Oncogene- and drug resistance-associated alternative exon usage in acute myeloid leukemia (AML)

// Aminetou Mint Mohamed 1 , Marie Balsat 1 , Morgan Thenoz 1 , Catherine Koering 1 , Lea Payen-Gay 2 , Meyling Cheok 3 , Hussein Mortada 4 , Didier Auboeuf 4 , Christiane Pinatel 5 , Mohamed El-Hamri 6 , Charles Dumontet 7 , Emeline Cros 7 , Pascale Flandrin-Gresta 1, 8 , Olivier Nibourel 4 , Claude Preudhomme 4 , Mauricette Michallet 1, 6 , Xavier Thomas 6 , Franck Nicolini 6 , Francoise Solly 1, 8 , Denis Guyotat 1, 9 , Lydia Campos 1, 8 , Eric Wattel 1, 6, * , Franck Mortreux 1, * 1 Universite Lyon 1, CNRS UMR5239, Oncovirologie et Biotherapies, Faculte de Medecine Lyon Sud, ENS – HCL, Pierre Benite, France 2 INSERM, UMR-S1052, Centre de Recherche en Cancerologie de Lyon, Lyon, France 3 Jean-Pierre Aubert Center, INSERM U837, Facteurs de persistance des cellules leucemiques, Institute for Cancer Research in Lille, Lille cedex, France 4 Centre de Recherche sur le Cancer de Lyon, Inserm, Epissage alternatif et progression tumorale, Lyon, France 5 Centre de Recherche sur le Cancer de Lyon, Inserm, Echappement aux systemes de sauvegarde et plasticite cellulaire, Lyon, France 6 Universite Lyon I, Service d’Hematologie, Pavillon Marcel Berard, Centre Hospitalier Lyon-Sud, Pierre Benite, France 7 Centre de Recherche sur le Cancer de Lyon, Inserm, Anticorps anticancer, Lyon, France 8 Universite de Saint Etienne, Laboratoire d’Hematologie, CHU de Saint-Etienne, Saint-Etienne, France 9 Institut de Cancerologie de la Loire, CHU de Saint-Etienne, Saint Priest en Jarez, France * These authors have contributed equally to this work Correspondence to: Eric Wattel, e-mail: eric.wattel@chu-lyon.fr Franck Mortreux, e-mail: franck.mortreux@ens-lyon.fr Keywords: acute myeloid leukemia, alternative splicing, WT1, DEK, multidrug resistance Received: March 16, 2015 Accepted: April 28, 2015 Published: May 12, 2015 ABSTRACT In addition to spliceosome gene mutations, oncogene expression and drug resistance in AML might influence exon expression. We performed exon-array analysis and exon-specific PCR (ESPCR) to identify specific landscapes of exon expression that are associated with DEK and WT1 oncogene expression and the resistance of AML cells to AraC, doxorubicin or azacitidine. Data were obtained for these five conditions through exon-array analysis of 17 cell lines and 24 patient samples and were extended through qESPCR of samples from 152 additional AML cases. More than 70% of AEUs identified by exon-array were technically validated through ESPCR. In vitro , 1,130 to 5,868 exon events distinguished the 5 conditions from their respective controls while in vivo 6,560 and 9,378 events distinguished chemosensitive and chemoresistant AML, respectively, from normal bone marrow. Whatever the cause of this effect, 30 to 80% of mis-spliced mRNAs involved genes unmodified at the whole transcriptional level. These AEUs unmasked new functional pathways that are distinct from those generated by transcriptional deregulation. These results also identified new putative pathways that could help increase the understanding of the effects mediated by DEK or WT1, which may allow the targeting of these pathways to prevent resistance of AML cells to chemotherapeutic agents.