we are investigating the in vitro cytotoxicity of various demethylating agents in our laboratory to pave the way for future clinical trials.