Integrated molecular profiling of juvenile myelomonocytic leukemia

Abstract

Juvenile myelomonocytic leukemia (JMML), a rare and aggressive myelodysplastic/myeloproliferative neoplasm that occurs in infants and during early childhood, is characterized by excessive myelomonocytic cell proliferation. More than 80% of patients harbor germ line and somatic mutations in RAS pathway genes (eg, ,, ,, and ), and previous studies have identified several biomarkers associated with poor prognosis. However, the molecular pathogenesis of 10% to 20% of patients and the relationships among these biomarkers have not been well defined. To address these issues, we performed an integrated molecular analysis of samples from 150 JMML patients. RNA-sequencing identified tyrosine kinase fusions (, and ) in 3 of 16 patients (18%) who lacked canonical RAS pathway mutations. Crizotinib, an ALK/ROS1 inhibitor, markedly suppressed fusion-positive JMML cell proliferation in vitro. Therefore, we administered crizotinib to a chemotherapy-resistant patient with the fusion who subsequently achieved complete molecular remission. In addition, crizotinib also suppressed proliferation of JMML cells with canonical RAS pathway mutations. Genome-wide methylation analysis identified a hypermethylation profile resembling that of acute myeloid leukemia (AML), which correlated significantly with genetic markers with poor outcomes such as gene mutations, 2 or more genetic mutations, an AML-type expression profile, and expression. In summary, we identified recurrent activated fusions in JMML patients without canonical RAS pathway gene mutations and revealed the relationships among biomarkers for JMML. Crizotinib is a promising candidate drug for the treatment of JMML, particularly in patients with fusions.

PTPN11 mutation with additional somatic alteration indicates unfavorable outcome in juvenile myelomonocytic leukemia: a retrospective clinical study from a single center

“…The high methylation group was dominated by cases with PTPN11 mutation, resulting in poor outcome, suggesting RAS-pathway mutation patterns define epigenetic subclasses in JMML [10]. In addition, hinting at possible functional links between Ras activation and methylation classes, some research also reported that DNA hypermethylation was more pronounced when additional mutations in Ras-pathway genes or epigenetic modifier genes were present [10,17]. Furthermore, we have shown that secondary mutations providing additional activation of RAS-signaling and other signaling pathways were frequent in poor-outcome JMML.…”

CBL mutations promote activation of PI3K/AKT signaling via LYN kinase

“…Recurrent somatic mutations in the Casitas B-lineage Lymphoma (CBL) gene, which encodes an E3 ubiquitin ligase and signaling adaptor, occur in myelodysplastic syndromes (MDS) and other myeloid neoplasms (2)(3)(4)(5)(6)(7)(8)(9), including 10-20% of chronic myelomonocytic leukemia (CMML) patients (10,11). In addition, up to 20% of children diagnosed with juvenile myelomonocytic leukemia (JMML) harbor germline CBL mutations (12)(13)(14)(15). The presence of CBL mutations has been associated with poor prognosis (16)(17)(18), and a better understanding of the mechanisms by which CBL mutations promote myeloid disease is needed for the development of new and effective therapeutic strategies.…”

“…The RING domain, which binds E2 ubiquitin ligase proteins, and linker region are both essential for CBL's E3 ubiquitin ligase function. The majority of CBL mutations in myeloid malignancies are predicted to alter the ubiquitin ligase activity of CBL through single amino acid substitutions within the linker region or RING domain (3,(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15), or splice site alterations resulting in exclusion of most amino acids within the RING domain (15,20). Recurrent mutations predicted to affect CBL's signaling adaptor functions are exceptionally rare, implying that oncogenic CBL mutations result in selective loss of CBL's E3 ubiquitin ligase function.…”

Gene mutations do not operate in a vacuum: the increasing importance of epigenetics in juvenile myelomonocytic leukemia

“…Interestingly, the authors noted that the methylation profile of samples from children who experienced spontaneous resolution of the disease was more similar to healthy leukocytes than to other JMML cases. The Nagoya University generated genome-wide DNA methylation data of samples from 106 children with JMML [71]. Here the unsupervised cluster analysis revealed two rather than three categories of methylation, potentially due to a significantly lower number of cases with monosomy 7 in the cohort.…”

“…With the advent of technology permitting the genome-wide analysis of CpG methylation three large-scale epigenetic analyses in a total of 312 children with JMML or related myeloproliferative disorders were conducted by investigators in Europe, North America, and Japan [43,70,71]. Confirming and extending the conclusions derived from the preceding candidate gene studies, the EWOG-MDS demonstrated in a cohort of 167 cases that JMML can be subdivided in three characteristic categories with low, intermediate, and high DNA methylation, with the methylation differences being most pronounced in or near CpG islands [43].…”