Genome-Wide Single Nucleotide Polymorphism Analysis in Juvenile Myelomonocytic Leukemia Uncovers Long-Range Uniparental Disomy Surrounding the NF1 Locus in Cases Associated with Type 1 Neurofibromatosis but Not in Cases with Mutant RAS or PTPN11.
Authors: Flotho Christian , Steinemann Doris , Göhring Gudrun , Mullighan Charles , Neale Geoffrey , Schlegelberger Brigitte , Downing James , Niemeyer Charlotte Marie 
Published: October 2019

Abstract
Juvenile myelomonocytic leukemia (JMML) is a malignant hematopoietic disorder of early childhood with myeloproliferative and myelodysplastic properties. The proliferative component is a result of RAS pathway deregulation caused by somatic mutation in the RAS or PTPN11 oncogenes (60% of cases) or by underlying neurofibromatosis type 1 (NF-1) with a germline NF1 gene defect (clinically 11% of cases). To search for potential collaborating genetic abnormalities, we used Affymetrix GeneChip Mapping 50K arrays to analyze over 116,000 single nucleotide polymorphisms (SNPs) across the genome using DNA from bone marrow or peripheral blood granulocytes from 16 children with JMML and normal karyotype (mutant RAS, n=4; mutant PTPN11, n=7; NF-1, n=5). Quantitative evaluation of hybridization intensities at each SNP locus failed to identify recurrent allelic gains or losses in the 16 cases. We were specifically interested in chromosome 7 because monosomy 7 or interstitial/terminal 7q deletions are found in about 30% of JMML cases and it is conceivable that submicroscopic 7q lesions occur in the other cases but remain undetected by standard techniques. However, at the resolution provided by the arrays used here, we saw no evidence for genomic copy number alterations on chromosome 7. Interestingly, evaluation of the SNP allelotypes identified large regions of copy-neutral loss of heterozygosity (LOH) on chromosome 17q, including the NF1 locus, in 4 of the 5 samples from patients with JMML and NF-1. The LOH region spanned a genomic range of approximately 55 Mbp in each case and included more than 1,400 contiguous SNPs. Allelic copy numbers were normal within the homozygous regions, indicating uniparental isodisomy (UPD). Compatible with isodisomy, 17q was normal in the corresponding conventional karyotypes. By contrast, the array data provided no evidence for 17q UPD in any of the 12 JMML cases without NF-1. In all four cases with 17q UPD, the recombination breakpoints appeared to be confined to a 400-kbp region on 17q11.1–17q11.2; however, lack of parental or nonleukemic DNA precluded definitive mapping of the breakpoints. Of note, the 17p chromosomal arm retained heterozygosity in all cases, indicating that the p53 tumor suppressor was not affected by the UPD event. We confirmed 17q disomy in the four NF-1 samples using matrix-based comparative genomic hybridization and are currently verifying homozygosity of multiple microsatellites spaced across chromosome 17. Furthermore, NF1 mutational analysis is under way to show that the individual lesion within this tumor suppressor gene is biallelic in leukemic cells from patients with JMML and NF-1. In summary, we assume that a mitotic recombination event in an early hematopoietic progenitor cell led to UPD involving the NF1 locus. Our observations provide strong confirmatory evidence that it is indeed the NF1 gene that is responsible for the increased incidence of JMML in NF-1 patients. In addition, our data support the emerging role of mitotic recombination as a second hit in leukemogenesis and corroborate the concept that RAS pathway deregulation is central to JMML pathogenesis.