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2. Profils clinique, électrophysiologique et biologique des neuropathies anti-MAG en fonction du statut mutationnel MYD88 et de l’hémopathie sous-jacente

Author

Guérémy, Alexandre, primary, Delmont, Emilien, additional, Attarian, Shahram, additional, Grapperon, Aude-Marie, additional, Kouton, Ludivine, additional, Farnault, Laure, additional, Boudjarane, John, additional, Gabert, Jean, additional, Fortanier, Etienne, additional, and Boucraut, José, additional

Published
2024
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4. 3q29 duplications: A cohort of 46 patients and a literature review

Author

Massier, Marie, primary, Doco‐Fenzy, Martine, additional, Egloff, Matthieu, additional, Le Guillou, Xavier, additional, Le Guyader, Gwenaël, additional, Redon, Sylvia, additional, Benech, Caroline, additional, Le Millier, Karine, additional, Uguen, Kevin, additional, Ropars, Juliette, additional, Sacaze, Elise, additional, Audebert‐Bellanger, Séverine, additional, Apetrei, Andreea, additional, Molin, Arnaud, additional, Gruchy, Nicolas, additional, Vincent‐Devulder, Aline, additional, Spodenkiewicz, Marta, additional, Jacquin, Clémence, additional, Loron, Gauthier, additional, Thibaud, Marie, additional, Delplancq, Geoffroy, additional, Brisset, Sophie, additional, Lesieur‐Sebellin, Marion, additional, Malan, Valérie, additional, Romana, Serge, additional, Rio, Marlène, additional, Marlin, Sandrine, additional, Amiel, Jeanne, additional, Marquet, Valentine, additional, Dauriat, Benjamin, additional, Moradkhani, Kamran, additional, Mercier, Sandra, additional, Isidor, Bertrand, additional, Arpin, Stéphanie, additional, Pujalte, Mathilde, additional, Jedraszak, Guillaume, additional, Pebrel‐Richard, Céline, additional, Salaun, Gaëlle, additional, Laffargue, Fanny, additional, Boudjarane, John, additional, Missirian, Chantal, additional, Chelloug, Nora, additional, Toutain, Annick, additional, Chiesa, Jean, additional, Keren, Boris, additional, Mignot, Cyril, additional, Gouy, Evan, additional, Jaillard, Sylvie, additional, Landais, Emilie, additional, and Poirsier, Céline, additional

Published
2024
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5. The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11

Author

Lafage-Pochitaloff, Marina, Gerby, Bastien, Baccini, Véronique, Largeaud, Laetitia, Fregona, Vincent, Prade, Naïs, Juvin, Pierre-Yves, Jamrog, Laura, Bories, Pierre, Hébrard, Sylvie, Lagarde, Stéphanie, Mas, Véronique Mansat-De, Dovey, Oliver M, Yusa, Kosuke, Vassiliou, George S, Jansen, Joop H., Tekath, Tobias, Rombaut, David, Ameye, Geneviève, Barin, Carole, Bidet, Audrey, Boudjarane, John, Collonge-Rame, Marie-Agnès, Gervais, Carine, Ittel, Antoine, Lefebvre, Christine, Luquet, Isabelle, Michaux, Lucienne, Nadal, Nathalie, Poirel, Hélène A., Radford-Weiss, Isabelle, Ribourtout, Bénédicte, Richebourg, Steven, Struski, Stéphanie, Terré, Christine, Tigaud, Isabelle, Penther, Dominique, Eclache, Virginie, Fontenay, Michaela, Broccardo, Cyril, and Delabesse, Eric

Published
2021
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6. Clinical, biological, electrophysiological and therapeutic profile of patients with anti-MAG neuropathy according to MYD88L265P and CXCR4 mutations and underlying haemopathy.

Author

Guérémy, Alexandre, Boucraut, José, Boudjarane, John, Grapperon, Aude-Marie, Fortanier, Etienne, Farnault, Laure, Gabert, Jean, Vely, Frédéric, Lacroix, Romaric, Kouton, Ludivine, Attarian, Shahram, and Delmont, Emilien

Subjects
BRUTON tyrosine kinase, CXCR4 receptors, SOMATIC mutation, MUCOSA-associated lymphoid tissue lymphoma, ELECTROPHYSIOLOGY
Abstract

Introduction: Anti-MAG neuropathies are associated with an IgM monoclonal gammopathy of undetermined significance (MGUS) or with a malignant haemopathy. Our objective was to determine whether the presence of a haemopathy or somatic mutations of MYD88 and CXCR4 genes influences disease presentation and response to rituximab (RTX). Methods: We included 79 patients (mean age 74 years, disease duration 9.68 years) who had a bone marrow aspiration with morphologic and immunophenotypic analysis. MYD88L265P and CXCR4 mutations were analysed in peripheral B cells. Information collected included: inflammatory neuropathy cause and treatment sensory sum score (ISS), MRC testing, overall neuropathy limitation scale (ONLS), Rash-built Overall Disability Score (RODS), ataxia score, anti-MAG titres, peak IgM dosage, neurofilament light chain levels, motor and sensory amplitudes, motor unit index (MUNIX) and motor unit size index (MUSIX) sum scores. Efficacy of RTX was evaluated at 12 months in 26 patients. Results: Malignant haematological disorders were discovered in 17 patients (22%): 13 Waldenstrom macroglobulinemia, 3 marginal zone lymphoma and one mantle cell lymphoma. MYD88L265P mutation was detected in 29/60 (48%) patients and CXCR4 in 1 single patient. Disease severity, biological and electrophysiological data and response to RTX were comparable in patients with MGUS/lymphoma and patients with/without MYD88L265P mutation. ISS was lower and MUSIX higher in patients improved by RTX. Conclusions: MYD88L265P mutation and underlying haemopathies are not predictive of a more severe disease. However, in cases of resistant and progressive neuropathy, they provide an opportunity to prescribe newly available drugs such as Bruton tyrosine kinase inhibitors. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Antenatal ultrasound features of isolated recurrent copy number variation in 7q11.23 (Williams syndrome and 7q11.23 duplication syndrome)

Author

Courdier, Cécile, primary, Boudjarane, John, additional, Malan, Valérie, additional, Muti, Christine, additional, Sperelakis‐Beedham, Brian, additional, Odent, Sylvie, additional, Jaillard, Sylvie, additional, Quelin, Chloé, additional, Le Caignec, Cédric, additional, Patat, Olivier, additional, Dubucs, Charlotte, additional, Julia, Sophie, additional, Schluth‐Bolard, Caroline, additional, Goumy, Carole, additional, Redon, Sylvia, additional, Gaillard, Jean‐Baptiste, additional, Huynh, Minh Tuan, additional, Dupont, Céline, additional, Tabet, Anne‐Claude, additional, Cogan, Guillaume, additional, Vialard, François, additional, Dard, Rodolphe, additional, Jedraszak, Guillaume, additional, Jobic, Florence, additional, Lefebvre, Mathilde, additional, Quenum, Geneviève, additional, Inai, Saori, additional, Rama, Mélanie, additional, Sauvestre, Fanny, additional, Coatleven, Frédéric, additional, Thomas, Julie, additional, and Rooryck, Caroline, additional

Published
2023
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9. The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11

Author

Lafage-Pochitaloff, Marina, primary, Gerby, Bastien, additional, Baccini, Véronique, additional, Largeaud, Laetitia, additional, Fregona, Vincent, additional, Prade, Naïs, additional, Juvin, Pierre-Yves, additional, Jamrog, Laura, additional, Bories, Pierre, additional, Hébrard, Sylvie, additional, Lagarde, Stéphanie, additional, Mansat-De Mas, Véronique, additional, Dovey, Oliver M., additional, Yusa, Kosuke, additional, Vassiliou, George S., additional, Jansen, Joop H., additional, Tekath, Tobias, additional, Rombaut, David, additional, Ameye, Geneviève, additional, Barin, Carole, additional, Bidet, Audrey, additional, Boudjarane, John, additional, Collonge-Rame, Marie-Agnès, additional, Gervais, Carine, additional, Ittel, Antoine, additional, Lefebvre, Christine, additional, Luquet, Isabelle, additional, Michaux, Lucienne, additional, Nadal, Nathalie, additional, Poirel, Hélène A., additional, Radford-Weiss, Isabelle, additional, Ribourtout, Bénédicte, additional, Richebourg, Steven, additional, Struski, Stéphanie, additional, Terré, Christine, additional, Tigaud, Isabelle, additional, Penther, Dominique, additional, Eclache, Virginie, additional, Fontenay, Michaela, additional, Broccardo, Cyril, additional, and Delabesse,, Eric, additional

Published
2022
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10. NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework

Author

Duboc, Véronique, Pratella, David, Milanesio, Marco, Boudjarane, John, Descombes, Stéphane, Paquis-Flucklinger, Véronique, Bottini, Silvia, Hôpital Archet 2 [Nice] (CHU), Université Côte d'Azur (UCA), E-Patient : Images, données & mOdèles pour la médeciNe numériquE (EPIONE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Numerical modeling and high performance computing for evolution problems in complex domains and heterogeneous media (NACHOS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and Université Nice Sophia Antipolis (... - 2019) (UNS)

Subjects
bioinformatic pipeline, AcademicSubjects/SCI01060, Noninvasive Prenatal Testing, prenatal testing, Aneuploidy, benchmark, fetal aneuploidies prediction, fetal fraction, Pregnancy, Prenatal Diagnosis, Problem Solving Protocol, Humans, Female, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Cell-Free Nucleic Acids, Retrospective Studies
Abstract

International audience; Abstract Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis. To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.

Published
2021

11. Characterization of the novel Sezary lymphoma cell line BKP1

Author

Boudjarane, John, Essaydi, Arnaud, Farnault, Laure, Popovici, Cornel, Lafage-Pochitaloff, Marina, Beaufils, Nathalie, Berda-Haddad, Yaël, Lacroix, Romaric, Nicolino-Brunet, Corinne, Le Treut, Thérèse, Zattara, Hélène, Gabert, Jean, Kahn-Perlès, Brigitte, and Costello, Régis

Published
2015
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12. NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework.

Author

Duboc, Véronique, Pratella, David, Milanesio, Marco, Boudjarane, John, Descombes, Stéphane, Paquis-Flucklinger, Véronique, and Bottini, Silvia

Subjects
PRENATAL diagnosis, CELL-free DNA, PIPELINE inspection, PYTHON programming language, MEDICAL screening, PRINCIPAL components analysis, DATA analysis, QUALITY control
Abstract

Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis. To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis. [ABSTRACT FROM AUTHOR]

Published
2022
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14. The CADM1tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11

Author

Lafage-Pochitaloff, Marina, Gerby, Bastien, Baccini, Véronique, Largeaud, Laetitia, Fregona, Vincent, Prade, Naïs, Juvin, Pierre-Yves, Jamrog, Laura, Bories, Pierre, Hébrard, Sylvie, Lagarde, Stéphanie, Mansat-De Mas, Véronique, Dovey, Oliver M., Yusa, Kosuke, Vassiliou, George S., Jansen, Joop H., Tekath, Tobias, Rombaut, David, Ameye, Geneviève, Barin, Carole, Bidet, Audrey, Boudjarane, John, Collonge-Rame, Marie-Agnès, Gervais, Carine, Ittel, Antoine, Lefebvre, Christine, Luquet, Isabelle, Michaux, Lucienne, Nadal, Nathalie, Poirel, Hélène A., Radford-Weiss, Isabelle, Ribourtout, Bénédicte, Richebourg, Steven, Struski, Stéphanie, Terré, Christine, Tigaud, Isabelle, Penther, Dominique, Eclache, Virginie, Fontenay, Michaela, Broccardo, Cyril, and Delabesse, Eric

Abstract

Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis leading to peripheral cytopenias and in a substantial proportion of cases to acute myeloid leukemia. The deletion of the long arm of chromosome 11, del(11q), is a rare but recurrent clonal event in MDS. Here, we detail the largest series of 113 cases of MDS and myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) harboring a del(11q) analyzed at clinical, cytological, cytogenetic, and molecular levels. Female predominance, a survival prognosis similar to other MDS, a low monocyte count, and dysmegakaryopoiesis were the specific clinical and cytological features of del(11q) MDS. In most cases, del(11q) was isolated, primary and interstitial encompassing the 11q22-23 region containing ATM, KMT2A, and CBLgenes. The common deleted region at 11q23.2 is centered on an intergenic region between CADM1(also known as Tumor Suppressor in Lung Cancer 1) and NXPE2. CADM1was expressed in all myeloid cells analyzed in contrast to NXPE2. At the functional level, the deletion of Cadm1 in murine Lineage-Sca1+Kit+cells modifies the lymphoid-to-myeloid ratio in bone marrow, although not altering their multilineage hematopoietic reconstitution potential after syngenic transplantation. Together with the frequent simultaneous deletions of KMT2A, ATM, and CBLand mutations of ASXL1, SF3B1, and CBL, we show that CADM1may be important in the physiopathology of the del(11q) MDS, extending its role as tumor-suppressor gene from solid tumors to hematopoietic malignancies.

Published
2022
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15. Interphase FISH for BCR-ABL1 rearrangement on neutrophils: A decisive tool to discriminate a lymphoid blast crisis of chronic myeloid leukemia from a de novo BCR-ABL1 positive acute lymphoblastic leukemia

Author

Balducci, Estelle, primary, Loosveld, Marie, additional, Rahal, Ilhem, additional, Boudjarane, John, additional, Alazard, Emilie, additional, Missirian, Chantal, additional, Lafage-Pochitaloff, Marina, additional, Michel, Gérard, additional, and Zattara, Hélène, additional

Published
2017
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16. Interphase FISH for BCR-ABL1 rearrangement on neutrophils: A decisive tool to discriminate a lymphoid blast crisis of chronic myeloid leukemia from a de novo BCR-ABL1 positive acute lymphoblastic leukemia.

Author

Balducci, Estelle, Loosveld, Marie, Rahal, Ilhem, Boudjarane, John, Alazard, Emilie, Missirian, Chantal, Lafage‐Pochitaloff, Marina, Michel, Gérard, Zattara, Hélène, and Lafage-Pochitaloff, Marina

Abstract

Discrimination between lymphoid blast crisis of chronic myeloid leukemia (CML) and de novo BCR-ABL1 positive acute lymphoblastic leukemia (ALL) represents a diagnostic challenge because this distinction has a major incidence on the management of patients. Here, we report an uncommon pediatric case of ALL with cryptic ins(22;9)(q11;q34q34) and p190-type BCR-ABL1 transcript. We performed interphase fluorescence in situ hybridization (FISH) for BCR-ABL1 rearrangement on blood neutrophils, which was positive consistent with the diagnosis of lymphoid blast crisis of CML. This case illustrates the major interest of interphase FISH for BCR-ABL1 rearrangement on blood neutrophils as a decisive method to discriminate a lymphoid blast crisis of CML from a de novo BCR-ABL1 positive ALL. [ABSTRACT FROM AUTHOR]

Published
2018
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17. Characterization of the novel Sezary lymphoma cell line BKP1

Author

Boudjarane, John, primary, Essaydi, Arnaud, additional, Farnault, Laure, additional, Popovici, Cornel, additional, Lafage‐Pochitaloff, Marina, additional, Beaufils, Nathalie, additional, Berda‐Haddad, Yaël, additional, Lacroix, Romaric, additional, Nicolino‐Brunet, Corinne, additional, Le Treut, Thérèse, additional, Zattara, Hélène, additional, Gabert, Jean, additional, Kahn‐Perlès, Brigitte, additional, and Costello, Régis, additional

Published
2014
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18. The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11

Author

Lafage-Pochitaloff, Marina, Gerby, Bastien, Baccini, Véronique, Largeaud, Laetitia, Fregona, Vincent, Prade, Naïs, Juvin, Pierre-Yves, Jamrog, Laura, Bories, Pierre, Hébrard, Sylvie, Lagarde, Stéphanie, Mansat-De Mas, Véronique, Dovey, Oliver M, Yusa, Kosuke, Vassiliou, George S, Jansen, Joop H, Tekath, Tobias, Rombaut, David, Ameye, Geneviève, Barin, Carole, Bidet, Audrey, Boudjarane, John, Collonge-Rame, Marie-Agnès, Gervais, Carine, Ittel, Antoine, Lefebvre, Christine, Luquet, Isabelle, Michaux, Lucienne, Nadal, Nathalie, Poirel, Hélène A, Radford-Weiss, Isabelle, Ribourtout, Bénédicte, Richebourg, Steven, Struski, Stéphanie, Terré, Christine, Tigaud, Isabelle, Penther, Dominique, Eclache, Virginie, Fontenay, Michaela, Broccardo, Cyril, and Delabesse, Eric

Subjects
Leukemia, Myeloid, Acute, Mice, hemic and lymphatic diseases, Chromosomes, Human, Pair 11, Myelodysplastic Syndromes, Cell Adhesion Molecule-1, Animals, Humans, Female, Genes, Tumor Suppressor, Chromosome Deletion, 3. Good health
Abstract

Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis leading to peripheral cytopenias and in a substantial proportion of cases to acute myeloid leukemia. The deletion of the long arm of chromosome 11, del(11q), is a rare but recurrent clonal event in MDS. Here, we detail the largest series of 113 cases of MDS and myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) harboring a del(11q) analyzed at clinical, cytological, cytogenetic, and molecular levels. Female predominance, a survival prognosis similar to other MDS, a low monocyte count, and dysmegakaryopoiesis were the specific clinical and cytological features of del(11q) MDS. In most cases, del(11q) was isolated, primary and interstitial encompassing the 11q22-23 region containing ATM, KMT2A, and CBL genes. The common deleted region at 11q23.2 is centered on an intergenic region between CADM1 (also known as Tumor Suppressor in Lung Cancer 1) and NXPE2. CADM1 was expressed in all myeloid cells analyzed in contrast to NXPE2. At the functional level, the deletion of Cadm1 in murine Lineage-Sca1+Kit+ cells modifies the lymphoid-to-myeloid ratio in bone marrow, although not altering their multilineage hematopoietic reconstitution potential after syngenic transplantation. Together with the frequent simultaneous deletions of KMT2A, ATM, and CBL and mutations of ASXL1, SF3B1, and CBL, we show that CADM1 may be important in the physiopathology of the del(11q) MDS, extending its role as tumor-suppressor gene from solid tumors to hematopoietic malignancies.

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