Abstract 113: Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia
Authors: Padella Antonella , Simonetti Giorgia , Ferrari Anna , Paciello Giulia , Zago Elisa , Baldazzi Carmen , Guadagnuolo Viviana , Papayannidis Cristina , Robustelli Valentina , Imbrogno Enrica , Testoni Nicoletta , Delledonne Massimo , Iacobucci Ilaria , Storlazzi Tiziana Clelia , Ficarra Elisa , Lollini Pier-Luigi , Martinelli Giovanni 
Published: July 2016

Abstract
Acute Myeloid Leukemia (AML) is a highly heterogeneous disease and somatic mutations and fusion genes have a crucial diagnostic, prognostic and therapeutic role in AML. However, the leukemogenic potential of the fusions, their cooperation with somatic mutations and their prognostic role are still unknown.
The aim of the study was to identify novel rare gene fusions having a causative role in leukemogenesis and to identify cooperative somatic mutations as potential targets for personalized therapies in AML cases with rare and poorly described chromosomal translocations.
We performed RNAseq on bone marrow samples from 5 AML patients (#59810, #20, #84, #21 and #32). The presence of gene fusions was assessed with deFuse and Chimerascan. Putative fusion genes were prioritized using Pegasus and Oncofuse to select biologically relevant fusions. WES was performed on samples #59810, #20 and #21 and variants were detected using the software Mutect and GATK.
The CBFβ-MYH11 chimera was identified in sample #84, with inv(16), thus confirming the reliability of our analysis.
Sample #59810 carried the fusion transcript ZEB2-BCL11B (Driver Score, DS = 0.7), an in-frame fusion and a rare event in AML associated with t(2;14). The fusion transcript showed 3 splicing isoforms and ZEB2 and BCL11B transcripts were upregulated in patient's blasts, compared with 53 AML samples with no chromosomal aberrations in the 14q32 region. The WT1-CNOT2 chimera was also detected, which is a novel out-of-frame fusion (DS = 0.008) related to t(11;12) translocation. WES analysis showed SNVs in TET2 and BCOR genes.
In sample #20 we identified two different fusion transcripts: CPD-PXT1 (DS = 0.07), which was the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which was cryptic at cytogenetic analysis (DS = 0.8). Interestingly, the latter fusion involved a tumour suppressor gene. Moreover, mutations in BCOR and NRAS were detected by WES.
RNAseq on sample #21 identified a novel fusion event between chromosomes 19 and 7, involving the genes OAZ and MAFK (DS = 0.9). The 3’ partner gene is a transcription factor, a functional class recurrently altered in AML. This patient showed SNVs in CBL and SMC1A genes.
Finally, no chimeras were confirmed in sample #32 having a t(12;18) translocation.
Our data suggest that fusion events are frequent in AML and a number of them cannot be detected by current cytogenetic analyses. Gene fusions cooperate with somatic mutations in the genomic landscape driving AML pathogenesis and its heterogeneity. Moreover, the results indicate that different approaches, including WES, RNAseq bioinformatic and statistic tools need to be integrated in order to identify potential targets for personalized therapies.
Acknowledgements: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project.
Citation Format: Antonella Padella, Giorgia Simonetti, Anna Ferrari, Giulia Paciello, Elisa Zago, Carmen Baldazzi, Viviana Guadagnuolo, Cristina Papayannidis, Valentina Robustelli, Enrica Imbrogno, Nicoletta Testoni, Massimo Delledonne, Ilaria Iacobucci, Tiziana Clelia Storlazzi, Elisa Ficarra, Pier-Luigi Lollini, Giovanni Martinelli. Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 113.