AML with CBFB-MYH11 Rearrangement Is Characterized by RAS Pathway Alterations in 92% of Cases and Demonstrates a High Frequency of NF1 Deletions.
Authors: Haferlach Claudia , Dicker Frank , Kohlmann Alexander , Schindela Sonja , Weiss Tamara , Kern Wolfgang , Schnittger Susanne , Haferlach Torsten 
Published: October 2019

Abstract
Abstract 272
AML with abnormal bone marrow eosinophils and with inv(16)(p13q22) or t(16;16)(p13;q22) leading to a CBFB-MYH11 fusion gene have been classified as distinct entity in the WHO classification and are associated with a favorable outcome. Knock-in mouse models demonstrated that CBFB-MYH11 alone is not sufficient to cause a leukemic phenotype and that additional aberrations are essential for the development of AML. To decipher accompanying genetic lesions in AML with CBFB-MYH11 rearrangements we performed SNP microarray analyses and mutation analysis of KIT, NRAS, KRAS, FLT3, CBL and JAK2 in 37 newly diagnosed patients with CBFB-MYH11+ AML. Recurring gains of whole chromosomes observed both by chromosome banding analysis and SNP microarray assays included chromosomes 8 (n=5) and 22 (n=6). In one additional case SNP microarray analysis revealed also a partial gain of 8q ranging from 8q24.13 to 8q24.3. Recurring genomic losses identified by SNP microarrays but not by conventional karyotyping were deletions of 7q36.1 to 7q36.3 (n=2), 16p13 (n=5), 17q11 (n=6), and 18q23 (n=2). All five 16p13 deletions included the 5' part of the MYH11 gene located in the breakpoint region of the CBFB-MYH11 translocation/inversion, and in 4/5 cases also the ABCC1 gene, encoding a protein with relevance in multidrug resistance. Interestingly, the NF1 (neurofibromin 1) gene, which negatively regulates the RAS pathway, was found to be deleted in all cases with 17q11 loss as depicted by SNP microarrays (6/37). Therefore, we performed further molecular analyses of genes known to be also involved in the RAS pathway. The following mutations were detected: FLT3-ITD (3/37), FLT3-TKD (3/36), KITD816 (7/37), KIT exon 8 (2/37), KRAS (5/37), NRAS (14/37), CBL splice mutations (6/37). No mutations were found in cases screened for JAK2V617F (0/37) and in PTPN11 (0/6). Overall, 46 alterations were observed in the analyzed genes. In 10 cases two of these candidates and in one case three genes were affected. In summary, CBFB-MYH11 rearrangements are very frequently accompanied by molecular alterations leading to an aberrant activation of the RAS pathway. In 34 (92%) of 37 patients mutations within the RAS genes (KRAS, NRAS) or alterations in genes regulating RAS (FLT3, KIT, CBL, NF1) were observed. NF1, which was found to be deleted in 16% of cases in our cohort, was identified as a new target gene in AML with CBFB-MYH11 rearrangement. We conclude that these new insights implicate alterations of the RAS pathway as the principal cooperating mutation in CBFB-MYH11+ AML, and suggest to further evaluate the use of drugs targeting the RAS pathway into treatment regimens for this AML subtype.

Disclosures:
Haferlach: MLL Munich Leukemia Laboratory: Equity Ownership. Dicker:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Schindela:MLL Munich Leukemia Laboratory: Employment. Weiss:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership.