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

Aminetou Mint Mohamed,Didier Auboeuf,Lydia Campos,Françoise Solly,Marie Balsat,Franck Mortreux,Pascale Flandrin-Gresta,Denis Guyotat,Claude Preudhomme,Mauricette Michallet,Emeline Cros,Olivier Nibourel,Hussein Mortada,Christiane Pinatel,Catherine Koering,Meyling Cheok,Xavier Thomas,Charles Dumontet,Éric Wattel ,Mohamed Elhamri ,Franck E Nicolini ,Morgan Thénoz ,Léa Payen-Gay

doi:10.18632/oncotarget.3898

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.

Highlights

Acute myelogenous leukemia (AML) represents a heterogeneous spectrum of myeloid malignancies that harbor a constellation of chromosomal abnormalities and gene mutations as well as transcriptional, proteomic, metabolomic and epigenetic modifications
We used Affymetrix HTA2 exon arrays to examine the exon expression profiles of three AML cell lines (MOLM13, Kasumi-1 and KG1) that had normal or knocked-down levels of WT1 or DEK gene expression. shRNA-WT1 significantly reduced the level of WT1 mRNA and protein expression in the three cell lines (Figure S1A) and similar results were obtained with DEK
Several reports have found somatic mutations that occurred in splicing factors in AML, yet their frequency is significantly lower than that observed in other myeloid malignancies such as myelodysplastic syndromes [6]

Summary

Introduction

Acute myelogenous leukemia (AML) represents a heterogeneous spectrum of myeloid malignancies that harbor a constellation of chromosomal abnormalities and gene mutations as well as transcriptional, proteomic, metabolomic and epigenetic modifications. These abnormalities have enabled better understanding of disease mechanisms and generated diagnostic and prognostic tools that rely on key therapeutic targets. In patients for whom such intensive treatment is unsuitable, hypomethylating agents can prolong survival [2]. For both of these therapeutic approaches resistance can be an issue. The expression and activity of the ATP Binding Cassette B1 (ABC-B1; MDR1/Pgp) gene is significantly correlated with the response to intensive chemotherapy (IC) and disease outcome [3]

Methods

Results

Conclusion