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34 results on '"Elodie Bohers"'

1. Analysis of immunoglobulin/T‐cell receptor repertoires by high‐throughput RNA sequencing reveals a continuous dynamic of positive clonal selection in follicular lymphoma

Author: Victor Bobée, Mathieu Viennot, Vinciane Rainville, Liana Veresezan, Fanny Drieux, Pierre‐Julien Viailly, Victor Michel, Vincent Sater, Marie‐Delphine Lanic, Elodie Bohers, Vincent Camus, Hervé Tilly, Fabrice Jardin, and Philippe Ruminy
Subjects: Diseases of the blood and blood-forming organs, RC633-647.5
Abstract: Abstract Follicular lymphoma (FL) course is highly variable, making its clinical management challenging. In this incurable and recurring pathology, the interval between relapses tends to decrease while aggressiveness increases, sometimes resulting in the transformation to higher‐grade lymphoma. These evolutions are particularly difficult to anticipate, resulting from complex clonal evolutions where multiple subclones compete and thrive due to their capacity to proliferate and resist therapies. Here, to apprehend further these processes, we used a high‐throughput RNA sequencing approach to address simultaneously the B‐cell immunoglobulin repertoires and T‐cell immunoglobulin repertoires repertoires of lymphoma cells and their lymphoid microenvironment in a large cohort of 131 FL1/2‐3A patients. Our data confirm the existence of a high degree of intra‐clonal heterogeneity in this pathology, resulting from ongoing somatic hyper‐mutation and class switch recombination. Through the evaluation of the Simpson ecological‐diversity index, we show that the contribution of the cancerous cells increases during the course of the disease to the detriment of the reactive compartment, a phenomenon accompanied by a concomitant decrease in the diversity of the tumoral population. Clonal evolution in FL thus contrasts with many tumors, where clonal heterogeneity steadily increases over time and participates in treatment evasion. In this pathology, the selection of lymphoma subclones with proliferative advantages progressively outweighs clonal diversification, ultimately leading in extreme cases to transformation to high‐grade lymphoma resulting from the rapid emergence of homogeneous subpopulations.
Published: 2024
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2. Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers

Author: Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Elodie Bohers, Nicolas Vergne, Caroline Berard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, and Fabrice Jardin
Subjects: UMI, CNV calling, Next generation sequencing, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract: Abstract Background Recently, copy number variations (CNV) impacting genes involved in oncogenic pathways have attracted an increasing attention to manage disease susceptibility. CNV is one of the most important somatic aberrations in the genome of tumor cells. Oncogene activation and tumor suppressor gene inactivation are often attributed to copy number gain/amplification or deletion, respectively, in many cancer types and stages. Recent advances in next generation sequencing protocols allow for the addition of unique molecular identifiers (UMI) to each read. Each targeted DNA fragment is labeled with a unique random nucleotide sequence added to sequencing primers. UMI are especially useful for CNV detection by making each DNA molecule in a population of reads distinct. Results Here, we present molecular Copy Number Alteration (mCNA), a new methodology allowing the detection of copy number changes using UMI. The algorithm is composed of four main steps: the construction of UMI count matrices, the use of control samples to construct a pseudo-reference, the computation of log-ratios, the segmentation and finally the statistical inference of abnormal segmented breaks. We demonstrate the success of mCNA on a dataset of patients suffering from Diffuse Large B-cell Lymphoma and we highlight that mCNA results have a strong correlation with comparative genomic hybridization. Conclusion We provide mCNA, a new approach for CNV detection, freely available at https://gitlab.com/pierrejulien.viailly/mcna/ under MIT license. mCNA can significantly improve detection accuracy of CNV changes by using UMI.
Published: 2021
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3. Correlations between baseline 18F-FDG PET tumour parameters and circulating DNA in diffuse large B cell lymphoma and Hodgkin lymphoma

Author: Pierre Decazes, Vincent Camus, Elodie Bohers, Pierre-Julien Viailly, Hervé Tilly, Philippe Ruminy, Mathieu Viennot, Sébastien Hapdey, Isabelle Gardin, Stéphanie Becker, Pierre Vera, and Fabrice Jardin
Subjects: Positron emission tomography, B cell malignancies, Diffuse large B cell lymphoma, Hodgkin lymphoma, Circulating tumour DNA, Circulating free DNA, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract: Abstract Background 18F-FDG PET/CT is a standard for many B cell malignancies, while blood DNA measurements are emerging tools. Our objective was to evaluate the correlations between baseline PET parameters and circulating DNA in diffuse large B cell lymphoma (DLBCL) and classical Hodgkin lymphoma (cHL). Methods Twenty-seven DLBCL and forty-eight cHL were prospectively included. Twelve PET parameters were analysed. Spearman’s correlations were used to compare PET parameters each other and to circulating cell-free DNA ([cfDNA]) and circulating tumour DNA ([ctDNA]). p values were controlled by Benjamini–Hochberg correction. Results Among the PET parameters, three different clusters for tumour burden, fragmentation/massiveness and dispersion parameters were observed. Some PET parameters were significantly correlated with blood DNA parameters, including the total metabolic tumour surface (TMTS) describing the tumour–host interface (e.g. ρ = 0.81 p
Published: 2020
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4. Concomitant occurrence of genetically distinct Hodgkin lymphoma and primary mediastinal lymphoma

Author: Sydney Dubois, Philippe Ruminy, Elodie Bohers, Pierre‐Julien Viailly, Liana Veresezan, Jean‐Michel Picquenot, Victor Bobée, Mathieu Viennot, Dominique Penther, Vincent Camus, Catherine Thieblemont, Camille Pouaty, Hervé Tilly, and Fabrice Jardin
Subjects: Hodgkin lymphoma, molecular characterization, primary mediastinal lymphoma, Medicine, Medicine (General), R5-920
Abstract: Abstract Synchronous Hodgkin Lymphoma and Primary Mediastinal B‐cell Lymphoma is possible, with molecular analyses proving the absence of clonal filiation between both entities. This suggests a common etiology but the existence of two divergent clones.
Published: 2021
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5. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles

Author: Sydney Dubois, Bruno Tesson, Sylvain Mareschal, Pierre-Julien Viailly, Elodie Bohers, Philippe Ruminy, Pascaline Etancelin, Pauline Peyrouze, Christiane Copie-Bergman, Bettina Fabiani, Tony Petrella, Jean-Philippe Jais, Corinne Haioun, Gilles Salles, Thierry Jo Molina, Karen Leroy, Hervé Tilly, and Fabrice Jardin
Subjects: Medicine, Medicine (General), R5-920
Abstract: Background: Gene expression profiling (GEP), next-generation sequencing (NGS) and copy number variation (CNV) analysis have led to an increasingly detailed characterization of the genomic profiles of DLBCL. The aim of this study was to perform a fully integrated analysis of mutational, genomic, and expression profiles to refine DLBCL subtypes. A comparison of our model with two recently published integrative DLBCL classifiers was carried out, in order to best reflect the current state of genomic subtypes. Methods: 223 patients with de novo DLBCL from the prospective, multicenter and randomized LNH-03B LYSA clinical trials were included. GEP data was obtained using Affymetrix GeneChip arrays, mutational profiles were established by Lymphopanel NGS targeting 34 key genes, CNV analysis was obtained by array CGH, and FISH and IHC were performed. Unsupervised independent component analysis (ICA) was applied to GEP data and integrated analysis of multi-level molecular data associated with each component (gene signature) was performed. Findings: ICA identified 38 components reflecting transcriptomic variability across our DLBCL cohort. Many of the components were closely related to well-known DLBCL features such as cell-of-origin, stromal and MYC signatures. A component linked to gain of 19q13 locus, among other genomic alterations, was significantly correlated with poor OS and PFS. Through this integrated analysis, a high degree of heterogeneity was highlighted among previously described DLBCL subtypes. Interpretation: The results of this integrated analysis enable a global and multi-level view of DLBCL, as well as improve our understanding of DLBCL subgroups. Keywords: Diffuse large B-cell lymphoma, Independent component analysis, Transcriptomic variability, Gene signatures, prognosis
Published: 2019
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6. Targeted genotyping of circulating tumor DNA for classical Hodgkin lymphoma monitoring: a prospective study

Author: Vincent Camus, Mathieu Viennot, Justine Lequesne, Pierre-Julien Viailly, Elodie Bohers, Lucile Bessi, Bénédicte Marcq, Pascaline Etancelin, Sydney Dubois, Jean-Michel Picquenot, Elena-Liana Veresezan, Marie Cornic, Lucie Burel, Justine Loret, Stéphanie Becker, Pierre Decazes, Pascal Lenain, Stéphane Lepretre, Emilie Lemasle, Hélène Lanic, Anne-Lise Ménard, Nathalie Contentin, Hervé Tilly, Aspasia Stamatoullas, and Fabrice Jardin
Subjects: Diseases of the blood and blood-forming organs, RC633-647.5
Abstract: The relevance of circulating tumor DNA (ctDNA) analysis as a liquid biopsy and minimal residual disease tool in the management of classical Hodgkin Lymphoma (cHL) patients was demonstrated in retrospective settings and remains to be confirmed in a prospective setting. We developed a targeted Next-Generation sequencing (NGS) panel for fast analysis (AmpliSeq technology) of nine commonly mutated genes in biopies and ctDNA of cHL patients. We then conducted a prospective trial to assess ctDNA follow up at diagnosis and after 2 cycles of chemotherapy (C2). Sixty cHL patients treated by first line conventional chemotherapy (BEACOPPescalated [21.3%], ABVD/ABVD-like [73.5%] and other regimens [5.2%, for elderly patients] were assessed in this non-interventional study. Median age of the patients was 33.5 years (range 20-86). Variants were identified in 42 (70%) patients. Mutations of NFKBIE, TNFAIP3, STAT6, PTPN1, B2M, XPO1, ITPKB, GNA13 and SOCS1 were found in 13.3%, 31.7%, 23.3%, 5%, 33.3%, 10%, 23.3%, 13.3% and 50% of patients, respectively. ctDNA concentration and genotype are correlated with clinical characteristics and presentation. Regarding early therapeutic response, 45 patients (83%, NA=6) had a negative positron emission tomography (PET) after C2 (Deauville Score 1-3). Mean of DeltaSUVmax after C2 was -78.8%. We analyzed ctDNA after C2 for 54 patients (90%). ctDNA became rapidly undetectable in all cases after C2. Variant detection in ctDNA is suitable to depict the genetic features of cHL at diagnosis and may help to assess early treatment response, in association with PET. Clinical Trial reference: NCT02815137.
Published: 2020
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7. cfDNA Sequencing: Technological Approaches and Bioinformatic Issues

Author: Elodie Bohers, Pierre-Julien Viailly, and Fabrice Jardin
Subjects: cell-free DNA, circulating tumoral DNA, sequencing technologies, bioinformatics, Medicine, Pharmacy and materia medica, RS1-441
Abstract: In the era of precision medicine, it is crucial to identify molecular alterations that will guide the therapeutic management of patients. In this context, circulating tumoral DNA (ctDNA) released by the tumor in body fluids, like blood, and carrying its molecular characteristics is becoming a powerful biomarker for non-invasive detection and monitoring of cancer. Major recent technological advances, especially in terms of sequencing, have made possible its analysis, the challenge still being its reliable early detection. Different parameters, from the pre-analytical phase to the choice of sequencing technology and bioinformatic tools can influence the sensitivity of ctDNA detection.
Published: 2021
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8. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma

Author: Vincent Camus, Aspasia Stamatoullas, Sylvain Mareschal, Pierre-Julien Viailly, Nasrin Sarafan-Vasseur, Elodie Bohers, Sydney Dubois, Jean Michel Picquenot, Philippe Ruminy, Catherine Maingonnat, Philippe Bertrand, Marie Cornic, Valérie Tallon-Simon, Stéphanie Becker, Liana Veresezan, Thierry Frebourg, Pierre Vera, Christian Bastard, Hervé Tilly, and Fabrice Jardin
Subjects: Diseases of the blood and blood-forming organs, RC633-647.5
Abstract: Classical Hodgkin lymphoma is one of the most common lymphomas and shares clinical and genetic features with primary mediastinal B-cell lymphoma. In this retrospective study, we analyzed the recurrent hotspot mutation of the exportin 1 (XPO1, p.E571K) gene, previously identified in primary mediastinal B-cell lymphoma, in biopsies and plasma circulating cell-free DNA from patients with classical Hodgkin lymphoma using a highly sensitive digital PCR technique. A total of 94 patients were included in the present study. This widely expressed XPO1 E571K mutation is present in one quarter of classical Hodgkin lymphoma patients (24.2%). Mutated and wild-type classical Hodgkin lymphomas were similar regarding the main clinical features. Patients with a detectable XPO1 mutation at the end of treatment displayed a tendency toward shorter progression-free survival, as compared to patients with undetectable mutation in plasma cell-free DNA (2-year progression-free survival: 57.1%, 95% confidence interval: 30.1–100% versus 2-year progression-free survival: 90.5%, 95% confidence interval: 78.8–100%, respectively, P=0.0601). To conclude, the detection of the XPO1 E571K mutation in biopsy and plasma cell-free DNA by digital PCR may be used as a novel biomarker in classical Hodgkin lymphoma for both diagnosis and minimal residual disease, and pinpoints a crucial role of XPO1 in classical Hodgkin lymphoma pathogenesis. The detection of somatic mutation in the plasma cell-free DNA of patients represents a major technological advance in the context of liquid biopsies and noninvasive management of classical Hodgkin lymphoma.
Published: 2016
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9. Somatic mutations of cell-free circulating DNA detected by next-generation sequencing reflect the genetic changes in both germinal center B-cell-like and activated B-cell-like diffuse large B-cell lymphomas at the time of diagnosis

Author: Elodie Bohers, Pierre Julien Viailly, Sydney Dubois, Philippe Bertrand, Catherine Maingonnat, Sylvain Mareschal, Philippe Ruminy, Jean-Michel Picquenot, Christian Bastard, Fabienne Desmots, Thierry Fest, Karen Leroy, Hervé Tilly, and Fabrice Jardin
Subjects: Diseases of the blood and blood-forming organs, RC633-647.5
Published: 2015
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10. Concomitant occurrence of genetically distinct Hodgkin lymphoma and primary mediastinal lymphoma

Author: Catherine Thieblemont, Liana Veresezan, Hervé Tilly, Fabrice Jardin, Vincent Camus, Elodie Bohers, Dominique Penther, Pierre-Julien Viailly, Victor Bobée, Mathieu Viennot, Sydney Dubois, Philippe Ruminy, Camille Pouaty, Jean-Michel Picquenot, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Bohers, Elodie
Subjects: Pathology, medicine.medical_specialty, primary mediastinal lymphoma, business.industry, [SDV]Life Sciences [q-bio], Case Report, General Medicine, medicine.disease, Lymphoma, [SDV] Life Sciences [q-bio], molecular characterization, Primary Mediastinal Lymphoma, immune system diseases, Concomitant, hemic and lymphatic diseases, Etiology, Medicine, Hodgkin lymphoma, business, ComputingMilieux_MISCELLANEOUS
Abstract: Synchronous Hodgkin Lymphoma and Primary Mediastinal B‐cell Lymphoma is possible, with molecular analyses proving the absence of clonal filiation between both entities. This suggests a common etiology but the existence of two divergent clones.
Published: 2021

11. cfDNA Sequencing: Technological Approaches and Bioinformatic Issues

Author: Fabrice Jardin, Pierre-Julien Viailly, Elodie Bohers, Bohers, Elodie, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Pharmaceutical Science, Early detection, Context (language use), Computational biology, Review, cell-free DNA, 03 medical and health sciences, 0302 clinical medicine, Pharmacy and materia medica, Drug Discovery, bioinformatics, Precision medicine, 3. Good health, Biomarker (cell), [SDV] Life Sciences [q-bio], RS1-441, 030104 developmental biology, Cell-free fetal DNA, 030220 oncology & carcinogenesis, circulating tumoral DNA, sequencing technologies, Molecular Medicine, Medicine
Abstract: International audience; In the era of precision medicine, it is crucial to identify molecular alterations that will guide the therapeutic management of patients. In this context, circulating tumoral DNA (ctDNA) released by the tumor in body fluids, like blood, and carrying its molecular characteristics is becoming a powerful biomarker for non-invasive detection and monitoring of cancer. Major recent technological advances, especially in terms of sequencing, have made possible its analysis, the challenge still being its reliable early detection. Different parameters, from the pre-analytical phase to the choice of sequencing technology and bioinformatic tools can influence the sensitivity of ctDNA detection.
Published: 2021

12. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles

Author: Bettina Fabiani, Sylvain Mareschal, Pascaline Etancelin, Tony Petrella, Fabrice Jardin, Bruno Tesson, Sydney Dubois, Jean-Philippe Jais, Christiane Copie-Bergman, Gilles Salles, Elodie Bohers, Corinne Haioun, Pierre-Julien Viailly, Thierry Jo Molina, Philippe Ruminy, Karen Leroy, Hervé Tilly, Pauline Peyrouze, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Carnot CALYM [Pierre-Benite], Synergie Lyon Cancer-Platform of Bioinformatics-Gilles Thomas, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Université Lille 2 - Faculté de Médecine, INSERM U955, équipe 9, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Service de Pathologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre de pathologie, Service d'informatique médicale et biostatistiques [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Est Créteil Val-de-Marne - Faculté de médecine (UPEC Médecine), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'hématologie [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service d'anatomie pathologique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Département d'Hématologie, Institut Carnot Lymphome (CALYM), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Faculté de Médecine Henri Warembourg - Université de Lille, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Centre de pathologie [Dijon]
Subjects: 0301 basic medicine, Male, Research paper, Key genes, Transcriptomic variability, DNA Copy Number Variations, lcsh:Medicine, [SDV.CAN]Life Sciences [q-bio]/Cancer, Locus (genetics), Computational biology, Independent component analysis, Biology, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], hemic and lymphatic diseases, medicine, Biomarkers, Tumor, Humans, Genetic Predisposition to Disease, Copy-number variation, Gene signatures, prognosis, Genetic Association Studies, lcsh:R5-920, Gene Expression Profiling, lcsh:R, Gene signatures, Chromosome Mapping, Computational Biology, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Molecular Sequence Annotation, General Medicine, Diffuse large B-cell lymphoma, Gene signature, medicine.disease, Immunohistochemistry, Gene expression profiling, 030104 developmental biology, 030220 oncology & carcinogenesis, Affymetrix genechip, Female, prognosis, Lymphoma, Large B-Cell, Diffuse, lcsh:Medicine (General)
Abstract: Background: Gene expression profiling (GEP), next-generation sequencing (NGS) and copy number variation (CNV) analysis have led to an increasingly detailed characterization of the genomic profiles of DLBCL. The aim of this study was to perform a fully integrated analysis of mutational, genomic, and expression profiles to refine DLBCL subtypes. A comparison of our model with two recently published integrative DLBCL classifiers was carried out, in order to best reflect the current state of genomic subtypes. Methods: 223 patients with de novo DLBCL from the prospective, multicenter and randomized LNH-03B LYSA clinical trials were included. GEP data was obtained using Affymetrix GeneChip arrays, mutational profiles were established by Lymphopanel NGS targeting 34 key genes, CNV analysis was obtained by array CGH, and FISH and IHC were performed. Unsupervised independent component analysis (ICA) was applied to GEP data and integrated analysis of multi-level molecular data associated with each component (gene signature) was performed. Findings: ICA identified 38 components reflecting transcriptomic variability across our DLBCL cohort. Many of the components were closely related to well-known DLBCL features such as cell-of-origin, stromal and MYC signatures. A component linked to gain of 19q13 locus, among other genomic alterations, was significantly correlated with poor OS and PFS. Through this integrated analysis, a high degree of heterogeneity was highlighted among previously described DLBCL subtypes. Interpretation: The results of this integrated analysis enable a global and multi-level view of DLBCL, as well as improve our understanding of DLBCL subgroups. Keywords: Diffuse large B-cell lymphoma, Independent component analysis, Transcriptomic variability, Gene signatures, prognosis
Published: 2019

13. Combining gene expression profiling and machine learning to diagnose B-cell non-Hodgkin lymphoma

Author: Philippe Gaulard, Fabrice Jardin, Fanny Drieux, Vinciane Marchand, Corinne Haioun, Pierre-Julien Viailly, Victor Bobée, Marie-Delphine Lanic, Liana Veresezan, Christiane Copie-Bergman, Gilles Salles, Thierry Jo Molina, Elodie Bohers, Vincent Sater, Philippe Ruminy, Jean-Michel Picquenot, Lucie Oberic, Hervé Tilly, Mathieu Viennot, UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Service d'Hématologie [IUCT Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'anatomie pathologique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Est Créteil Val-de-Marne - Faculté de médecine (UPEC Médecine), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'hématologie [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Bohers, Elodie, Service Hématologie - IUCT-Oncopole [CHU Toulouse], Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle IUCT [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Service d'Hématologie [CHU Toulouse], and CHU Toulouse [Toulouse]
Subjects: Lymphoma, B-Cell, [SDV]Life Sciences [q-bio], Computational biology, lcsh:RC254-282, Article, Machine Learning, 03 medical and health sciences, 0302 clinical medicine, immune system diseases, hemic and lymphatic diseases, Cancer genomics, Biomarkers, Tumor, Tumor Microenvironment, Medicine, Humans, Clinical significance, Progression-free survival, Diagnosis, Computer-Assisted, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, business.industry, B-cell lymphoma, Gene Expression Profiling, Hematology, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, Progression-Free Survival, 3. Good health, Lymphoma, Random forest, [SDV] Life Sciences [q-bio], Gene expression profiling, Clinical trial, Oncology, Genetic marker, 030220 oncology & carcinogenesis, B-Cell Non-Hodgkin Lymphoma, business, Transcriptome
Abstract: Non-Hodgkin B-cell lymphomas (B-NHLs) are a highly heterogeneous group of mature B-cell malignancies. Their classification thus requires skillful evaluation by expert hematopathologists, but the risk of error remains higher in these tumors than in many other areas of pathology. To facilitate diagnosis, we have thus developed a gene expression assay able to discriminate the seven most frequent B-cell NHL categories. This assay relies on the combination of ligation-dependent RT-PCR and next-generation sequencing, and addresses the expression of more than 130 genetic markers. It was designed to retrieve the main gene expression signatures of B-NHL cells and their microenvironment. The classification is handled by a random forest algorithm which we trained and validated on a large cohort of more than 400 annotated cases of different histology. Its clinical relevance was verified through its capacity to prevent important misclassification in low grade lymphomas and to retrieve clinically important characteristics in high grade lymphomas including the cell-of-origin signatures and the MYC and BCL2 expression levels. This accurate pan-B-NHL predictor, which allows a systematic evaluation of numerous diagnostic and prognostic markers, could thus be proposed as a complement to conventional histology to guide the management of patients and facilitate their stratification into clinical trials.
Published: 2020

14. EBV+ diffuse large B-cell lymphoma associated with chronic inflammation expands the spectrum of breast implant-related lymphomas

Author: Vincent Camus, Daniel Birnbaum, Luc Xerri, Arnaud Guille, Cyrielle Robe, Camille Laurent, Isabelle Brenot-Rossi, Jean-Michel Picquenot, José Adélaïde, Jean-Marc Schiano, Fabrice Jardin, Elodie Bohers, Marie Bannier, Reda Bouabdallah, Lénaïg Mescam, Pierre-Julien Viailly, Andrew Wotherspoon, Philippe Gaulard, Philippe Ruminy, Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Royal Marsden NHS Foundation Trust
Subjects: Immunology, Inflammation, Biochemistry, law.invention, 03 medical and health sciences, 0302 clinical medicine, law, medicine, T-cell lymphoma, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, business.industry, Cell Biology, Hematology, medicine.disease, 3. Good health, Lymphoma, Chronic disease, 030220 oncology & carcinogenesis, Mutation (genetic algorithm), Breast implant, Cancer research, [SDV.IMM]Life Sciences [q-bio]/Immunology, medicine.symptom, business, Diffuse large B-cell lymphoma
Abstract: International audience
Published: 2020

15. XPO1E571K Mutation Modifies Exportin 1 Localisation and Interactome in B-cell Lymphoma

Author: Brigitte Sola, François Guillonneau, Vincent Cabaud Gibouin, Antoine Taly, Pierre-Julien Viailly, Hadjer Miloudi, Elodie Bohers, Luca Grumolato, Fabrice Jardin, Gaëtan Jego, Sola, Brigitte, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plateforme protéomique 3P5 [Institut Cochin] (3P5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Différenciation et communication neuronale et neuroendocrine (DC2N), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Centre National de la Recherche Scientifique (CNRS), and Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Cancer Research, Mutant, XPO1/CRM1, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], CRISPR–Cas9, [SDV.BC.IC] Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], lcsh:RC254-282, Article, 03 medical and health sciences, XPO1, 0302 clinical medicine, proteomics, [SDV.CAN] Life Sciences [q-bio]/Cancer, immune system diseases, Exportin-1, hemic and lymphatic diseases, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], B-cell lymphoma, Nuclear export signal, proximity ligation assay, 030304 developmental biology, 0303 health sciences, importin β1, Chemistry, Point mutation, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, Molecular biology, nuclear import, indirect immunofluorescence, Oncology, 030220 oncology & carcinogenesis, Mutation (genetic algorithm), nuclear export, Nuclear transport, CRISPR-Cas9
Abstract: The XPO1 gene encodes exportin 1 (XPO1) that controls the nuclear export of cargo proteins and RNAs. Almost 25% of primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) cases harboured a recurrent XPO1 point mutation (NM_003400, chr2:g61718472C&gt, T) resulting in the E571K substitution within the hydrophobic groove of the protein, the site of cargo binding. We investigated the impact of the XPO1E571K mutation using PMBL/cHL cells having various XPO1 statuses and CRISPR&ndash, Cas9-edited cells in which the E571K mutation was either introduced or knocked-out. We first confirmed that the mutation was present in both XPO1 mRNA and protein. We observed that the mutation did not modify the export capacity but rather the subcellular localisation of XPO1 itself. In particular, mutant XPO1 bound to importin &beta, 1 modified the nuclear export/import dynamics of relevant cargoes.
Published: 2020

16. Combining Gene Expression Profiling and Artificial Intelligence to Diagnose B-Cell Non-Hodgkin Lymphoma

Author: Corinne Haioun, Pierre-Julien Viailly, Vinciane Marchand, Marie-Delphine Lanic, Mathieu Viennot, Fabrice Jardin, Fanny Drieux, Gilles Salles, Philippe Ruminy, Philippe Gaulard, Elodie Bohers, Vincent Sater, Jean-Michel Picquenot, Thierry Molina, Victor Bobée, Christiane Copie-Bergman, Liana Veresezan, Hervé Tilly, Lucie Oberic, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'Anatomie et Cytologie Pathologique [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de pathologie [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service d'hématologie clinique, and Hospices Civils de Lyon (HCL)
Subjects: [SDV]Life Sciences [q-bio], Immunology, Follicular lymphoma, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, International Prognostic Index, immune system diseases, hemic and lymphatic diseases, Medicine, 030304 developmental biology, 0303 health sciences, business.industry, Cell Biology, Hematology, medicine.disease, BCL6, 3. Good health, Lymphoma, Gene expression profiling, B-Cell Non-Hodgkin Lymphoma, Mantle cell lymphoma, Artificial intelligence, business, Diffuse large B-cell lymphoma, 030215 immunology
Abstract: Introduction Non-Hodgkin B-cell lymphomas (B-NHLs) are a highly heterogeneous group of mature B-cell malignancies associated with very diverse clinical behaviors. They rely on the activation of different signaling pathways for proliferation and survival which might be amenable to targeted therapies, increasing the need for precision diagnosis. Unfortunately, their accurate classification can be challenging, even for expert hemato-pathologists, and secondary reviews recurrently differ from initial diagnosis. To address this issue we have developed a pan-B-NHL classifier based on a middle throughput gene expression assay coupled with a random forest algorithm. Material and Methods Five hundred ten B-NHL diagnosed according to the WHO criteria were studied, with 325 diffuse large B-cell lymphomas (DLBCL), 43 primary mediastinal B-cell lymphomas (PMBL), 55 follicular lymphomas (FL), 31 mantle cell lymphomas (MCL), 17 small lymphocytic lymphomas (SLL), 20 marginal zone lymphomas (MZL), 11 marginal zone lymphomas of mucosa-associated lymphoid tissue (MALT) and 8 lymphoplasmacytic lymphomas (LPL). To train and validate the predictor the samples were randomly split into a training (2/3) and an independent validation cohort (1/3). A panel of 137 genes was designed by purposely selecting the differentiation markers identified in the WHO classification for their capacity to provide diagnostic and prognostic information in NHLs. Gene expression profiles were generated by ligation dependent RT-PCR applied to RNA extracted from frozen or FFPE tissue and analyzed on a MiSeq sequencer. For analysis, the sequencing reads were de-multiplexed, aligned with the sequences of the LD-RTPCR probes and counted. Results were normalized using unique molecular indexes counts to correct PCR amplification biases. Results In DLBCL, unsupervised gene expression analysis retrieved the expected GCB, ABC and PMBL signatures (Fig A). These tumors also showed higher expressions of the KI67 (proliferation), CD68 and CD163 (tumor associated macrophages), and PD-L1/2 (immune response) markers. We also observed that the dual expression of MYC and BCL2 at the mRNA level significantly associates with inferior PFS and OS, independent from the International Prognostic Index and from the GCB/ABC cell-of-origin signature, validating the capacity of the assay to identify these highly aggressive lymphomas (Fig C). Overall, low-grade lymphomas were characterized by a significant T cell component. FLs associated with the GCB (BCL6, MYBL1, CD10 and LMO2) and Tfh (CD3, CD5, CD28, ICOS, CD40L, CXCL13) signatures. Other small B-cell lymphomas tended to overexpress activated B-cell markers (LIMD1, TACI, IRF4,FOXP1...), and the expected CD5, CD10, CD23 and CCND1 differential expressions in SLL, MCL and MZL were correctly retrieved (Fig B). Surprisingly, our analysis revealed that the Ie-Ce sterile transcript, expressed from the IGH locus during IgE isotype switching, is almost exclusively expressed by FLs, constituting one of the most discriminant markers for this pathology. We next trained a random forest classifier to discriminate the 7 principal subtypes of B-NHLs. The training cohort comprised 162 DLBCLs (ABC or GCB), 28 PMBL, 35 FLs (grade 1-3A), 21 MCLs, 12 SLLs, and 25 NHLs grouped into the MZL category (13 MZLs, 8 MALT and 4 LPLs). The independent validation series comprised 90 DLBCLs classified as GCB or ABC DLBCLs by the Lymph2Cx assay, 15 PMBLs, 12 FLs (grade 1-3A), 10 MCLs, 5 SLLs and 14 MZLs (7 MZL, 3 MALT and 4 LPL). The RF algorithm classified all cases of the training series into the expected subtype, as well as 94.5% samples of the independent validation cohort (Fig D). For ABC and GCB DLBCLs, the concordance with the Lymph2Cx assay in the validation cohort was 94.3%. Conclusion We have developed a comprehensive gene expression based solution which allows a systematic evaluation of multiple diagnostic and prognostic markers expressed by the tumor and by the microenvironment in B-NHLs. This assay, which does not require any specific platform, could be implemented in complement to histology in many diagnostic laboratories and, with the current development of targeted therapies, enable a more accurate and standardized B-NHL diagnosis. Together, our data illustrate how the integration of gene expression profiling and artificial intelligence can increase precision diagnosis in cancers. Figure Disclosures Oberic: Takeda: Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria; Roche: Membership on an entity's Board of Directors or advisory committees. Haioun:Miltenyi: Honoraria; Takeda: Honoraria; Servier: Honoraria; F. Hoffmann-La Roche Ltd: Honoraria; Novartis: Honoraria; Amgen: Honoraria; Celgene: Honoraria; Gilead: Honoraria; Janssen: Honoraria. Salles:Roche, Janssen, Gilead, Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Educational events; Amgen: Honoraria, Other: Educational events; BMS: Honoraria; Merck: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis, Servier, AbbVie, Karyopharm, Kite, MorphoSys: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Educational events; Autolus: Consultancy, Membership on an entity's Board of Directors or advisory committees; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Educational events; Epizyme: Consultancy, Honoraria. Tilly:roche: Membership on an entity's Board of Directors or advisory committees; servier: Honoraria; merck: Honoraria; Roche: Consultancy; Celgene: Consultancy, Research Funding; Astra-Zeneca: Consultancy; Karyopharm: Consultancy; BMS: Honoraria; Janssen: Honoraria; Gilead: Honoraria. Jardin:celgene: Honoraria; roche: Honoraria; amgen: Honoraria; Servier: Honoraria; janssen: Honoraria.
Published: 2019

17. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort

Author: Hélène Lanic, Pierre-Julien Viailly, Philippe Bertrand, Philippe Ruminy, Stéphanie Becker, Louis-Ferdinand Pepin, Vincent Camus, Emilie Lemasle, Julie Libraire, Elodie Bohers, Stéphane Leprêtre, Vinciane Marchand, Sandrine Vaudaux, Catherine Maingonnat, Pascaline Etancelin, Pascal Lenain, Jean-Michel Picquenot, Anne-Lise Menard, Fabrice Jardin, Pierre Vera, Aspasia Stamatoullas, Nathalie Contentin, Hervé Tilly, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de médecine nucléaire [Rouen], CRLCC Haute Normandie-CRLCC Henri Becquerel, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Service d'Hématologie, CRLCC Henri Becquerel, Service d'hématologie, Unité de recherche clinique, Equipe Quantification en Imagerie Fonctionnelle (QuantIF-LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU), CRLCC Haute Normandie-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Unité de recherche clinique [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU), This research was supported by grants from the Cancéropole Nord-Ouest, the Ligue Contre le Cancer, and Henri Becquerel Center., and Breton, Céline
Subjects: Male, 0301 basic medicine, Oncology, 0302 clinical medicine, Positron Emission Tomography Computed Tomography, Antineoplastic Combined Chemotherapy Protocols, Prospective Studies, Prospective cohort study, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, medicine.diagnostic_test, High-Throughput Nucleotide Sequencing, DNA, Neoplasm, Hematology, Middle Aged, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Cell-free fetal DNA, 030220 oncology & carcinogenesis, Female, Lymphoma, Large B-Cell, Diffuse, Cell-Free Nucleic Acids, Adult, medicine.medical_specialty, DNA Copy Number Variations, Genotype, [SDV.CAN]Life Sciences [q-bio]/Cancer, Context (language use), lcsh:RC254-282, Article, Young Adult, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, Internal medicine, Biopsy, Biomarkers, Tumor, medicine, Humans, Clinical significance, Liquid biopsy, Alleles, Aged, business.industry, Liquid Biopsy, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, Lymphoma, 030104 developmental biology, business, Diffuse large B-cell lymphoma
Abstract: From a liquid biopsy, cell-free DNA (cfDNA) can provide information regarding basal tumoral genetic patterns and changes upon treatment. In a prospective cohort of 30 diffuse large B-cell lymphomas (DLBCL), we determined the clinical relevance of cfDNA using targeted next-generation sequencing and its correlation with PET scan imaging at the time of diagnosis and during treatment. Using a dedicated DLBCL panel, mutations were identified at baseline for 19 cfDNAs and profiles were consistent with expected DLBCL patterns. Tumor burden-related clinical and PET scan features (LDH, IPI, and metabolic tumor volume) were significantly correlated with the quantity of tumoral cfDNA. Among the four patients presenting additional mutations in their cfDNAs, three had high metabolic tumor volumes, suggesting that cfDNA more accurately reflects tumor heterogeneity than tissues biopsy itself. Mid-treatment, four patients still had basal mutations in their cfDNAs, including three in partial response according to their Deauville scores. Our study highlights the major interests in liquid biopsy, in particular in the context of bulky tumors where cfDNA allows capturing the entire tumoral mutation profile. Therefore, cfDNA analysis in DLBCL represents a complementary approach to PET scan imaging.
Published: 2018

18. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries

Author: Philippe Ruminy, Fabrice Jardin, Hélène Dauchel, Élise Prieur-Gaston, Vincent Sater, Pierre Vera, Pierre-Julien Viailly, Mathieu Viennot, Elodie Bohers, Thierry Lecroq, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Equipe Traitement de l'information en Biologie Santé (TIBS - LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU), and Equipe Quantification en Imagerie Fonctionnelle (QuantIF-LITIS)
Subjects: Statistics and Probability, Computer science, Pipeline (computing), computer.software_genre, Biochemistry, Polymerase Chain Reaction, law.invention, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, law, Molecular Biology, Polymerase chain reaction, Paired-end tag, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, High-Throughput Nucleotide Sequencing, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, chemistry, Filter (video), 030220 oncology & carcinogenesis, Data mining, Noise (video), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, DNA, Algorithms
Abstract: Motivation Next-generation sequencing has become the go-to standard method for the detection of single-nucleotide variants in tumor cells. The use of such technologies requires a PCR amplification step and a sequencing step, steps in which artifacts are introduced at very low frequencies. These artifacts are often confused with true low-frequency variants that can be found in tumor cells and cell-free DNA. The recent use of unique molecular identifiers (UMI) in targeted sequencing protocols has offered a trustworthy approach to filter out artefactual variants and accurately call low-frequency variants. However, the integration of UMI analysis in the variant calling process led to developing tools that are significantly slower and more memory consuming than raw-reads-based variant callers. Results We present UMI-VarCal, a UMI-based variant caller for targeted sequencing data with better sensitivity compared to other variant callers. Being developed with performance in mind, UMI-VarCal stands out from the crowd by being one of the few variant callers that do not rely on SAMtools to do their pileup. Instead, at its core runs an innovative homemade pileup algorithm specifically designed to treat the UMI tags in the reads. After the pileup, a Poisson statistical test is applied at every position to determine if the frequency of the variant is significantly higher than the background error noise. Finally, an analysis of UMI tags is performed, a strand bias and a homopolymer length filter are applied to achieve better accuracy. We illustrate the results obtained using UMI-VarCal through the sequencing of tumor samples and we show how UMI-VarCal is both faster and more sensitive than other publicly available solutions. Availability and implementation The entire pipeline is available at https://gitlab.com/vincent-sater/umi-varcal-master under MIT license. Supplementary information Supplementary data are available at Bioinformatics online.
Published: 2019
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19. TARGETED GENOTYPING OF CIRCULATING TUMOR DNA FOR CLASSICAL HODGKIN LYMPHOMA MONITORING: A PROSPECTIVE STUDY

Author: Vincent Camus, Hélène Lanic, Emilie Lemasle, Fabrice Jardin, Jean-Michel Picquenot, Hervé Tilly, Pascaline Etancelin, Elodie Bohers, Stéphanie Becker, Aspasia Stamatoullas, B. Marcq, Mathieu Viennot, L. Burel, Stéphane Leprêtre, Anne-Lise Menard, Pascal Lenain, Marie Cornic, L. Bessi, Nathalie Contentin, Pierre-Julien Viailly, J. Loret, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)
Subjects: 0303 health sciences, Cancer Research, business.industry, [SDV]Life Sciences [q-bio], Hematology, General Medicine, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Oncology, Circulating tumor DNA, 030220 oncology & carcinogenesis, Cancer research, Classical Hodgkin lymphoma, Medicine, business, Prospective cohort study, Genotyping, 030304 developmental biology
Abstract: International audience; About Related Information ePDFPDF Request permission Export citation Add to favorites Track citationShare a linkShare on Email Facebook Twitter LinkedIn RedditIntroduction: The relevance of circulating tumor DNA (ctDNA) analysis as a liquid biopsy and minimal residual disease tool in the management of classical Hodgkin Lymphoma (cHL) patients was demonstrated in retrospective settings and remains to be confirmed.Methods: We developed a targeted Next‐Generation sequencing (NGS) panel for fast analysis (AmpliSeq® technology) of nine commonly mutated genes in biopsy and ctDNA of cHL patients. We then conducted a prospective trial to assess ctDNA follow up at diagnosis and after 2 cycles of chemotherapy (C2). A dedicated bioinformatics pipeline to optimize detections of variants with low rates and minimize artefactual misinterpretations was built. Sixty cHL patients treated by first line conventional chemotherapy (BEACOPPescalated [21.3%], ABVD/ABVD‐like [73.5%] and other regimens [5.2%, for elderly patients] were included in this non‐interventional study (NCT02815137).Results: Median age of the patients was 33.5 years (range 20‐86) with a predominance of male patients, scleronodular subtype and ECOG 0‐1 (53.3%, 70% and 88.3%, respectively). Variants were identified in 33 (55%) patients, precisely in 16/30 (53.3%) and 30/60 (50%) of available biopsy and ctDNA samples respectively. Concordance between genetic profiles of biopsy and ctDNA was accurate for 22/30 patients (73.3%). Mutations of NFKBIE, TNFAIP3, STAT6, PTPN1, B2M, XPO1, ITPKB, GNA13 and SOCS1were found in 11.7% (mean number of variants by sample [range]: 1 [0‐1]), 25% (1.1 [0‐2]), 21.7% (1.4 [0‐2]), 1.7% (1 [0‐1]), 25% (1.3 [0‐3]), 6.7% (1 [0‐1]), 15% (1.4 [0‐3]), 5% (1.3 [0‐2]) and 31.7% (1.8 [0‐7]) of all patients, respectively. Unsupervised hierarchical clustering was performed among the 9 genes to represent the association of alterations (See Figure 1).Higher level of [ctDNA] at diagnosis was associated with adverse characteristics: age ≥45 years, presence of anemia (hemoglobin
Published: 2019

20. Somatic mutations of cell-free circulating DNA detected by targeted next-generation sequencing and digital droplet PCR in classical Hodgkin lymphoma

Author: Marie Cornic, Catherine Maingonnat, Lucile Bessi, Pascaline Etancelin, Pierre-Julien Viailly, Philippe Bertrand, Ludivine Beaussire, Philippe Ruminy, Aspasia Stamatoullas, Vincent Camus, NasrinSarafan Vasseur, Elodie Bohers, Jean-Michel Picquenot, Hervé Tilly, Fabrice Jardin, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), service d'anatomo-pathologie, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), and Service d'hématologie
Subjects: Cancer Research, Somatic cell, [SDV]Life Sciences [q-bio], macromolecular substances, Cell free, Biology, Polymerase Chain Reaction, DNA sequencing, Circulating Tumor DNA, 03 medical and health sciences, 0302 clinical medicine, Refractory, immune system diseases, hemic and lymphatic diseases, polycyclic compounds, Classical Hodgkin lymphoma, Biomarkers, Tumor, Humans, Genetic Predisposition to Disease, Digital droplet pcr, Genetic Association Studies, ComputingMilieux_MISCELLANEOUS, food and beverages, High-Throughput Nucleotide Sequencing, Hematology, DNA, Neoplasm, Hodgkin Disease, 3. Good health, Oncology, 030220 oncology & carcinogenesis, Mutation, Cancer research, Circulating DNA, 030215 immunology
Abstract: Classical Hodgkin lymphoma (cHL) accounts for 30% of all lymphomas [1]. Currently, 20–25% of cHL cases relapse or are refractory after first-line standard treatments, leading to the need to better ...
Published: 2018

21. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma

Author: Fabrice Jardin, Hervé Tilly, Elodie Bohers, Annie Laquerrière, Maxime Fontanilles, Florent Marguet, Catherine Maingonnat, Jean Michel Picquenot, Stéphane Derrey, Sylvain Mareschal, Elena Liana Veresezan, Pierre-Julien Viailly, Philippe Bertrand, Sydney Dubois, Vincent Camus, Philippe Ruminy, Stéphane Leprêtre, Laboratoire d'hématologie [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Pathology, Rouen University Hospital, Service d'Hématologie Becquerel, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Département de Pathologie [CHU Rouen], Service de neurochirurgie [CHU Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Normandie Université (NU)-Normandie Université (NU), and Service d'Anatomie et Cytologie Pathologique [CHU Rouen]
Subjects: 0301 basic medicine, Oncology, Male, Pathology, Lymphoma, Biopsy, [SDV]Life Sciences [q-bio], DNA Mutational Analysis, Central Nervous System Neoplasms, circulating cell-free tumor DNA, 0302 clinical medicine, Gene Frequency, somatic mutation, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, Primary central nervous system lymphoma, High-Throughput Nucleotide Sequencing, DNA, Neoplasm, Genomics, Middle Aged, Magnetic Resonance Imaging, 3. Good health, 030220 oncology & carcinogenesis, Female, DNA, Circular, Personal genomics, Research Paper, medicine.medical_specialty, Sensitivity and Specificity, DNA sequencing, 03 medical and health sciences, Germline mutation, Internal medicine, medicine, Humans, Liquid biopsy, Alleles, Aged, primary central nervous system lymphoma, liquid biopsy, business.industry, Cancer, Ion semiconductor sequencing, medicine.disease, 030104 developmental biology, Case-Control Studies, Mutation, next-generation sequencing, Personalized medicine, business
Abstract: // Maxime Fontanilles 1, 2 , Florent Marguet 3, 4 , Elodie Bohers 2 , Pierre-Julien Viailly 2 , Sydney Dubois 2 , Philippe Bertrand 2 , Vincent Camus 1, 2 , Sylvain Mareschal 2 , Philippe Ruminy 2 , Catherine Maingonnat 2 , Stephane Lepretre 1 , Elena-Liana Veresezan 5 , Stephane Derrey 6 , Herve Tilly 1, 2 , Jean-Michel Picquenot 5 , Annie Laquerriere 3, 4 and Fabrice Jardin 1, 2 1 Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France 2 INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France 3 INSERM U1245 and Hopital Charles Nicolle, NeoVasc Team, University of Normandy, UNIVROUEN, CHU-Hopitaux de Rouen, 76031 Rouen, France 4 Department of Neuropathology, Hopital Charles Nicolle, Normandy Center for Genomic and Personalized Medicine, CHU-Hopitaux de Rouen, 76031 Rouen, France 5 Department of Pathology, Cancer Center Henri Becquerel, 76000 Rouen, France 6 Department of Neurosurgery, Hopital Charles Nicolle, CHU-Hopitaux de Rouen, 76031 Rouen, France Correspondence to: Fabrice Jardin, email: fabrice.jardin@chb.unicancer.fr Keywords: primary central nervous system lymphoma, circulating cell-free tumor DNA, somatic mutation, liquid biopsy, next-generation sequencing Received: March 08, 2017 Accepted: May 03, 2017 Published: June 01, 2017 ABSTRACT Purpose: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). Patients and Methods: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies ® ). First, patient-specific targeted sequencing of identified somatic mutations in tDNA was performed. Then, a second sequencing targeting MYD88 c.T778C was performed and compared to plasma samples from 25 age-matched control patients suffering from other types of cancer. Results: According to the patient-specific targeted sequencing, eight patients (32% [95% CI 15-54%]) had detectable somatic mutations in cfDNA. Considering MYD88 sequencing, six patients had the specific c.T778C alteration detected in plasma. Using a control group, the sensitivity was 24% [9-45%] and the specificity was 100%. Tumor volume or deep brain structure involvement did not influence the detection of somatic mutations in plasma. Conclusion: This pilot study provided evidence that somatic mutations can be detected by NGS in the cfDNA of a subset of patients suffering from PCNSL.
Published: 2017

22. THE LANDSCAPE OF SOMATIC MUTATIONS OF PRIMARY CUTANEOUS DIFFUSE LARGE B-CELL LYMPHOMA, LEG-TYPE

Author: Philippe Ruminy, Pascal Joly, Fabrice Jardin, Anne Pham-Ledard, Hervé Tilly, Anne Benedicte Duval, Thierry Frebourg, B. Vergier, L. Verneuil, Elodie Bohers, Catherine Maingonnat, Sydney Dubois, Martina Carlotti, Emilie Andrieu, M. Fontanillles, Philippe Courville, Philippe Bertrand, Marie Beylot-Barry, Jean-Philippe Merlio, Sylvain Mareschal, Isabelle Tournier, Pierre-Julien Viailly, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Research In Translational Oncology [Bordeaux] (BaRITOn), Université de Bordeaux (UB)-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de dermatologie [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Service de Dermatologie [CHU Caen], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Service de Dermatologie [Rouen], Normandie Université (NU)-Normandie Université (NU)-Hôpital Charles Nicolle [Rouen], and Hôpital Charles Nicolle [Rouen]
Subjects: Cancer Research, Pathology, medicine.medical_specialty, Somatic cell, [SDV]Life Sciences [q-bio], Hematology, General Medicine, Leg type, Biology, 3. Good health, Oncology, hemic and lymphatic diseases, Primary Cutaneous Diffuse Large B-Cell Lymphoma, medicine
Abstract: International audience; Introduction: Primary cutaneous diffuse large B‐cell lymphoma leg‐type (PCLBCL‐LT) is recognized by the World Health Organization (WHO) classification as a rare and aggressive disease accounting for 5 to 10% of primary cutaneous lymphoma. It displays original clinical features occurring mostly in the elderly and preferentially involving the legs but date the genetic specificities of this entities, as compared to other B‐cell aggressive lymphoma is unknown.Methods: 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 (DLBCL) subtypes, we analyzed a total cohort of 28 PCLBCL‐LT cases by next generation sequencing with a Lymphopanel designed for DLBCL. 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 Lymphopanel: TBL1XR1, KLHL6 and IKZF3. To pinpoint specificities, comparison with a cohort of DLBCL and Primary central nervous System lymphoma (PCNSL) analyzed by the same targeted panel was performed.Results: 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, NFKB activation or DNA modeling were found altered notably TBL1XR1 (33%), MYC (26%) CREBBP (26%) and IRF4 (21%) or HIST1H1E(41%). MYD88L265P variant was associated with copy number variations or copy neutral loss of heterozygosity in 60% of cases. The most frequent genetic losses involved CDKN2A/2B, TNFAIP3/A20, PRDM1, TCF3 and CIITA. The high recurrence of specific gene mutations such as MYD88 and the absence of mutations of KMT2D or FOXO1 are distinct features from nodal DLBCLs of either GC or ABC subtypes. Interestingly PCLBCL‐LT exhibits a mutational pattern that is closer to PCNSL than to ABC‐type nodal DLBCL but also has distinctive features, such as a very high mutational rate for PIM1, a higher rate of CD79B mutations and other original mutations such as CREBBP, MYC and IRF4 mutations (figure 1).Conclusion: This study describes for the first time the genomic landscape of a series of untreated PCLBCL‐LT. Our results obtained by WES and targeted sequencing underscore several similarities with ABC‐DBCL and more specifically with PCNSL subtypes. On the other hand, we pinpoint specificities that may sustain distinctive clinical features and guide therapeutic strategies according to an individual genetic analysis.
Published: 2017

23. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases

Author: Thierry Jo Molina, Fabrice Jardin, Marc André, Richard Delarue, Sylvain Mareschal, Philippe Bertrand, Thierry Fest, Corinne Haioun, Pierre-Julien Viailly, Martin Figeac, Philippe Ruminy, Dominique Penther, Vinciane Marchand, Sydney Dubois, Frederic Peyrade, Jean-Michel Picquenot, Karen Leroy, Jean-Philippe Jais, Christiane Copie-Bergman, Bruno Tesson, Catherine Maingonnat, Bettina Fabiani, Elodie Bohers, Fabienne Desmots, Hervé Tilly, Nicolas Ketterer, Thierry Lamy, Pauline Peyrouze, Gilles Salles, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Res Ctr, Institut Curie, Institut Curie [Paris], Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Institut Curie [Paris]-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Lille 2 - Faculté de Médecine, Plateforme de génomique fonctionnelle et structurelle [Lille], Institut pour la recherche sur le cancer de Lille [Lille] (IRCL)-Université de Lille, Droit et Santé, CHU Pontchaillou [Rennes], Microenvironment, Cell Differentiation, Immunology and Cancer (MICMAC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Etablissement français du sang [Rennes] (EFS Bretagne), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service d’immunologie, de thérapie cellulaire et d’hématopoïèse, Hôpital Pontchaillou, Service d'hématologie clinique, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de pathologie [Mondor], Service de Pathologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), UNICANCER-Université Côte d'Azur (UCA), Cliniques Universitaires UCL Mont-Godinne, Department of Oncology, Lausanne Hospital, Lausanne Hospital, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Service d’Hématologie [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'anatomie pathologique [CHU Necker], Service d'informatique médicale et biostatistiques [CHU Necker], Institut Carnot Lymphome (CALYM), Faculté de Médecine Henri Warembourg - Université de Lille, Interactions cellulaires et moléculaires (ICM), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Microenvironnement et cancer (MiCa), Service d'Hématologie, Immunologie et de Thérapie Cellulaire (HITC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'Anatomie et cytologie pathologiques [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Département de Pathologie [CHU Necker], Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Groupe d'étude des proliférations lymphoïdes ( GPL ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes ( LITIS ), Université Le Havre Normandie ( ULH ), Normandie Université ( NU ) -Normandie Université ( NU ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Institut national des sciences appliquées Rouen Normandie ( INSA Rouen Normandie ), Normandie Université ( NU ), HEMATOLOGIE, CRLCC Henri Becquerel, Centre de Recherche des Cordeliers ( CRC ), Université Paris Diderot - Paris 7 ( UPD7 ) -École pratique des hautes études ( EPHE ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Dept Translat Res, Breast Canc Biol Grp, Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -INSTITUT CURIE, Institut pour la recherche sur le cancer de Lille [Lille] ( IRCL ) -Université de Lille, Droit et Santé, Microenvironment, Cell Differentiation, Immunology and Cancer ( MICMAC ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Etablissement français du sang [Rennes] ( EFS Bretagne ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Centre d'Investigation Clinique [Rennes] ( CIC ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Saint-Antoine [APHP], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Centre Antoine Lacassagne, CRLCC Antoine Lacassagne, Institut Mondor de Recherche Biomédicale ( IMRB ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Centre Hospitalier Lyon Sud [CHU - HCL] ( CHLS ), Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Carnot CALYM [Pierre-Benite], Service d'anatomie et cytologie pathologiques [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Saint-Antoine [AP-HP], Université Côte d'Azur (UCA)-UNICANCER, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Sorbonne Université (SU)-CHU Saint-Antoine [APHP], Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU), MINES ParisTech - École nationale supérieure des mines de Paris, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), MINES ParisTech - École nationale supérieure des mines de Paris-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP], Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Oncology, 0301 basic medicine, Cancer Research, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Bioinformatics, medicine.disease_cause, Biochemistry, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Targeted therapy, 0302 clinical medicine, CDKN2A, hemic and lymphatic diseases, Copy-number variation, Aged, 80 and over, Genetics, 0303 health sciences, Mutation, NF-kappa B, High-Throughput Nucleotide Sequencing, hemic and immune systems, Genomics, Hematology, Middle Aged, Prognosis, 3. Good health, 030220 oncology & carcinogenesis, Female, Lymphoma, Large B-Cell, Diffuse, Signal Transduction, Adult, medicine.medical_specialty, Adolescent, DNA Copy Number Variations, Immunology, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Genetic Heterogeneity, 03 medical and health sciences, Internal medicine, medicine, Humans, Aged, 030304 developmental biology, Genome, Human, Genetic heterogeneity, Germinal center, Cancer, Cell Biology, CD79B, medicine.disease, Lymphoma, Gene expression profiling, 030104 developmental biology, Myeloid Differentiation Factor 88, Diffuse large B-cell lymphoma, 030215 immunology
Abstract: Introduction: MYD88 mutations, 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 MYD88 mutations in DLBCL and other hematologic malignancies is well described; however, there has not yet been a large-scale study of a MYD88 mutated 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 MYD88 mutations in order to delineate patients potentially sensitive to targeted therapies, and to define the prognostic value of MYD88 mutations according to different genomic contexts. Methods: A cohort of 361 DLBCL patients (94 MYD88 mutant and 267 MYD88 wild-type) was selected among the prospective, multicenter and randomized LNH-03B and LNH09-7B (NCT01195714) LYSA trials, as well as among patients sequenced at our institution as part of routine procedure. Cell of origin (COO) classification was obtained with HGU133+2.0 Affymetrix GeneChip arrays for 214 patients, with RT-MLPA for 77 patients1 and with Hans immunohistochemistry (IHC) method for 49 patients. All cases were submitted to next generation sequencing (NGS) focusing on 34 genes (Lymphopanel2) in order to analyze associated mutations and copy number variations (CNVs), as well as IHC, FISH, and clinical and prognostic analyses. Results: Importantly, we highlighted different genomic profiles for MYD88 L265P and MYD88 non-L265P mutant DLBCL, shedding light on their divergent backgrounds. Clustering analysis segregated subgroups according to associated genetic alterations among patients with either MYD88 L265P or non-L265P mutations. As such, clustering separated MYD88 L265P mutated DLBCL with associated PIM1 (52%), CD79B (52%), KMT2D (42%), and PRDM1 (32%) mutations, as well as MYD88 L265P mutated DLBCL with CDKN2A/B (67%/50%), PRDM1 (57%) and TNFAIP3 (52%) CNVs. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFkB pathway activation, although the majority of ABC MYD88 L265P mutant cases harbor downstream NFkB alterations, which can potentially predict BTK inhibitor resistance. Of note, although the MYD88 L265P variant was not an independent prognostic factor in ABC DLBCL, associated CD79B mutations significantly improved the survival of MYD88 L265P mutant ABC DLBCL in our cohort both in OS (p=0.02) and PFS (p=0.01), whereas the association of CARD11 or TNFAIP3 alterations did not impact survival. Interestingly, MYD88 mutant DLBCL cases were significantly more likely to experience central nervous system (CNS) relapse than MYD88 WT cases (p=0.02), as were MYD88 L265P mutant cases specifically (p=0.03). This result still tended toward statistical significance when considering only ABC patients (7 of 11 ABC CNS-relapsing cases were MYD88 mutant, p=0.1) but would have to be confirmed in a larger cohort. Conclusions: This study highlights the relative heterogeneity of MYD88 mutant DLBCBL, adding to the field's knowledge of the distinct genetic backgrounds of these subgroups. Our data highlights the theranostic and prognostic relevance of examining MYD88 and associated genomic alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. 1. Mareschal S, Ruminy P, Bagacean C, et al. Accurate Classification of Germinal Center B-Cell-Like/Activated B-Cell-Like Diffuse Large B-Cell Lymphoma Using a Simple and Rapid Reverse Transcriptase-Multiplex Ligation-Dependent Probe Amplification Assay: A CALYM Study. The Journal of molecular diagnostics : JMD. 2015;17(3):273-283. 2. Dubois S, Viailly P-J, Mareschal S, et al. Next Generation Sequencing in Diffuse Large B Cell Lymphoma Highlights Molecular Divergence and Therapeutic Opportunities: a LYSA Study. Clinical cancer research : an official journal of the American Association for Cancer Research. 2016;22(12):2919-2928. Disclosures 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.
Published: 2017

24. Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier

Author: Corinne Haioun, Pierre-Julien Viailly, Victor Bobée, Thierry Jo Molina, Sylvain Mareschal, Gilles Salles, Caroline Bérard, Jean-Philippe Jais, Philippe Ruminy, Ahmad Abdel Sater, Jean-Michel Picquenot, Karen Leroy, Fabrice Jardin, Hervé Tilly, Martin Figeac, Fanny Drieux, Sydney Dubois, Liana Veresezan, Elodie Bohers, Vinciane Marchand, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Groupe d'étude des proliférations lymphoïdes (GPL), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Service d'Anatomie et Cytologie Pathologique [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Equipe Traitement de l'information en Biologie Santé (TIBS - LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Service d'informatique médicale et biostatistiques [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Plateforme de génomique fonctionnelle et structurelle [Lille], Institut pour la recherche sur le cancer de Lille [Lille] (IRCL)-Université de Lille, Droit et Santé, service d'anatomo-pathologie, Hôpital Hôtel Dieu, Service d’Hématologie [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service d'hématologie clinique, Université Le Havre Normandie (ULH), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Groupe d'étude des proliférations lymphoïdes ( GPL ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), CRLCC Henri Becquerel, Service d'Anatomie et Cytologie Pathologique [Rouen], CHU Rouen-Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ), Mathématiques et Informatique Appliquées ( MIA-Paris ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Institut pour la recherche sur le cancer de Lille [Lille] ( IRCL ) -Université de Lille, Droit et Santé, Assistance publique - Hôpitaux de Paris (AP-HP), Centre Hospitalier Lyon Sud [CHU - HCL] ( CHLS ), Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), and Service hématologie
Subjects: 0301 basic medicine, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, hemic and lymphatic diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Biomarkers, Tumor, medicine, Humans, Multiplex, Multiplex ligation-dependent probe amplification, Oligonucleotide Array Sequence Analysis, Paraffin Embedding, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Germinal center, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, medicine.disease, Molecular biology, Reverse transcriptase, 3. Good health, Lymphoma, Gene Expression Regulation, Neoplastic, Gene expression profiling, 030104 developmental biology, 030220 oncology & carcinogenesis, Mutation, Cancer research, Molecular Medicine, Lymphoma, Large B-Cell, Diffuse, Multiplex Polymerase Chain Reaction, Diffuse large B-cell lymphoma, Classifier (UML)
Abstract: International audience; Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. It includes three major subtypes termed germinal center B-cell-like, activated B-cell-like, and primary mediastinal B-cell lymphoma. With the emergence of novel targeted therapies, accurate methods capable of interrogating this cell-of-origin classification should soon become essential in the clinics. To address this issue, we developed a novel gene expression profiling DLBCL classifier based on reverse transcriptase multiplex ligation-dependent probe amplification. This assay simultaneously evaluates the expression of 21 markers, to differentiate primary mediastinal B-cell lymphoma, activated B-cell-like, germinal center B-cell-like, and also Epstein-Barr virus-positive DLBCLs. It was trained using 70 paraffin-embedded biopsies and validated using >160 independent samples. Compared with a reference classification established from Affymetrix U133 + 2 data, reverse transcriptase multiplex ligation-dependent probe amplification classified 85.0% samples into the expected subtype, comparing favorably with current diagnostic methods. This assay also proved to be highly efficient in detecting the MYD88 L265P mutation, even in archival paraffin-embedded tissues. This reliable, rapid, and cost-effective method uses common instruments and reagents and could thus easily be implemented into routine diagnosis workflows, to improve the management of these aggressive tumors.
Published: 2017

25. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma

Author: Sydney Dubois, Vincent Camus, Philippe Bertrand, Elodie Bohers, Jean Michel Picquenot, Pierre-Julien Viailly, Fabrice Jardin, Marie Cornic, Philippe Ruminy, Thierry Frebourg, Aspasia Stamatoullas, Christian Bastard, Liana Veresezan, Nasrin Sarafan-Vasseur, Sylvain Mareschal, Catherine Maingonnat, Pierre Vera, Hervé Tilly, Valérie Tallon-Simon, Stéphanie Becker, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique du cancer et des maladies neuropsychiatriques (GMFC), service d'anatomo-pathologie, Service de médecine nucléaire [Rouen], CRLCC Haute Normandie-Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Equipe Quantification en Imagerie Fonctionnelle (QuantIF-LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU), and Génétique médicale et fonctionnelle du cancer et des maladies neuropsychiatriques
Subjects: 0301 basic medicine, Male, Receptors, Cytoplasmic and Nuclear, medicine.disease_cause, 0302 clinical medicine, Recurrence, immune system diseases, Neoplasms, Positron Emission Tomography Computed Tomography, hemic and lymphatic diseases, Mutation, medicine.diagnostic_test, High-Throughput Nucleotide Sequencing, Hematology, DNA, Neoplasm, Articles, Middle Aged, Prognosis, Combined Modality Therapy, Hodgkin Disease, 3. Good health, Tumor Burden, Treatment Outcome, 030220 oncology & carcinogenesis, Biomarker (medicine), Female, Adult, Context (language use), [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Karyopherins, 03 medical and health sciences, Young Adult, Germline mutation, Cell Line, Tumor, Biopsy, medicine, Biomarkers, Tumor, Humans, Codon, Survival analysis, Neoplasm Staging, Retrospective Studies, medicine.disease, Minimal residual disease, Survival Analysis, Lymphoma, 030104 developmental biology, Amino Acid Substitution, Cancer research
Abstract: International audience; Classical Hodgkin lymphoma is one of the most common lymphomas and shares clinical and genetic features with primary mediastinal B-cell lymphoma. In this retrospective study, we analyzed the recurrent hotspot mutation of the exportin 1 (XPO1, p.E571K) gene, previously identified in primary mediastinal B-cell lymphoma, in biopsies and plasma circulating cell-free DNA from patients with classical Hodgkin lymphoma using a highly sensitive digital PCR technique. A total of 94 patients were included in the present study. This widely expressed XPO1 E571K mutation is present in one quarter of classical Hodgkin lymphoma patients (24.2%). Mutated and wild-type classical Hodgkin lymphomas were similar regarding the main clinical features. Patients with a detectable XPO1 mutation at the end of treatment displayed a tendency toward shorter progression-free survival, as compared to patients with undetectable mutation in plasma cell-free DNA (2-year progression-free survival: 57.1%, 95% confidence interval: 30.1-100% versus 2-year progression-free survival: 90.5%, 95% confidence interval: 78.8-100%, respectively, P=0.0601). To conclude, the detection of the XPO1 E571K mutation in biopsy and plasma cell-free DNA by digital PCR may be used as a novel biomarker in classical Hodgkin lymphoma for both diagnosis and minimal residual disease, and pinpoints a crucial role of XPO1 in classical Hodgkin lymphoma pathogenesis. The detection of somatic mutation in the plasma cell-free DNA of patients represents a major technological advance in the context of liquid biopsies and noninvasive management of classical Hodgkin lymphoma.
Published: 2016

26. Multiplexed targeted sequencing of recurrent fusion genes in acute leukaemia

Author: Emilie Lemasle, Marie Cornic, Vannier Jp, Pierre-Julien Viailly, Dominique Penther, Sydney Dubois, Stéphane Leprêtre, N. Buchbinder, Camus, Fabrice Jardin, Girod C, Philippe Ruminy, Philippe Bertrand, Sylvain Mareschal, Jean-Michel Picquenot, Pascale Schneider, Larson T, G Buchonnet, David Rizzo, Joly B, Pascaline Etancelin, Angot E, Christian Bastard, Elodie Bohers, Marchand, Hervé Tilly, Florian Clatot, Mathieu Viennot, Groupe d'étude des proliférations lymphoïdes (GPL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Rouen, Normandie Université (NU), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Argelander-Institut für Astronomie (AlfA), and Rheinische Friedrich-Wilhelms-Universität Bonn
Subjects: 0301 basic medicine, Cancer Research, Oncogene Proteins, Oncogene Proteins, Fusion, Chromosomes, Human, Pair 21, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Chromosomal translocation, Biology, Translocation, Genetic, Fusion gene, 03 medical and health sciences, Text mining, Humans, Base sequence, ComputingMilieux_MISCELLANEOUS, Retrospective Studies, Genetics, Chromosomes, Human, Pair 15, Leukemia, Base Sequence, business.industry, Reverse Transcriptase Polymerase Chain Reaction, High-Throughput Nucleotide Sequencing, Hematology, 030104 developmental biology, Oncology, Acute Disease, Cytogenetic Analysis, Biological Assay, business, Oligonucleotide Probes, Chromosomes, Human, Pair 17
Abstract: International audience
Published: 2016

27. Digital PCR for quantification of recurrent and potentially actionable somatic mutations in circulating free DNA from patients with diffuse large B-cell lymphoma

Author: Pierre-Julien Viailly, Philippe Ruminy, Catherine Maingonnat, Philippe Bertrand, Emilie Lemasle, Ludivine Beaussire, Sylvain Mareschal, Aspasia Stamatoullas, Christian Bastard, Hervé Tilly, Nasrin Sarafan-Vasseur, Fabrice Jardin, Thierry Frebourg, Marie Cornic, Sydney Dubois, Jean-Michel Picquenot, Vincent Camus, Elodie Bohers, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Génétique du cancer et des maladies neuropsychiatriques (GMFC), and Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)
Subjects: 0301 basic medicine, Adult, Male, Cancer Research, Somatic cell, [SDV]Life Sciences [q-bio], Receptors, Cytoplasmic and Nuclear, Biology, Karyopherins, medicine.disease_cause, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, 0302 clinical medicine, Germline mutation, Recurrence, hemic and lymphatic diseases, Antineoplastic Combined Chemotherapy Protocols, medicine, Biomarkers, Tumor, Humans, Digital polymerase chain reaction, Liquid biopsy, ComputingMilieux_MISCELLANEOUS, Aged, Neoplasm Staging, Aged, 80 and over, Mutation, Liquid Biopsy, High-Throughput Nucleotide Sequencing, Hematology, DNA, Neoplasm, Middle Aged, medicine.disease, 3. Good health, Lymphoma, 030104 developmental biology, Real-time polymerase chain reaction, Oncology, 030220 oncology & carcinogenesis, Positron-Emission Tomography, Myeloid Differentiation Factor 88, Cancer research, Female, Lymphoma, Large B-Cell, Diffuse, Diffuse large B-cell lymphoma
Abstract: Diffuse large B-cell lymphoma (DLBCL) is an aggressive and heterogeneous malignancy harboring frequent targetable activating somatic mutations. Emerging evidence suggests that circulating cell-free DNA (cfDNA) can be used to detect somatic variants in DLBCL using Next-Generation Sequencing (NGS) experiments. In this proof-of-concept study, we chose to develop simple and valuable digital PCR (dPCR) assays for the detection of recurrent exportin-1 (XPO1) E571K, EZH2 Y641N, and MYD88 L265P mutations in DLBCL patients, thereby identifying patients most likely to potentially benefit from targeted therapies. We demonstrated that our dPCR assays were sufficiently sensitive to detect rare XPO1, EZH2, and MYD88 mutations in plasma cfDNA, with a sensitivity of 0.05%. cfDNA somatic mutation detection by dPCR seems to be a promising technique in the management of DLBCL, in addition to NGS experiments.
Published: 2015

28. Somatic Mutations Detected in Plasma Cell-Free DNA By Targeted Sequencing: Assessment of Liquid Biopsy in Primary Central Nervous System Lymphoma

Author: Philippe Ruminy, Maxime Fontanilles, Fabrice Jardin, Vincent Camus, Florent Marguet, Jean-Michel Picquenot, Sylvain Mareschal, Annie Laquerrière, Elena-Liana Veresezan, Pierre-Julien Viailly, Hervé Tilly, Elodie Bohers, Philippe Bertrand, Sydney Dubois, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Service d'Anatomie et Cytologie Pathologique [CHU Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Département de Pathologie [CHU Rouen], and Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel)
Subjects: Oncology, Pathology, medicine.medical_specialty, [SDV]Life Sciences [q-bio], Immunology, Plasma cell, Biology, medicine.disease_cause, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Germline mutation, CDKN2A, Internal medicine, medicine, Liquid biopsy, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Mutation, Primary central nervous system lymphoma, Cell Biology, Hematology, CD79B, medicine.disease, 3. Good health, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Diffuse large B-cell lymphoma
Abstract: Background Primary Central Nervous System Lymphoma (PCNSL) are rare and aggressive primary brain tumors. Histological diagnosis can be difficult at initial stages or at relapse due to deep brain structure involvement. Finding a minimally invasive biomarker aiding the diagnosis remains an unsolved question. Plasma Cell-Free DNA (cfDNA) seems to have shown its diagnostic and prognostic value in nodal Diffuse Large B Cell Lymphomas (DLBCL) [Roschewski et al, Lancet Oncology, 2015; Kurtz et al, Blood, 2015]. Our main objective was to demonstrate that targeted sequencing of cfDNA in plasma at time of diagnosis could identify PCNSL somatic mutations. Methods 30 immuno-competent patients suffering from newly diagnosed PCNSL, without any extranevraxic lesions, were enrolled from 2008 to 2014. Tumor tissues and plasma samples were collected at the time of diagnosis and frozen until use. High throughput sequencing was performed on primitive tumors using a panel of 34 genes relevant to lymphomagenesis, as previously reported [Dubois et al, Oncotarget, 2015; Bohers et al, Haematologica, 2015]. We next performed patient-specific targeted sequencing of identified somatic mutations in cfDNA. The detection sensitivity threshold was set at 1% for all SNVs, except for MYD88 L265P, which was set at 0.1%. The primary endpoint was the proportion of patients having at least one somatic mutation found in the plasma. Results Among 24 available plasmas, 15 patients (63%) had at least one detected somatic mutation in cfDNA. All plasmas had detectable cfDNA (mean concentration 1.6 ng/µL). No correlation was found between tumor volume and cfDNA concentration (R squared coefficient 0.01). Regarding the whole sequenced cohort (n=30) 21 (70%) were classified as nonGC subtype, 8 (27%) as GC subtype and 1 patient (3%) as unclassifiable, according to the Hans algorithm. 29 tumors had at least one somatic mutation, mainly nonsynonymous single nucleotide variants (SNV). The NF-kB pathway was the most affected by mutations: MYD88 (n=23, 77%), PIM1 (n=11, 37%), TNFAIP3 (n=6, 20%), IRF4 (n=3, 10%), CARD11 (n=3, 10%) and PRDM1 (n=3, 10%). Among the 23 tumors harboring a MYD88 mutation, the L265P variant was the most frequent (20 patients, 67%); mean tumor variant allele frequency was 46% [min 8%, max 91%]. One tumor harbored a single MYD88 L265P mutation with no other detectable abnormality. Among patients with both available plasma and a somatic MYD88 L265P mutation in the tumor, 15 patients (88%) had an identifiable L265P variant in cfDNA, with a mean variant allele frequency of 4% [min 0.1%, max 28%]. PIM1 and TNFAIP3 SNVs were also detected in cfDNA for respectively two and one patient. The second most affected pathway was the apoptotic pathway: genes affected by mutations included GNA13 (n=7, 23%), TP53 (n=2, 7%), MYC (n=1, 3%), CDKN2A (n=2, 7%) and BCL2 (n=1, 3%). The B Cell Receptor (BCR) pathway was also affected, mainly due to mutations targeting CD79B (n=10, 33%) and ITPKB (n=3, 10%) mutations. 8 tumors (27%) harbored a dual alteration affecting MYD88 and CD79B. One tumor of the GC subtype had one EZH2 SNV (Y646H), but the mutation was not found in cfDNA. There was no significant difference in overall survival (OS) between patients with and without mutations detected in cfDNA: mean OS 27 months versus 18 months (HR 0.6; IC95% [0.2 - 1.6], p value 0.3). Tumor gene copy number variations were detected in 29/30 patients with either homo or heterozygous deletions or copy gains. CDKN2A/2B deletions were detected in 23 cases (77%). Conclusion To our knowledge this is the first study that provides evidence that somatic mutations can be detected in cfDNA in patients suffering from PCNSL, therefore constituting a minimally invasive tool helping for diagnosis. Further studies are now required to improve prognosis and predictive values of this new promising procedure for PCNSL patient care. Disclosures No relevant conflicts of interest to declare.
Published: 2015

29. Recurrent Mutations of the Exportin 1 Gene (XPO1) in Primary Mediastinal B-Cell Lymphoma: A Lysa Study

Author: Diane Damotte, Corinne Haioun, Pierre-Julien Viailly, Alexandra Traverse-Glehen, Christian Argueta, Sylvain Mareschal, Aspasia Stamatoullas, Martin Figeac, Karen Leroy, Fabrice Jardin, Catherine Maingonnat, Peter Moeller, Philippe Gaulard, Hervé Tilly, Christer Sundström, Elodie Bohers, Thierry Jo Molina, Laura Pelletier, Philippe Bertrand, Sydney Dubois, Vincent Camus, Emilie Lemasle, Thierry Fest, Christian Bastard, Gilles Salles, Noel Milpied, Jean-Michel Picquenot, Jean-Philippe Jais, François Lemonnier, Marie Cornic, Anaïs Pujals, Christiane Copie-Bergman, Marlene Ochman, Richard Delarue, William Senapedis, Martin J. S. Dyer, Yosef Landesman, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Microenvironnement et cancer (MiCa), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'Anatomie Pathologique, Hospices Civils de Lyon (HCL), Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie Pharmacie Pathologie, Sorbonne Paris Cité-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5), Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service d'hématologie clinique, Service d'informatique médicale et biostatistiques [CHU Necker], Plateforme de génomique fonctionnelle et structurelle [Lille], Institut pour la recherche sur le cancer de Lille [Lille] (IRCL)-Université de Lille, Droit et Santé, INSERM U955, équipe 9, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service d'Anatomo-Pathologie, service d'anatomo-pathologie, Service d'Hématologie et Thérapie Cellulaire, CHU Bordeaux [Bordeaux]-Hôpital Haut-Lévêque [CHU Bordeaux], CHU Bordeaux [Bordeaux], Service d'Hématologie, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Pathology, Uppsala University Hospital, Service de Pathologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service d'Hématologie Biologique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Service d'anatomo-pathologie [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), CHU Henri Mondor, Karyopharm Therapeutics Inc., Newton, MA, U918, CHU Necker - Enfants Malades [AP-HP], Service d'Hématologie, Immunologie et de Thérapie Cellulaire (HITC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Universitätsklinikum Ulm - University Hospital of Ulm, Department of Cancer Studies and Molecular Medicine, University of Leicester, Service de génétique oncologique, Groupe d'étude des proliférations lymphoïdes ( GPL ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Institut Mondor de Recherche Biomédicale ( IMRB ), Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10, Microenvironnement et cancer ( MiCa ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Laboratoire de Biologie Moléculaire de la Cellule ( LBMC ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Hospices Civils de Lyon ( HCL ), Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Centre de Recherche des Cordeliers ( CRC ), Université Paris Diderot - Paris 7 ( UPD7 ) -École pratique des hautes études ( EPHE ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Sorbonne Paris Cité-CHU Cochin [AP-HP]-Université Paris Descartes - Paris 5 ( UPD5 ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Institut pour la recherche sur le cancer de Lille [Lille] ( IRCL ) -Université de Lille, Droit et Santé, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Institut Mondor de Recherche Biomédicale ( IMRB ), Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10, Assistance publique - Hôpitaux de Paris (AP-HP), CRLCC Henri Becquerel, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne Paris Cité-CHU Cochin [AP-HP]-Université Paris Descartes - Paris 5 (UPD5), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bohers, Elodie, Jonchère, Laurent, Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Henri Mondor [Créteil], and Université de Rennes (UR)-Hôpital Pontchaillou-CHU Pontchaillou [Rennes]
Subjects: Mutation, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], Immunology, Mutant, Wild type, Cell Biology, Hematology, Biology, medicine.disease, medicine.disease_cause, Biochemistry, 3. Good health, Lymphoma, [SDV] Life Sciences [q-bio], International Prognostic Index, medicine, Cancer research, Missense mutation, Primary mediastinal B-cell lymphoma, Nuclear export signal, ComputingMilieux_MISCELLANEOUS
Abstract: Background and aim of the study Primary mediastinal B-cell lymphoma (PMBL) is an entity of aggressive B-cell lymphoma that is clinically and biologically distinct from the other molecular subtypes of diffuse large B-cell lymphoma (DLBCL). We recently detected by Whole exome sequencing a recurrent point mutation in the XPO1 (exportin 1) gene (also referred to as chromosome region maintenance 1; CRM1), which resulted in the Glu571Lys (p.E571K) missense substitution in 2 refractory/relapsed PMBL (Dubois et al., ICML 2015; Mareschal et al. AACR 2015). XPO1 is a member of the Karyopherin-b superfamily of nuclear transport proteins. XPO1 mediates the nuclear export of numerous RNAs and cellular regulatory proteins, including tumor suppressor proteins. This mutation is in the hydrophobic groove of XPO1 that binds to the leucine-rich nuclear export signal (NES) of cargo proteins. In this study, we investigated the prevalence, specificity, and biological / clinical relevance of XPO1 mutations in PMBL. Patients and methods High-throughput targeted or Sanger sequencing of 117 PMBL patients and 3 PMBL cell lines were performed. PMBL cases were defined either molecularly by gene expression profile (mPMBL cohort) or by standard histological method (hPMBL cohort) and enrolled in various LYSA (LYmphoma Study Association) clinical trials. To assess the frequency and specificity of XPO1 mutations, cases of classical Hodgkin lymphoma (cHL) and primary mediastinal grey zone lymphoma (MGZL) were analysed. Cell experiments were performed to assess the impact of the E571 mutation on the activity of selective inhibitor of nuclear export (SINE) molecules. Results XPO1 mutations were present in 28/117 (24%) PMBL cases but were rare in cHL cases (1/19, 5%) and absent from MGZL cases (0/20). A higher prevalence (50%) of the recurrent codon 571 variant (p.E571K) was observed in PMBL cases defined by gene expression profiling (n = 32), as compared to hPMBL cases (n = 85, 13%). No difference in age, International Prognostic Index (IPI) or bulky mass was observed between the PMBL patients harboring mutant and wild-type XPO1 in the overall cohort whereas a female predominance was noticed in the mPMBL cohort. Based on a median follow-up duration of 42 months, XPO1 mutant patients exhibited significantly decreased PFS (3y PFS = 74% [CI95% 55-100]) compared to wild-type patients (3y PFS = 94% [CI95% 83-100], p=0.049) in the mPMBL cohort. In 4/4 tested cases, the E571K variant was also detected in cell-free circulating plasmatic DNA, suggesting that the mutation can be used as a biomarker at the time of diagnosis and during follow-up. Importantly, the E571K variant was detected as a heterozygous mutation in MedB-1, a PMBL-derived cell line, whereas the two other PMBL cell lines tested, Karpas1106 and U-2940, did not display any variants in XPO1 exon 15. KPT-185, the SINE compound that blocks XPO1-dependent nuclear export, induced a dose-dependent decrease in cell proliferation and increased cell death in the PMBL cell lines harbouring wild type or mutated alleles. To test directly if XPO1 mutation from E571 to E571K alters XPO1 inhibition by SINE compounds, the mutated protein was tested in vitro. The E571XPO1 mutated allele was transiently transfected into osteosarcoma U2OS cells which stably express the fluorescently labelled XPO1 cargo REV. Cells were treated with the clinical SINE compound selinexor, which is currently in phase I/II clinical trials and nuclear localization of REV-GFP was analysed in red transfected cells. The results showed that the nuclear export of the mutated XPO1 protein was inhibited by selinexor similarly to the wild-type XPO1 protein (Figure 1). Conclusion Although the oncogenic properties of XPO1 mutations remain to be determined, their recurrent selection in PMBL strongly supports their involvement in the pathogenesis of this curable aggressive B-cell lymphoma. XPO1 mutations were primarily observed in young female patients who displayed a typical PMBL molecular signature. The E571K XPO1 mutation represents a novel hallmark of PMBL but does not seem to interfere with SINE activity. Rev-GFP (green fluorescent) expressing U2OS cells were transfected with wild type XPO1-RFP (red fluorescent protein), XPO1-C528S-RFP, XPO1-E571K-mCherry, and XPO1-E571G-mCherry. The cells were then treated with 1µM KPT-330 for 8 hours. Figure 1. Rev-GFP expressing U2OS cells transfected with XPO1 variants. Figure 1. Rev-GFP expressing U2OS cells transfected with XPO1 variants. Disclosures Landesman: Karyopharm Therapeutics: Employment. Senapedis:Karyopharm Therapeutics, Inc.: Employment, Patents & Royalties. Argueta:Karyopharm Therapeutics: Employment. Milpied:Celgene: Honoraria, Research Funding.
Published: 2015

30. Immunohistochemical and genomic profiles of diffuse large B-cell lymphomas: Implications for targeted EZH2 inhibitor therapy?

Author: Philippe Ruminy, Elena Liana Veresezan, Catherine Maingonnat, Marie Cornic, Hervé Tilly, Philippe Bertrand, Fabrice Jardin, Vinciane Marchand, Sydney Dubois, Dominique Penther, Hélène Lanic, Elodie Bohers, Jean-Michel Picquenot, Pierre-Julien Viailly, Sylvain Mareschal, Christian Bastard, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), service d'anatomo-pathologie, Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Service d'Hématologie, and Département d'Oncologie Génétique [Rouen] (CLCC Henri Becquerel)
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, [SDV.CAN]Life Sciences [q-bio]/Cancer, macromolecular substances, Biology, medicine.disease_cause, Methylation, Histones, Young Adult, Internal medicine, medicine, Humans, Enhancer of Zeste Homolog 2 Protein, EZH2, Epigenetics, ComputingMilieux_MISCELLANEOUS, Aged, Aged, 80 and over, Mutation, Hematology, Polycomb Repressive Complex 2, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Middle Aged, medicine.disease, Immunohistochemistry, 3. Good health, Lymphoma, DNA-Binding Proteins, Gene Expression Regulation, Neoplastic, Oncology, DLBCL, NGS, Cancer research, Female, Lymphoma, Large B-Cell, Diffuse, Clinical Research Paper, Diffuse large B-cell lymphoma
Abstract: // Sydney Dubois 1 , Sylvain Mareschal 1 , Jean-Michel Picquenot 1, 2 , Pierre-Julien Viailly 1 , Elodie Bohers 1 , Marie Cornic 2 , Philippe Bertrand 1 , Elena Liana Veresezan 1, 2 , Philippe Ruminy 1 , Catherine Maingonnat 1 , Vinciane Marchand 1 , Helene Lanic 1, 3 , Dominique Penther 1 , Christian Bastard 1 , Herve Tilly 1, 3 , Fabrice Jardin 1, 3 1 INSERM U918, Centre Henri Becquerel, Universite de Rouen, IRIB, Rouen, France 2 Department of Pathology, Centre Henri Becquerel, Rouen, France 3 Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France Correspondence to: Fabrice Jardin, e-mail: fabrice.jardin@chb.unicancer.fr Keywords: DLBCL, EZH2, Methylation, Immunohistochemistry, NGS Received: October 20, 2014 Accepted: January 15, 2015 Published: February 05, 2015 ABSTRACT Enhancer of Zeste Homolog 2 (EZH2) plays an essential epigenetic role in Diffuse Large B Cell Lymphoma (DLBCL) development. Recurrent somatic heterozygous gain-of-function mutations of EZH2 have been identified in DLBCL, most notably affecting tyrosine 641 (Y641), inducing hyper-trimethylation of H3K27 (H3K27me3). Novel EZH2 inhibitors are being tested in phase 1 and 2 clinical trials but no study has examined which patients would most benefit from this treatment. We evaluated the immunohistochemical (IHC) methylation profiles of 82 patients with DLBCL, as well as the mutational profiles of 32 patients with DLBCL using NGS analysis of a panel of 34 genes involved in lymphomagenesis. A novel IHC score based on H3K27me2 and H3K27me3 expression was developed, capable of distinguishing patients with wild-type (WT) EZH2 and patients with EZH2 Y641 mutations ( p = 10 −5 ). NGS analysis revealed a subclonal EZH2 mutation pattern in EZH2 mutant patients with WT-like IHC methylation profiles, while associated mutations capable of upregulating EZH2 were detected in WT EZH2 patients with mutant-like IHC methylation profiles. IHC and mutational profiles highlight in vivo hyper-H3K27me3 and hypo-H3K27me2 status, pinpoint associated activating mutations and determine EZH2 mutation clonality, maximizing EZH2 inhibitor potential by identifying patients most likely to benefit from treatment.
Published: 2015

31. Abstract 4810: Exome sequencing of refractory diffuse large B-cell lymphomas highlights candidate genes for targeted resequencing

Author: Fabrice Jardin, Martin Figeac, Philippe Bertrand, Jean-Philippe Jais, Gilles Salles, Thierry Molina, Sylvain Mareschal, Karen Leroy, Hervé Tilly, Thierry Fest, Fabienne Desmots, Corinne Haioun, Pierre-Julien Viailly, Elodie Bohers, Groupe d'étude des proliférations lymphoïdes ( GPL ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Service d'informatique médicale et biostatistiques [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Plateforme de génomique fonctionnelle et structurelle [Lille], Institut pour la recherche sur le cancer de Lille [Lille] ( IRCL ) -Université de Lille, Droit et Santé, Microenvironnement et cancer ( MiCa ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Lyon Sud [CHU - HCL] ( CHLS ), Hospices Civils de Lyon ( HCL ), Laboratoire de Biologie Moléculaire de la Cellule ( LBMC ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Service d'hématologie clinique, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Service de Pathologie, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor, Institut Mondor de Recherche Biomédicale ( IMRB ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut pour la recherche sur le cancer de Lille [Lille] (IRCL)-Université de Lille, Droit et Santé, Microenvironnement et cancer (MiCa), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: Genetics, 0303 health sciences, Cancer Research, Candidate gene, Mutation rate, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], Biology, medicine.disease, Genome, 3. Good health, Lymphoma, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Oncology, 030220 oncology & carcinogenesis, CIITA, medicine, EP300, Exome sequencing, 030304 developmental biology
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 < 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 < 0.01) but not in the comparative series (FDR > 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
Published: 2015

32. Activating somatic mutations in diffuse large B-cell lymphomas: lessons from next generation sequencing and key elements in the precision medicine era

Author: Sylvain Mareschal, Pierre-Julien Viailly, Hervé Tilly, Sydney Dubois, Elodie Bohers, Fabrice Jardin, Catherine Maingonnat, Philippe Ruminy, Philippe Bertrand, Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND)
Subjects: Cancer Research, Somatic cell, [SDV]Life Sciences [q-bio], B-cell receptor, Biology, immune system diseases, hemic and lymphatic diseases, medicine, Humans, Genetic Predisposition to Disease, Molecular Targeted Therapy, Precision Medicine, Exome sequencing, B cell, ComputingMilieux_MISCELLANEOUS, Genetics, breakpoint cluster region, High-Throughput Nucleotide Sequencing, Genomics, Hematology, Cell cycle, medicine.disease, 3. Good health, Lymphoma, Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, Oncology, Mutation, Cancer research, Lymphoma, Large B-Cell, Diffuse, Diffuse large B-cell lymphoma, Signal Transduction
Abstract: Diff use large B-cell lymphoma (DLBCL) is the most common form of lymphoma, accounting for 30 - 40% of newly diagnosed non-Hodgkin lymphomas. Historically, DLBCL has been thought to involve recurrent translocations of the immunoglobulin heavy (IGH) locus and the deregulation of rearranged oncogenes. Whole exome sequencing (WES) of more than 200 DLBCLs has completely redefi ned the genetic landscape of the disease by identifying recurrent single nucleotide variants and providing new therapeutic opportunities in DLBCL molecular subtypes. Some of these somatic mutations target genes that play a crucial role in B-cell function (B cell receptor (BCR) signaling, nuclear factor κ B (NF- κ B) pathway, Toll-like receptor (TLR) signaling and phosphatidylinositol 3-kinase (PI3K) pathway), immunity, cell cycle/apoptosis or chromatin modifi cation. In this review, following an overview of the somatic mutations reported in DLBCL, we focus on activating and clustered mutations targeting genes including MYD88 , CD79A/B , EZH2 and CARD11 and discuss their clinical and therapeutic relevance in the precision medicine era.
Published: 2014

33. Multiple sequence variants of BRCA2 exon 7 alter splicing regulation

Author: Dominique Vaur, Elodie Bohers, Jean-Philippe Peyrat, Mario Tosi, Pascaline Gaildrat, Alexandra Martins, Françoise Révillion, Danielle Ledemeney, Etienne Rouleau, Agnès Hardouin, Estelle Jamard, Thierry Frebourg, Daniela Di Giacomo, Sophie Krieger, Rosette Lidereau, Claude Houdayer, Julie Abdat, Sandrine M. Caputo, Génétique du cancer et des maladies neuropsychiatriques (GMFC), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Interaction virus-hôte et maladies du foie, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Experimental Medicine, Università degli Studi dell'Aquila = University of L'Aquila (UNIVAQ), Laboratoire d'Oncologie Moléculaire Humaine, Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université de Lille-UNICANCER-Université de Lille-UNICANCER, DIEP/DSV (DIEP/DSV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre Régional de Lutte contre le Cancer François Baclesse [Caen] (UNICANCER/CRLC), Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Curie [Paris], Genetique Moleculaire des Cancers d'Origine Epitheliale, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de biologie clinique et oncologique, Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN), Università degli Studi dell'Aquila (UNIVAQ), Université Lille Nord de France (COMUE)-UNICANCER-Université Lille Nord de France (COMUE)-UNICANCER, UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU), Service de Biochimie et de Biologie Moléculaire [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie [Paris], and UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)
Subjects: [SDV]Life Sciences [q-bio], Genes, BRCA2, Molecular Sequence Data, Exonic splicing enhancer, Biology, 03 medical and health sciences, Exon, 0302 clinical medicine, Cell Line, Tumor, Gene Order, Genetics, Humans, splice, Gene Silencing, Genetics (clinical), Alleles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Splice site mutation, Base Sequence, RNA, Computational Biology, Genetic Variation, Exons, Exon skipping, Gene Expression Regulation, Neoplastic, Alternative Splicing, Enhancer Elements, Genetic, 030220 oncology & carcinogenesis, RNA splicing, Mutation, France, RNA Splice Sites, Databases, Nucleic Acid, Minigene
Abstract: Background Exonic variants of unknown biological significance (VUS) identified in patients can affect mRNA splicing, either by changing 5′ or 3′ splice sites or by modifying splicing regulatory elements. Bioinformatic predictions of these elements are still inaccurate and only few such elements have been functionally mapped in BRCA2 . We studied the effect on splicing of eight exon 7 VUS, selected from the French UMD- BRCA2 mutation database. Methods We performed splicing minigene assays and analyses of patient RNA. We also developed a pyrosequencing-based quantitative assay, to measure, in patient RNA, the relative contribution of each allele to the production of exon 7-containing transcripts. Moreover, an exonic splicing enhancer (ESE)-dependent minigene assay was used to evaluate the splicing regulatory properties of wild-type and mutant segments. Results Six out of the eight variants induced splicing defects. In the minigene assay, c.517G>T and c.631G>A altered the natural splice sites, c.572A>G created a new 5′ splice site, and c.520C>T, c.587G>A and c.617C>G induced exon 7 skipping (66%, 25% and 46%, respectively). Pyrosequencing of patient RNA confirmed these levels of exon skipping for c.520C>T and c.617C>G. Results from the ESE-dependent minigene assay indicated that c.520C>T and c.587G>A disturb splicing regulatory elements. Conclusions BRCA2 exon 7 splicing is regulated by multiple exonic elements and is sensitive to disease-associated sequence variations. Measurements of allelic imbalance in patient-derived RNA and/or quantitative analyses using minigene assays provide valuable estimates of the extent of partial splicing defects. Assessment of pathogenicity of variants with partial splicing effect awaits additional evidence and especially the completion of segregation analyses.
Published: 2012

34. interim positron emission tomography scan associated with international prognostic index and germinal center B cell-like signature as prognostic index in diffuse large B-cell lymphoma

Author: Jean-Michel Picquenot, Fabrice Jardin, Stéphanie Becker, Philippe Ruminy, Elodie Bohers, Hélène Lanic, Pierre Vera, Hervé Tilly, Stéphane Leprêtre, Florian Clatot, Christian Bastard, Catherine Maingonnat, Vinciane Rainville, Aspasia Stamatoullas, Marie Cornic, Ferial Mechken, Philippe Bertrand, Sylvain Mareschal, service d'anatomo-pathologie, CRLCC Henri Becquerel, Groupe d'étude des proliférations lymphoïdes ( GPL ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), laboratoire de génétique oncologique, Service d'Hématologie, Equipe Quantification en Imagerie Fonctionnelle ( QuantIF-LITIS ), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes ( LITIS ), Université Le Havre Normandie ( ULH ), Normandie Université ( NU ) -Normandie Université ( NU ) -Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Institut national des sciences appliquées Rouen Normandie ( INSA Rouen Normandie ), Normandie Université ( NU ) -Université Le Havre Normandie ( ULH ), Normandie Université ( NU ), Centre de Lutte Contre le Cancer Henri Becquerel Normandie Rouen (CLCC Henri Becquerel), Groupe d'étude des proliférations lymphoïdes (GPL), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Equipe Quantification en Imagerie Fonctionnelle (QuantIF-LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU), and Breton, Céline
Subjects: Oncology, Male, Cancer Research, Pathology, CHOP, 030218 nuclear medicine & medical imaging, 0302 clinical medicine, International Prognostic Index, Antineoplastic Combined Chemotherapy Protocols, Outcome Assessment, Health Care, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Aged, 80 and over, B-Lymphocytes, medicine.diagnostic_test, Hematology, Middle Aged, Prognosis, 3. Good health, Gene Expression Regulation, Neoplastic, Positron emission tomography, Vincristine, 030220 oncology & carcinogenesis, Female, Lymphoma, Large B-Cell, Diffuse, medicine.drug, Adult, medicine.medical_specialty, Standardized uptake value, Disease-Free Survival, 03 medical and health sciences, Young Adult, Internal medicine, medicine, Humans, Cyclophosphamide, Aged, Proportional Hazards Models, business.industry, Gene Expression Profiling, Germinal center, medicine.disease, Germinal Center, Lymphoma, Doxorubicin, Positron-Emission Tomography, Multivariate Analysis, Prednisone, business, Diffuse large B-cell lymphoma
Abstract: [(18)F]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging is essential to optimize the initial staging and to predict the prognosis of diffuse large B-cell lymphoma (DLBCL). To assess the relationship between the germinal center B cell-like/activated B cell-like (GCB/ABC) classification and PET scan features in DLBCL, 57 cases treated with rituximab and a cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP)/CHOP-like regimen were analyzed. The expression profile of 18 GCB/ABC related genes and five genes coding for glucose transporters (GLUTs) was determined from frozen tissues using DASL (cDNA-mediated Annealing, Selection, Ligation and extension) technology. According to the gene expression profile (GEP), 30 cases of DLBCL were classified as GCB subtype (2-year progression-free survival [PFS] 76%) and 27 cases as ABC subtype (2-year PFS 51%, p = 0.03). Using a semiquantitative assessment of the decrease in standard uptake value (SUV) at interim PET performed after 3-4 cycles of chemotherapy, we defined fast (n = 36) and slow (n = 9) metabolic responders. In multivariate analysis, GCB/ABC subtype, age-adjusted international prognostic index (aaIPI) and slow/fast metabolic response were independent variables that predicted outcome. A score incorporating aaIPI, fast/slow metabolic response and GCB/ABC classification was used to define two groups with highly significantly distinct outcomes. Our study suggests that the combination of GEP, aaIPI and interim PET more accurately predicts DLBCL prognosis and is therefore suitable for tailoring therapeutic strategies.
Published: 2012

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34 results on '"Elodie Bohers"'

1. Analysis of immunoglobulin/T‐cell receptor repertoires by high‐throughput RNA sequencing reveals a continuous dynamic of positive clonal selection in follicular lymphoma

2. Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers

3. Correlations between baseline 18F-FDG PET tumour parameters and circulating DNA in diffuse large B cell lymphoma and Hodgkin lymphoma

4. Concomitant occurrence of genetically distinct Hodgkin lymphoma and primary mediastinal lymphoma

5. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles

6. Targeted genotyping of circulating tumor DNA for classical Hodgkin lymphoma monitoring: a prospective study

7. cfDNA Sequencing: Technological Approaches and Bioinformatic Issues

8. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma

9. Somatic mutations of cell-free circulating DNA detected by next-generation sequencing reflect the genetic changes in both germinal center B-cell-like and activated B-cell-like diffuse large B-cell lymphomas at the time of diagnosis

10. Concomitant occurrence of genetically distinct Hodgkin lymphoma and primary mediastinal lymphoma

11. cfDNA Sequencing: Technological Approaches and Bioinformatic Issues

12. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles

13. Combining gene expression profiling and machine learning to diagnose B-cell non-Hodgkin lymphoma

14. EBV+ diffuse large B-cell lymphoma associated with chronic inflammation expands the spectrum of breast implant-related lymphomas

15. XPO1E571K Mutation Modifies Exportin 1 Localisation and Interactome in B-cell Lymphoma

16. Combining Gene Expression Profiling and Artificial Intelligence to Diagnose B-Cell Non-Hodgkin Lymphoma

17. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort

18. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries

19. TARGETED GENOTYPING OF CIRCULATING TUMOR DNA FOR CLASSICAL HODGKIN LYMPHOMA MONITORING: A PROSPECTIVE STUDY

20. Somatic mutations of cell-free circulating DNA detected by targeted next-generation sequencing and digital droplet PCR in classical Hodgkin lymphoma

21. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma

22. THE LANDSCAPE OF SOMATIC MUTATIONS OF PRIMARY CUTANEOUS DIFFUSE LARGE B-CELL LYMPHOMA, LEG-TYPE

23. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases

24. Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier

25. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma

26. Multiplexed targeted sequencing of recurrent fusion genes in acute leukaemia

27. Digital PCR for quantification of recurrent and potentially actionable somatic mutations in circulating free DNA from patients with diffuse large B-cell lymphoma

28. Somatic Mutations Detected in Plasma Cell-Free DNA By Targeted Sequencing: Assessment of Liquid Biopsy in Primary Central Nervous System Lymphoma

29. Recurrent Mutations of the Exportin 1 Gene (XPO1) in Primary Mediastinal B-Cell Lymphoma: A Lysa Study

30. Immunohistochemical and genomic profiles of diffuse large B-cell lymphomas: Implications for targeted EZH2 inhibitor therapy?

31. Abstract 4810: Exome sequencing of refractory diffuse large B-cell lymphomas highlights candidate genes for targeted resequencing

32. Activating somatic mutations in diffuse large B-cell lymphomas: lessons from next generation sequencing and key elements in the precision medicine era

33. Multiple sequence variants of BRCA2 exon 7 alter splicing regulation

34. interim positron emission tomography scan associated with international prognostic index and germinal center B cell-like signature as prognostic index in diffuse large B-cell lymphoma

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