International Consensus Definition of DNA Methylation Subgroups in Juvenile Myelomonocytic Leukemia

Abstract

Purpose: Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML on the basis of DNA methylation patterns are lacking. We, therefore, sought to define an international consensus for DNA methylation subgroups in JMML and develop classification methods for clinical implementation. Experimental Design: Published DNA methylation data from 255 patients with JMML were used to develop and internally validate a classifier model. Accuracy across platforms (EPIC-arrays and MethylSeq) was tested using a technical validation cohort (32 patients). The suitability of both methods for single-patient classification was demonstrated using an independent cohort (47 patients). Results: Analysis of pooled, published data established three DNA methylation subgroups as a de facto standard. Unfavorable prognostic parameters (PTPN11 mutation, elevated fetal hemoglobin, and older age) were significantly enriched in the high methylation (HM) subgroup. A classifier was then developed that predicted subgroups with 98% accuracy across different technological platforms. Applying the classifier to an independent validation cohort confirmed an association of HM with secondary mutations, high relapse incidence, and inferior overall survival (OS), while the low methylation subgroup was associated with a favorable disease course. Multivariable analysis established DNA methylation subgroups as the only significant factor predicting OS. Conclusions: This study provides an international consensus definition for DNA methylation subgroups in JMML. We developed and validated methods which will facilitate the design of risk-stratified clinical trials in JMML.

Current Treatment of Juvenile Myelomonocytic Leukemia

“…However, long-term survival without HSCT has not yet been observed in this group, so that proceeding to transplant and inception of therapy with azacitidine is advisable as in patients with somatic PTPN11 mutation. Consistent with this recommendation, JMML/NF-1 cases almost always have an intermediate or high methylation profile [ 88 ].…”

“…The North American study defined three similar methylation classes in 39 patients [ 65 ]. Interestingly, some JMML patients with good transplantation-free outcome and all patients with NS/MPD exhibited a DNA methylation signature closer to healthy controls than to other JMML cases [ 65 , 88 ], again underlining the significance of disrupted epigenetic control for the biology of JMML. The fact that all three methylome studies had used a comparable technical platform provided the unique opportunity for a comprehensive overarching meta-analysis.…”

“…The fact that all three methylome studies had used a comparable technical platform provided the unique opportunity for a comprehensive overarching meta-analysis. These collaborative efforts succeeded in developing and validating an international standard classifier of three different methylation categories matching those above and correlating with disease biology and outcome [ 88 ]. The prospective use of methylation analysis as a biomarker in JMML will aid in adapting treatment strategies, e.g., use of pretransplant therapy or low-intensity graft-versus-host disease (GVHD) prophylaxis, and support the generation of internationally comparable JMML study data.…”

“…Interestingly, monosomy 7 is observed more frequently in European compared to Japanese patients with JMML [ 33 ]. In a large international series, all patients with monosomy 7 and intermediate methylation class carried KRAS mutations, in contrast to an association between monosomy 7 and PTPN11 or NF1 in the high methylation group, and the absence of monosomy 7 in patients with low methylation pattern [ 88 ]. The mechanistic connection between this particular chromosomal lesion and aberrant DNA methylation patterns is not understood.…”

Mutant SETBP1 enhances NRAS-driven MAPK pathway activation to promote aggressive leukemia

“…SETBP1 mutations are known to co-occur with both PTPN11 and NRAS mutations (such as PTPN11 E76K and NRAS G12D ) 1, 2, 8 . We find that, in the absence of exogenous cytokines, both PTPN11 E76K (Fig.1A, B) and NRAS G12D (Fig.1C, D) formed a modest number of murine hematopoietic colony forming units (CFU).…”