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Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing–based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)–defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA–related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss ≥200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2A rearrangements while showing limitations in detecting lowly expressed PML-RARA fusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing–based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.

Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing–based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)–defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA–related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss ≥200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2Arearrangements while showing limitations in detecting lowly expressed PML-RARAfusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing–based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.

To determine whether the mutational profile of primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) is unique by comparison with other diffuse large B-cell lymphoma subtypes, we analyzed a total cohort of 20 PCLBCL-LT patients by using next-generation sequencing with a lymphoma panel designed for diffuse large B-cell lymphoma. We also analyzed 12 pairs of tumor and control DNA samples by whole-exome sequencing, which led us to perform resequencing of three selected genes not included in the lymphoma panel: TBL1XR1, KLHL6,and IKZF3. Our study clearly identifies an original mutational landscape of PCLBCL-LT with a very restricted set of highly recurrent mutations (>40%) involving MYD88(p.L265P variant), PIM1,and CD79B. Other genes involved in B-cell signaling, NF-κB activation, or DNA modeling were found altered, notably TBL1XR1(33%), MYC(26%) CREBBP(26%), and IRF4(21%) or HIST1H1E(41%). MYD88L265Pvariant was associated with copy number variations or copy neutral loss of heterozygosity in 60% of patients. The most frequent genetic losses involved CDKN2A/2B, TNFAIP3/A20, PRDM1, TCF3,and CIITA.Together, these results show that PCLBCL-LT exhibits a unique mutational landscape, combining highly recurrent hotspot mutations in genes involved in NF-kB and B-cell signaling pathways, which provides a rationale for using selective inhibitors of the B-cell receptor.

Background:

Sibon: Janssen: Consultancy; Abbvie: Consultancy; iQone: Consultancy; Takeda: Consultancy; Roche: Consultancy. Drieux: Genexpath: Patents & Royalties: The author is a potential inventor on a patent application for the LymphoSign, which has been licensed for by Genexpath Patents & Royalties.. Ruminy: Genexpath: Patents & Royalties: The author is a potential inventor on a patent application for the LymphoSign, which has been licensed for by Genexpath Patents & Royalties. . Salles: Takeda: Consultancy; Velosbio: Consultancy; Ipsen: Consultancy; Allogene: Consultancy; Miltneiy: Consultancy; Genentech/Roche: Consultancy; Genmab: Consultancy; Janssen: Consultancy; Loxo: Consultancy; Kite/Gilead: Consultancy; Regeneron: Consultancy, Honoraria; Morphosys: Consultancy, Honoraria; Novartis: Consultancy; Incyte: Consultancy; Rapt: Consultancy; Epizyme: Consultancy, Honoraria; Debiopharm: Consultancy; BMS/Celgene: Consultancy; Beigene: Consultancy; Abbvie: Consultancy, Honoraria; Bayer: Honoraria. Gaulard: Alderaan: Research Funding; Sanofi: Research Funding; Innate Pharma: Research Funding; Gilead: Consultancy; Takeda: Consultancy, Honoraria. Bachy: Kite, a Gilead Company: Honoraria; Novartis: Honoraria; Daiishi: Research Funding; Roche: Consultancy; Takeda: Consultancy; Incyte: Consultancy.

RNA splicing is a fundamental biological process that generates protein diversity from a finite set of genes. Recurrent somatic mutations of genes involved in RNA splicing are present at high frequency in Myelodysplasia (up to 70%) but less so in Acute Myeloid Leukemia (AML; less than 20%). To investigate whether there were aberrant and recurrent RNA splicing events in the AML transcriptome that were associated with poor prognosis in the absence of splicing factor mutations, we developed a bioinformatics pipeline to systematically annotate and quantify alternative splicing events from RNA-sequencing data (Fig A).

Unnikrishnan: Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Lehmann:TEVA: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Abbive: Membership on an entity's Board of Directors or advisory committees. Pimanda:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.

Salles: Novartis: Consultancy, Honoraria; Mundipharma: Honoraria; Amgen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Gilead: Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Roche/Genentech: Consultancy, Honoraria, Research Funding.

Haioun: Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sandoz: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees. Salles:Mundipharma: Honoraria; Janssen: Consultancy, Honoraria; Gilead: Honoraria, Research Funding; Novartis: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Roche/Genentech: Consultancy, Honoraria, Research Funding.

The molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) has been highlighted by gene expression profiling (GEP), dividing DLBCL into the following three main molecular subtypes with different clinical outcomes and responses to immunochemotherapy: the germinal center B-cell-like (GCB) subtype, the activated B-cell-like (ABC) subtype and the primary mediastinal B-cell lymphoma (PMBL) subtype. Despite frequent translocations involving the IGH(heavy chain) locus, B-cell receptor (BCR) expression is retained in almost all DLBCL, indicating that BCR signaling is crucial for the survival of malignant cells. Furthermore, DLBCL are characterized by recurrent somatic mutations that are supposed to be oncogenic drivers. Here, with the aim to more accurately define the DLBCL pathogenic subgroups, we report a detailed immunogenetic analysis of IGHrearrangements in a well-defined GEP DLBCL cohort and correlate these features with the somatic mutation status of recurrently mutated genes involved in lymphomagenesis. Methods: 204 DLBCL enrolled in the prospective LYSA LNH03 trial program were classified into molecular subtypes by GEP using Affymetrix arrays [82 ABC (40.2%), 77 GCB (37.7%), 29 (14.2%) unclassified and 16 PMBL (7.8%)]. The amplification of complete VDJrearrangements was realized using BIOMED-2 protocols. Somatic hypermutation (SHM) characteristics were studied (mutation rate, glycosylation N-X-S/T sites, RGYW hotspots, composition of CDR3) and correlated with the molecular subtypes. To obtain a more comprehensive molecular portrait of the DLBCL cases, GEP and IGH VDJanalyses were correlated with the mutational status of a panel of 34 recurrently mutated genes in DLBCL such as MYD88, EZH2, CD79B, TNFAIP3, CARD11and GNA13 (Dubois et al. Clinical Cancer Research 2016). Results: A total of 153/204 (75%) clonal VDJrearrangements were successfully determined. Failures to detect clonotypic sequences were predominantly seen in PMBL (56%) and unclassified (31%) cases. The ABC subtype display a significantly lower SHM rate than the 3 other subtypes, especially in contrast to the PMBL subgroup that was characterized by a higher SHM rate (p<0.0001 for each). While IGHVgene usage generally reflected that of normal B cells, a marked increase in IGHV4-34in ABC cases (30%) was confirmed and those cases tended to have less SHM. Acquisition of new N-glycosylation (N-Gly) sites, a hallmark of follicular lymphoma, was more prevalent in the GCB cases (48%) than in ABC (22%) (p=0.012) but was also observed in 5/7 (71%) PMBL cases with functional IGHrearrangement. This acquisition is correlated with a more frequent t(14;18)(q24;q32) in GCB subtype. As reported in FL, this suggests that lectin binding signals via surface Ig that contain N-Gly sites may provide an extrinsic antigen-independent signal in some DLBCL, and more specifically in t(14;18) DLBCL (Linley et al. Blood 2015). Finally, we correlated these immunogenetic features with the mutational status of some drivers genes frequently mutated in DLBCL. Within ABC subtype patients, MYD88or TNFAIP3mutated cases displayed a higher SHM rate (13.4% vs 8.4%, p <0.0001; 15.44% vs 11.13%, p=0.03), without any IGHfamily distribution bias.9/56 (16%) GCB DLBCLharbored an EZH2 mutation. All expressed an IGHV3 rearrangement (100% vs 52% for the GCB-EZH2 wt, p=0.014). By contrast to MYD88 status, a similar IGSHM rate was observed in mutated and wt patients regarding EZH2, CARD11 or GNA13 genes. Conclusion: The IG characterization and the driver gene mutation analysis according to the cell of origin of the tumor allowed us to refine DLBCL subgroups. Our data suggest that there is a strong interaction between extrinsic mechanisms, including lectin-mediated antigen-independent activation or, in the IGHV4-34cases, via N-acetyl lactosamine ligands, and intrinsic mechanisms to activate the BCR/NFKB pathway. These data could help us classify the different subgroups of DLBCL more accurately and, in particular, to identify new molecular features for BCR target therapy.

Introduction: MYD88mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of Activated B-Cell like (ABC) Diffuse Large B Cell Lymphoma (DLBCL), leading to constitutive NFkB pathway activation. The frequency of MYD88mutations in DLBCL and other hematologic malignancies is well described; however, there has not yet been a large-scale study of a MYD88mutated patient cohort with additional Next Generation Sequencing (NGS), copy number variation (CNV), and gene expression data, in order to thoroughly characterize the associated genomic profiles of these patients. The aims of our study were to compare the L265P and non-L265P mutations in terms of pathological and genetic features, to better detail the genomic background associated with MYD88mutations in order to delineate patients potentially sensitive to targeted therapies, and to define the prognostic value of MYD88mutations according to different genomic contexts.

Briere: St. Louis Hospital, Paris, France: Employment. Salles:Celgene Corporation; Roche: Speakers Bureau; Calistoga Pharmaceuticals, Inc.; Celgene Corporation; Genentech, Inc.; Janssen Pharmaceutica Products, L.P.; Roche: Consultancy; Celgene Corporation; Roche and Gilead Sciences: Research Funding.

Landesman: Karyopharm Therapeutics: Employment. Senapedis:Karyopharm Therapeutics, Inc.: Employment, Patents & Royalties. Argueta:Karyopharm Therapeutics: Employment. Milpied:Celgene: Honoraria, Research Funding.

No relevant conflicts of interest to declare.

Background

Introduction

Background and aim of the study

Ruminy: Centre Henri Becquerel: Patents & Royalties. Marchand:Centre Henri Becquerel: Patents & Royalties.

No relevant conflicts of interest to declare.

In acute leukemia, recurrent chromosomal translocations which result in the fusion of two genes are frequent. Some of these markers have a well established prognostic and therapeutic impact and are routinely screened at diagnosis by cytogenetics and RT-PCR. Yet, due to the limitations of these methods, only a few among the dozens of known rearrangements are systematically tested. Many abnormalities which could provide important clinical information thus remain ignored, mainly due to the impossibility of performing a cost effective multi-targeted screening. To overcome this obstacle, we have developed a simple and parsimonious assay which allows a reliable detection of dozens of fusion genes in only a few hours.

No relevant conflicts of interest to declare.

Diffuse large B-cell lymphoma (DLBCL) is the most common non-hodgkin lymphoma. It is subdivided into two molecular subtypes called germinal center B cell-like (GCB) and Activated B cell-like (ABC), deriving from different stages of B-cell differentiation. Recent studies have shown that ABC DLBCLs, which are associated with inferior survival, could benefit from new therapies targeting the NFkB pathway. Unfortunately, gene expression profiling methods to distinguish these lymphomas are not available in routine diagnosis and alternative immunohistochemical algorithms are often considered poorly reproducible. To circumvent these limitations we have developed a simple assay which allows a rapid and efficient classification of these tumours. By comparing gene expression data from the literature and from our own studies, we established a 10 genes expression signature which discriminates ABC from GCB cases (ABC: IRF4, FOXP1, IGHM, TNFRSF13B, CCND2; GCB: LMO2, MYBL1, BCL6, NEK6, TNFRSF9). These genes were incorporated into a Reverse Transcriptase Multiplex Ligation-dependant Probe Amplification assay (RT-MLPA), together with cMYC and BCL2, whose co-expression was recently shown to be prognostic in these diseases, and the CCND1and MS4A1(encoding CD20) genes used as controls (Figure 1A-B). We next applied this assay on a training series of 50 cases previously identified as belonging to the ABC or GCB subtypes by gene expression profiling using the Wright's algorithm to construct a Bayesian predictor. Within this first series, this predictor classified 44 cases within the expected subtypes, 5 were considered unclassified and only one ABC case was misclassified. The efficiency of this predictor was next verified on an independent validation series of 50 cases, where 46 cases were classified within the expected subtype, 3 were considered unclassified and again only one ABC case was misclassified. To test the prognostic strength of this assay we next included 85 additional cases, to reach a total of 185 DLBCLs (Figure 1C). 141 of these tumours, all treated between 2001 and 2011 at the centre H. Becquerel, Rouen, France, by a combination of Rituximab and chemotherapy, were retained for this analysis. Within this series, the RT-MLPA predictor identified 49 GCB and 64 ABC DLBCLs, and 28 cases remained unclassified. As expected, ABC cases were significantly associated with a worst event free survival (EFS)(P=0.015) and showed a trend toward a lower overall survival (OS)(P=0.060). Univariate analysis confirmed that the expression of several individual genes within this signature is significantly associated with poor prognosis (LMO2 low: OS P=0.005; BCL6 low: OS P=0.012; IRF4 high: OS P=0.008; TNFRSF13B high: OS P=0.004). We could also verify that the double MYC+/BCL2+ signature is significantly associated with a worst outcome (OS P=0.012) and identified a group of patients with particularly poor prognosis within the ABC subtype (OS P=0.004). Finally, we could demonstrate the robustness of our assay by classifying correctly 12 DLBCLs (6 ABC and 6 GCB) starting from RNA extracted from paraffin embedded (FFPE) biopsies. In conclusion, our RT-MLPA assay is a rapid (it can be achieved in less than one day, and we repeatedly tested up to 40 patients in parallel), cheap (the cost of one test is less than 5 dollars), and efficient gene expression profiling method to discriminate ABC from GCB DLBCLs and to obtain important information on others prognosis markers. It does not require specific equipments (only one conventional PCR module and one capillary genetic analyser), can be achieved from FFPE samples, and could easily be transferred in many routine diagnosis laboratories.

Genomic gains and losses play a crucial role in the development and progression of DLBCL and are closely related to gene expression profiles (GEP), including the germinal center B-cell like (GCB) and activated B-cell like (ABC) cell of origin (COO) molecular signatures. To identify new oncogenes or tumor suppressor genes (TSG) involved in DLBCL pathogenesis and to determine their prognostic values, an integrated analysis of high-resolution gene expression and copy number profiling was performed.Two hundred and eight adult patients with de novo CD20+ DLBCL enrolled in the prospective multicentric randomized LNH-03 GELA trials (LNH03-1B, -2B, -3B, 39B, -5B, -6B, -7B) with available frozen tumour samples, centralized reviewing and adequate DNA/RNA quality were selected. 116 patients were treated by Rituximab(R)-CHOP/R-miniCHOP and 92 patients were treated by the high dose (R)-ACVBP regimen dedicated to patients younger than 60 years (y) in frontline. Tumour samples were simultaneously analysed by high resolution comparative genomic hybridization (CGH, Agilent, 144K) and gene expression arrays (Affymetrix, U133+2). Minimal common regions (MCR), as defined by segments that affect the same chromosomal region in different cases, were delineated. Gene expression and MCR data sets were merged using Gene expression and dosage integrator algorithm (GEDI, Lenz et al. PNAS 2008) to identify new potential driver genes.A total of 1363 recurrent (defined by a penetrance > 5%) MCRs within the DLBCL data set, ranging in size from 386 bp, affecting a single gene, to more than 24 Mb were identified by CGH. Of these MCRs, 756 (55%) showed a significant association with gene expression: 396 (59%) gains, 354 (52%) single-copy deletions, and 6 (67%) homozygous deletions. By this integrated approach, in addition to previously reported genes (CDKN2A/2B, PTEN, DLEU2, TNFAIP3, B2M, CD58, TNFRSF14, FOXP1, REL…), several genes targeted by gene copy abnormalities with a dosage effect and potential physiopathological impact were identified, including genes with TSG activity involved in cell cycle (HACE1, CDKN2C) immune response (CD68, CD177, CD70, TNFSF9, IRAK2), DNA integrity (XRCC2, BRCA1, NCOR1, NF1, FHIT) or oncogenic functions (CD79b, PTPRT, MALT1, AUTS2, MCL1, PTTG1…) with distinct distribution according to COO signature.The CDKN2A/2B tumor suppressor locus (9p21) was deleted homozygously in 27% of cases and hemizygously in 9% of cases. Biallelic loss was observed in 49% of ABC DLBCL and in 10% of GCB DLBCL. This deletion was strongly correlated to age and associated to a limited number of additional genetic abnormalities including trisomy 3, 18 and short gains/losses of Chr. 1, 2, 19 regions (FDR < 0.01), allowing to identify genes that may have synergistic effects with CDKN2A/2B inactivation. With a median follow-up of 42.9 months, only CDKN2A/2B biallelic deletion strongly correlates (FDR p.value < 0.01) to a poor outcome in the entire cohort (4y PFS = 44% [32–61] respectively vs. 74% [66–82] for patients in germline configuration; 4y OS = 53% [39–72] vs 83% [76–90]). In a Cox proportional hazard prediction of the PFS, CDKN2A/2B deletion remains predictive (HR = 1.9 [1.1–3.2], p = 0.02) when combined with IPI (HR = 2.4 [1.4–4.1], p = 0.001) and GCB status (HR = 1.3 [0.8–2.3], p = 0.31). This difference remains predictive in the subgroup of patients treated by R-CHOP (4y PFS = 43% [29–63] vs. 66% [55–78], p=0.02), in patients treated by R-ACVBP (4y PFS = 49% [28–84] vs. 83% [74–92], p=0.003), and in GCB (4y PFS = 50% [27–93] vs. 81% [73–90], p=0.02), or ABC/unclassified (5y PFS = 42% [28–61] vs. 67% [55–82] p = 0.009) molecular subtypes (Figure 1).We report for the first time an integrated genetic analysis of a large cohort of DLBCL patients included in a prospective multicentric clinical trial program allowing identifying new potential driver genes with pathogenic impact. However CDKN2A/2B deletion constitutes the strongest and unique prognostic factor of chemoresistance to R-CHOP, regardless the COO signature, which is not overcome by a more intensified immunochemotherapy. Patients displaying this frequent genomic abnormality warrant new and dedicated therapeutic approaches.Salles: roche: Consultancy.

No relevant conflicts of interest to declare.

Abstract 418

Abstract 415This icon denotes a clinically relevant abstract