Abstract A15: The landscape of somatic mutations in the core-binding factor acute myeloid leukemias

Acute myeloid leukemia (AML) results from mutations that promote aberrant self-renewal, proliferation and differentiation. The specific combination of mutations not only influences the phenotype of the leukemia but also its response to therapy. The core-binding factor (CBF) leukemias represent one of the most common forms of AML and are defined by genetic lesions that target the RUNX1(AML1)/CBFβ transcription factor complex. These include t(8;21)[RUNX1-ETO], inv(16) and t(16;16)[CBFβ-MYH11], point mutations in RUNX1, and several other rarer translocations that target RUNX1. The AML1/CBFβ transcription factor complex functions as a master transcriptional regulator that is essential for the generation of definitive hematopoietic stem cells during development, and plays an important role in the differentiation of a number of hematopoietic lineages including T cells and megakaryocytes. Using a conditional Runx1-Eto murine knock-in model, we previously demonstrated that the expression of Runx1-Eto was insufficient to induce leukemia. To define the landscape of mutation that cooperate with RUNX1-ETO in leukemogenesis, the St. Jude Children9s Research Hospital - Washington University Pediatric Cancer Genome Project performed whole genome DNA Sequencing (WGS) on a cohort of 17 pediatric CBF leukemia [7 t(8;21) and 10 inv(16) cases. Somatic mutations were identified using the PCGP analytical pipeline and all identified mutations were experimentally validated. The frequency of the identified mutations were then assessed by performing exome sequencing on a validation cohort consisting of 151 pediatric and adult CBF leukemias [79 t(8;21) and 72 inv(16)]. The combined analyses identified very few copy number alterations (CNAs) or structural alterations per case, and an average of only 12.5 somatic non-synonymous single nucleotide variations or insertions/deletions per case. Despite the low burden of mutations, recurrent activating mutations in the Kinase/RAS signaling pathway (NRAS, KIT, FLT3, KRAS, and PTPN11, and inactivating mutations in NF1) were collectively identified in >67% of cases An even more striking result was the identification of a high frequency of loss-of-function mutations in genes that encode key epigenetic regulatory proteins (28% including ASXL2, EZH2, UTX, SETD2, MLL2/3), and missense and loss of function mutations in genes that encode components of the cohesin complex (10% including SMC1A, SMC2, RAD21). Moreover, the frequency of both classes of mutations were significantly higher in the t(8;21) versus inv(16) containing cases (epigenetic regulatory mutations 48% vs 6.25% and cohesin mutations 20% vs 0%). No significant difference was noted in the frequency of cohesin mutations between pediatric and adult cases. The identified mutations targeted genes encoding core components of the cohesion complex required to generate the ring shaped DNA binding structure, SMC1A, SMC3, and RAD21, as well as a single case with a mutation in the SMC3 acetyl transferase ESCO2. In addition, loss of the X chromosome is a frequent somatic event in female patients with t(8;21) leukemia and SMC1A is located on Chr. X and is not subjected to X inactivation, suggesting that loss of Chr. X leads to haploinsufficiency. The majority of leukemias with cohesion mutations also contain activating mutation in the RAS/Kinase signaling pathway, suggesting that these mutations cooperate with AML1-ETO to induce leukemia. Collectively, these data provide an unprecedented view of the range of cooperating mutations that occur in the CBF leukemias and highlight fundamental differences between t(8;21) and inv(16) containing cases. Citation Format: Amanda Larson Gedman, Jinjun Cheng, Xiang Chen, Ina Radtke, Anna Andersson, Heather Mulder, Kristy Boggs, Bhavin Vadodaria, Donald Yergeau, Joy Nakitandwe, Lars Bullinger, Michael Kuehn, Hartmut Doehner, Konstanze Doehner, Sheila Shurtleff, John Easton, Richard Wilson, Jinghui Zhang, James R. Downing. The landscape of somatic mutations in the core-binding factor acute myeloid leukemias. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A15.