Deletion of the Tumor Suppressor Gene NF1 Is An Alternative Mechanism for Aberrant Activation of the RAS Pathway and Is Found in 11% of Acute Myeloid Leukemia.

Abstract 401

The NF1 gene encodes neurofibromin 1, a Ras-specific guanosine triphosphatase-activating protein (GAP) that negatively regulates the p21ras (Ras) family of signaling proteins by accelerating GTP hydrolysis. Germline loss of function mutations of NF1 lead to Neurofibromatosis type I. Carriers of the mutations develop benign neurofibromas and are predisposed to neuronal tumors, but also to juvenile myelomonocytic leukemia (JMML), MDS, and AML. In addition, in children suffering from CMML without germline NF1 mutations, acquired loss of function mutations of NF1 have been reported. In contrast, the role of NF1 in adult myeloid malignancies has not been studied in detail. Therefore, we first evaluated NF1 gene expression in 272 AML cases which were analyzed by Affymetrix HG-U133 Plus 2.0 microarrays. These included cases with t(15;17)(q22;q12) (n=15), t(8;21)(q22;q22) (n=16), inv(16)(p13q22) (n=7), t(11q23)/MLL-rearrangement (n=10), complex aberrant karyotype (n=47), normal karyotype (n=97), and with various other genetic abnormalities (n=80). The median NF1 expression intensity was 131.6 (range 35.2 - 457.5). 68 cases showed an expression intensity of NF1 below 98.6 (first quartile). In this cohort cases with t(8;21) (n=10) or complex karyotype (n=18) were over-represented (Chi-square: p<0.0001 and p=0.021, respectively), while cases with normal karyotype (n=16) were under-represented (Chi-square: p=0.016). In 54/68 of the latter cases with low expression material was availabel for FISH analysis with a probe spanning the NF1 locus. Remarkably, in 11/54 of these cases (20.4%) a NF1 deletion was observed by interphase FISH (% of cells with NF1 deletion median 90% (range: 60-99%). The mean±SD NF1 expression intensity in cases with NF1 deletion was 60.4±17.7 as compared to 75.5±18.0 in cases with 2 NF1 copies (p=0.023). Chromosome banding analysis in these 11 cases revealed a complex karyotype (n=7), a normal karyotype (n=2), an inv(3)(q21q26), and a 5q-deletion accompanied by trisomy 21, respectively. To further investigate the incidence of NF1 deletion in myeloid malignancies 425 additional patients were analyzed by FISH for NF1 deletion using a 420 kb probe spanning the NF1 gene. A heterozygous NF1 deletion was observed in 30/425 (7.1%) patients: de novo AML: 13/142 (9.2%), s-AML: 5/39 (12.8%), t-AML: 4/13 (31%), CMML: 5/99 (5.6%), MDS: 0/122 (0%), MPN: 3/10 (30%). Chromosome banding analysis in the NF1-deleted cases revealed a normal karyotype (n=4), an inv(16)(p13q22) (n=6), an inv(3)(q21q26) (n=6), a complex aberrant karyotype (n=5) or other abnormalities (n=9). In conclusion, NF1 deletions occur in 11% of AML, 5% of CMML and 3/10 MPN and therefore are a frequent and important alternative genetic mechanism for activating the RAS pathway in adult myeloid malignancies.