Abstract 4810: Exome sequencing of refractory diffuse large B-cell lymphomas highlights candidate genes for targeted resequencing
Authors: Mareschal Sylvain , Viailly Pierre-Julien , Bertrand Philippe , Bohers Elodie , Jais Jean-Philippe , Figeac Martin , Molina Thierry J. , Desmots Fabienne , Fest Thierry , Salles Gilles , Haioun Corinne , Tilly Hervé , Leroy Karen , Jardin Fabrice 
Published: August 2015

Abstract
As the most common lymphoid malignancy, Diffuse Large B-Cell Lymphoma (DLBCL) has largely benefited from immunochemotherapy combinations developed in the past decade. However 30% to 40% of patients still do not respond to treatment, or relapse in a few months. The mechanisms involved in short term treatment failure are poorly understood, and biomarkers to predict refractoriness in newly diagnosed patients are still lacking.
To address this issue, 14 normal / tumoral pairs of exomes from patients who progressed or relapsed within 12 months were sequenced on a HiSeq2500 platform. Somatic events were called using VarScan2, and significantly mutated pathways were highlighted by PathScan (False Discovery Rate, FDR &lt; 0.001). Genes from 175 pathways were found to be more mutated than expected according to the background mutation rate observed throughout the exomes (2.68 non synonymous mutations per megabase, ranging from 0.69 to 4.66), including genes encoding histone monomers (HIST1H1/2) and transcription regulators (CREBBP, EP300, TP53), members and relatives of the NFKB signaling pathway (MYD88, TNFAIP3, NFKBIA/E), or other signaling cascades (IRF4, CIITA, SOCS1).
To pinpoint genes and pathways unusually enriched in such refractory patients, a published series of 39 DLBCL genome pairs was used (Morin et al, Blood 2013). Variant annotation and filtering was reapplied to enforce target region consistency, and Fisher tests were conducted independently in the two series. 22 of the 175 pathways selected by PathScan were found to be enriched in refractory patients (FDR &lt; 0.01) but not in the comparative series (FDR &gt; 0.5). One of the most relevant was “IL4 mediated signaling events”, which includes genes such as STAT6, IRF4 or SOCS1.
These 3 genes, along with 31 other genes frequently mutated in DLBCL, were sequenced in a series of 216 DLBCLs with an orthogonal method (PGM sequencer). Although the survival impact of IL4 related gene mutations could not be confirmed, their prevalence (17.5%) was far above what was previously described in DLBCL. Molecular profiling by Affymetrix U133+2 arrays revealed a strong association with the Primary Mediastinal B-Cell lymphoma (PMBL) subtype (Fisher p = 5e-10), a molecular subtype observed in 4/14 and 22/216 patients of the refractory and extended series respectively.
We propose here an exhaustive description of mutations found in 14 exomes from refractory DLBCL patients, compared to 39 previously published genomes. The extension to 216 patients enrolled in the LNH03 LYSA (LYmphoma Study Association) clinical trial program using targeted resequencing and transcriptomic arrays allowed us to refine these results, and highlight the high prevalence of somatic mutations in IL4 signaling related genes in PMBLs.
Citation Format: Sylvain Mareschal, Pierre-Julien Viailly, Philippe Bertrand, Elodie Bohers, Jean-Philippe Jais, Martin Figeac, Thierry J. Molina, Fabienne Desmots, Thierry Fest, Gilles Salles, Corinne Haioun, Hervé Tilly, Karen Leroy, Fabrice Jardin. Exome sequencing of refractory diffuse large B-cell lymphomas highlights candidate genes for targeted resequencing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4810. doi:10.1158/1538-7445.AM2015-4810