Frequent Inactivating Mutations of TET2 and CBL Are Associated with Acquired Uniparental Disomy in Atypical Chronic Myeloid Leukemia and Related Disorders.

Abstract 3258

Poster Board III-1

Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) such as atypical BCR-ABL negative chronic myeloid leukemia (aCML) and chronic myelomonocytic leukemia (CMML) combine dysplastic morphology with features of a CML-like myeloproliferative disorder. The underlying pathomechanism of these related disorders is poorly understood. Recent evidence has shown that acquired uniparental disomy (aUPD) is a novel mechanism by which pathogenetic mutations in cancer may be reduced to homozygosity. In this study we sought to investigate if aUPD characterizes MDS/MPN of unknown molecular etiology, and whether it could be used as a tool to help identify novel driver mutations. Genome wide high resolution SNP 6.0 array analysis was performed on total leukocyte DNA from 148 patients with aCML (n=54), CMML (n=69), and unclassified MDS/MPN (n=25). All patients were negative for BCR-ABL, JAK2 V617F, FIP1L1-PDGFRA and cytogenetic indicators of other tyrosine kinase fusion genes. Homozygous copy neutral SNP calls >20 Mb, considered indicative of aUPD, were seen in 39 (26%) patients. In total, 15 different chromosomes were involved with the most common recurrent abnormalities being seen at 4q (n=7), 7q (n=12), and 11q (n=8). Sequencing of candidate genes in the minimally affected regions excluded the involvement of tyrosine kinases and several other genes. Following the identification of TET2 at 4q24 as a putative novel tumor suppressor gene of unknown function in patients with classic MPN and MDS we identified homozygous TET2 variants in 6 cases with 4q aUPD. Analysis of 210 additional patients revealed TET2 variants in aCML (16/53; 30%), CMML (28/70; 40%), unclassified MDS/MPN (5/17, 29%), hypereosinophilic syndrome (4/30; 13%) but none in blast crisis CML (n=40). In total, 70 TET2 variants were identified that were spread throughout the coding region. Of these, 35 were likely causative changes predicted to result in premature chain termination (nonsense, n=18; deletion, n=10; insertion, n=7) and 35 were missense substitutions that have not been reported as SNPs. 20 missense mutations (57%) clustered in two conserved regions. TET2 mutations were not associated with a change of overall or progression-free survival compared to mutation negative cases. Mutations in CBL, encoding a key regulator of tyrosine kinase signaling, were identified in 5 cases with 11q aUPD and analysis of 574 additional MPN and MDS/MPN patients revealed a total of 27 CBL variants in 26 patients with aCML (12/152; 8%), CMML (10/78; 13%), myelofibrosis (n=3/53; 6%) or hypereosinophilic syndrome (n=1/96; 1%). Most variants were missense substitutions in exons 8 or 9 (encoding the linker/RING domain) that abrogated CBL ubiquitin ligase activity and conferred a proliferative advantage to 32D cells that overexpressed FLT3. Patients with CBL mutations had a shorter overall survival and progression-free survival compared to mutation negative cases (OS: 33 months vs. 39 months; PFS: 22 months vs 32 months) but the differences were not significant. We conclude that aUPD is common in atypical CML and related disorders and that inactivating mutations of TET2 and CBL are associated with aUPD at 4q and 11q, respectively.