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Bobée V, Viennot M, Rainville V, Veresezan L, Drieux F, Viailly P, Michel V, Sater V, Lanic M, Bohers E, Camus V, Tilly H, Jardin F, Ruminy P. Analysis of immunoglobulin/T-cell receptor repertoires by high-throughput RNA sequencing reveals a continuous dynamic of positive clonal selection in follicular lymphoma. Hemasphere 2024; 8:e50. [PMID: 38435425 PMCID: PMC10896008 DOI: 10.1002/hem3.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024] Open
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.
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Affiliation(s)
- Victor Bobée
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of Biological HematologyRouen University HospitalRouenFrance
| | - Mathieu Viennot
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Vinciane Rainville
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Liana Veresezan
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of PathologyCentre Henri BecquerelRouenFrance
| | - Fanny Drieux
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of PathologyCentre Henri BecquerelRouenFrance
| | | | - Victor Michel
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Vincent Sater
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Marie‐Delphine Lanic
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
| | - Vincent Camus
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of Clinical HematologyCentre Henri BecquerelRouenFrance
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of Clinical HematologyCentre Henri BecquerelRouenFrance
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
- Department of Clinical HematologyCentre Henri BecquerelRouenFrance
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, UNIROUENUniversity of NormandieRouenFrance
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Al Jamal I, Parquet M, Guiyedi K, Aoufouchi S, Le Guillou M, Rizzo D, Pollet J, Dupont M, Boulin M, Faumont N, Boutouil H, Jardin F, Ruminy P, El Hamel C, Lerat J, Al Hamaoui S, Makdissy N, Feuillard J, Gachard N, Peron S. IGH 3'RR recombination uncovers a non-germinal center imprint and c-MYC-dependent IGH rearrangement in unmutated chronic lymphocytic leukemia. Haematologica 2024; 109:466-478. [PMID: 37496419 PMCID: PMC10828775 DOI: 10.3324/haematol.2023.282897] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable indolent non-Hodgkin lymphoma characterized by tumor B cells that weakly express a B-cell receptor. The mutational status of the variable region (IGHV) within the immunoglobulin heavy chain (IGH) locus is an important prognosis indicator and raises the question of the CLL cell of origin. Mutated IGHV gene CLL are genetically imprinted by activation-induced cytidine deaminase (AID). AID is also required for IGH rearrangements: class switch recombination and recombination between switch Mu (Sμ) and the 3' regulatory region (3'RR) (Sμ-3'RRrec). The great majority of CLL B cells being unswitched led us to examine IGH rearrangement blockade in CLL. Our results separated CLL into two groups on the basis of Sμ-3'RRrec counts per sample: Sμ-3'RRrecHigh cases (mostly unmutated CLL) and Sμ-3'RRrecLow cases (mostly mutated CLL), but not based on the class switch recombination junction counts. Sμ-3'RRrec appeared to be ongoing in Sμ-3'RRrecHigh CLL cells and comparison of Sμ-3'RRrec junction structural features pointed to different B-cell origins for both groups. In accordance with IGHV mutational status and PIM1 mutation rate, Sμ-3'RRrecHigh CLL harbor a non-germinal center experienced B-cell imprint while Sμ-3'RRrecLow CLL are from AID-experienced B cells from a secondary lymphoid organ. In addition to the proposals already made concerning the CLL cell of origin, our study highlights that analysis of IGH recombinatory activity can identify CLL cases from different origins. Finally, on-going Sμ-3'RRrec in Sμ-3'RRrecHigh cells appeared to presumably be the consequence of high c-MYC expression, as c-MYC overexpression potentiated IGH rearrangements and Sμ-3'RRrec, even in the absence of AID for the latter.
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Affiliation(s)
- Israa Al Jamal
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Milene Parquet
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Kenza Guiyedi
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Said Aoufouchi
- CNRS UMR9019, Gustave Roussy, B-cell and Genome Plasticity Team, Villejuif, France and Universite Paris-Saclay, Orsay
| | - Morwenna Le Guillou
- CNRS UMR9019, Gustave Roussy, B-cell and Genome Plasticity Team, Villejuif, France and Universite Paris-Saclay, Orsay
| | - David Rizzo
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Justine Pollet
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Marine Dupont
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Melanie Boulin
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Nathalie Faumont
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Hend Boutouil
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges
| | - Fabrice Jardin
- Inserm U1245 and Department of Henri-Becquerel Hematology Center and Normandie Univ UNIROUEN, Rouen
| | - Philippe Ruminy
- Inserm U1245 and Department of Henri-Becquerel Hematology Center and Normandie Univ UNIROUEN, Rouen
| | - Chahrazed El Hamel
- Collection Biologique Hopital de la Mere et de l'Enfant (CB-HME), Department of Pediatrics, Limoges University Hospital, Limoges
| | - Justine Lerat
- Department of Otorinolaryngology, Limoges University Hospital, Limoges
| | - Samar Al Hamaoui
- Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Nehman Makdissy
- Faculty of Sciences, GSBT Genomic Surveillance and Biotherapy Team, Mont Michel Campus, Lebanese University, Tripoli
| | - Jean Feuillard
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Nathalie Gachard
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges, France; Laboratoire d'Hematologie Biologique, Centre Hospitalier Universitaire de Limoges, Limoges
| | - Sophie Peron
- Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 7276/INSERM U1262, Universite de Limoges, Limoges.
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Gross Z, Veyrat-Masson R, Grange B, Huet S, Verney A, Traverse-Glehen A, Ruminy P, Baseggio L. Diagnosis of chronic B-cell lymphoproliferative disease in peripheral blood = how machine learning may help to the interpretation of flow cytometry data. Hematol Oncol 2024; 42:e3245. [PMID: 38287532 DOI: 10.1002/hon.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/27/2023] [Accepted: 12/02/2023] [Indexed: 01/31/2024]
Abstract
Flow cytometry (FCM) has become a method of choice for immunologic characterization of chronic lymphoproliferative disease (CLPD). To reduce the potential subjectivities of FCM data interpretation, we developed a machine learning random forest algorithm (RF) allowing unsupervised analysis. This assay relies on 16 parameters obtained from our FCM screening panel, routinely used in the exploration of peripheral blood (PB) samples (mean fluorescence intensity values (MFI) of CD19, CD45, CD5, CD20, CD200, CD23, HLA-DR, CD10 in CD19-gated B cells, ratio of kappa/Lambda, and different ratios of MFI B-cells/T-cells [CD20, CD200, CD23]). The RF algorithm was trained and validated on a large cohort of more than 300 annotated different CLPD cases (chronic B-cell leukemia, mantle cell lymphoma, marginal zone lymphoma, follicular lymphoma, splenic red pulp lymphoma, hairy cell leukemia) and non-tumoral selected from PB samples. The RF algorithm was able to differentiate tumoral from non-tumoral B-cells in all cases and to propose a correct CLPD classification in more than 90% of cases. In conclusion the RF algorithm could be proposed as an interesting help to FCM data interpretation allowing a first B-cells CLPD diagnostic hypothesis and/or to guide the management of complementary analysis (additional immunologic markers and genetic).
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Affiliation(s)
- Zofia Gross
- Service clinique d'hématologie, Groupement Hospitalier Lyon-Sud/Hospices Civils de Lyon, Pierre-Bénite, France
| | | | - Béatrice Grange
- Laboratoire d'hématologie spécialisée, Groupement Hospitalier Lyon-Sud/Hospices Civils de Lyon, Pierre-Bénite, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie (CIRI) INSERM U1111 - CNRS UMR5308, Lyon, France
| | - Sarah Huet
- Laboratoire d'hématologie spécialisée, Groupement Hospitalier Lyon-Sud/Hospices Civils de Lyon, Pierre-Bénite, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie (CIRI) INSERM U1111 - CNRS UMR5308, Lyon, France
| | - Aurélie Verney
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie (CIRI) INSERM U1111 - CNRS UMR5308, Lyon, France
| | - Alexandra Traverse-Glehen
- Service d'anatomie-pathologique, Groupement Hospitalier Lyon-Sud/Hospices Civils de Lyon, Pierre-Bénite, France
- INSERM U1245, Centre Henri Becquerel, UNIROUEN, University of Normandie, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, UNIROUEN, University of Normandie, Rouen, France
| | - Lucile Baseggio
- Laboratoire d'hématologie spécialisée, Groupement Hospitalier Lyon-Sud/Hospices Civils de Lyon, Pierre-Bénite, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie (CIRI) INSERM U1111 - CNRS UMR5308, Lyon, France
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Camus V, Viailly PJ, Drieux F, Veresezan EL, Sesques P, Haioun C, Durot E, Patey M, Rossi C, Martin L, Rainville V, Bohers E, Ruminy P, Penther D, Kaltenbach S, Bruneau J, Paillassa J, Tournilhac O, Willaume A, Antier C, Lazarovici J, Lévêque E, Decazes P, Becker S, Tonnelet D, Berriolo-Riedinger A, Gaulard P, Tilly H, Molina TJ, Traverse-Glehen A, Jardin F. High PDL1/PDL2 gene expression correlates with worse outcome in primary mediastinal large B-cell lymphoma. Blood Adv 2023; 7:7331-7345. [PMID: 37862676 PMCID: PMC10701594 DOI: 10.1182/bloodadvances.2023011169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
Primary mediastinal B-cell lymphoma (PMBL) is an uncommon entity of aggressive B-cell lymphoma with an unusually good prognosis, except for 10-15% of chemotherapy-refractory cases. To identify earlier these higher risk patients, we performed molecular characterization of a retrospective multicenter cohort of patients treated with firstline immunochemotherapy. The traits of the patients with gene-expression profiling data (n = 120) were as follows: median age of 34 years (range, 18-67 years); female sex, 58.3%; elevated lactate dehydrogenase, 82.5%; Eastern Cooperative Oncology Group performance status score of 0 to 1, 85.7%; Ann Arbor stage I/II, 55%; International Prognostic Index score of 1 to 2, 64.4%; and median metabolic tumor volume, 290.4 cm3 (range, 15.7-1147.5 cm3). Among all 137 markers tested for correlation with survival data, only programmed death-ligand (PDL) 1 and PDL2 expression showed a prognostic impact. Overall, both PDL1 and PDL2 genes were highly expressed in 37 patients (30.8%; PDL1high/PDL2high). The baseline clinical characteristics of patients with PDL1high/PDL2high were similar to those of other patients. In univariate analysis, PDL1high/PDL2high status was associated with poor progression-free survival (PFS) (hazard ratio [HR], 4.292) and overall survival (OS; HR, 8.24). In multivariate analysis, PDL1high/PDL2high status was an independent prognostic factor of adverse outcomes (PFS: HR, 5.22; OS: HR, 10.368). We validated these results in an independent cohort of 40 patients and confirmed the significant association between PDL1high/PDL2high status and inferior PFS (HR, 6.11). High PDL1/PDL2 gene expression defines a population with strong immune privilege and poorer outcomes from standard chemotherapy who might benefit from firstline checkpoint inhibitor therapy.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Fanny Drieux
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Pierre Sesques
- Department of Hematology, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Corinne Haioun
- Lymphoid malignancies Unit, Henri Mondor University Hospital, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Eric Durot
- Department of Hematology, Centre Hospitalier Universitaire (CHU) de Reims, Reims, France
| | - Martine Patey
- Department of Pathology, CHU de Reims, Reims, France
| | - Cédric Rossi
- Department of Hematology, Dijon University Hospital, Dijon, France
| | - Laurent Martin
- Department of Pathology, Dijon University Hospital, Dijon, France
| | - Vinciane Rainville
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Dominique Penther
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
- Department of Genetic Oncology, Centre Henri Becquerel, Rouen France
| | - Sophie Kaltenbach
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Julie Bruneau
- Université de Paris, Institut Imagine, Laboratory of Hematological Disorders, INSERM UMR1163, Paris, France
- Department of Pathology, Université Paris Cité, Assistance Publique-Hôpitaux de Paris, Necker and Robert Debré, Paris, France
| | - Jérome Paillassa
- Department of Hematology, Angers University Hospital, Angers, France
| | - Olivier Tournilhac
- Department of Hematology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Alexandre Willaume
- Department of Hematology, Lille University Hospital – Hôpital Claude Hurriez, Lille, France
| | - Chloé Antier
- Department of Hematology, University Hospital, Nantes, France
| | - Julien Lazarovici
- Department of Hematology, Institut Gustave Roussy, Villejuif, France
| | - Emilie Lévêque
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Pierre Decazes
- Department of Nuclear Medicine and QuantIF-LITIS-EA4108, University of Rouen, Centre Henri Becquerel, Rouen, France
| | - Stéphanie Becker
- Department of Nuclear Medicine and QuantIF-LITIS-EA4108, University of Rouen, Centre Henri Becquerel, Rouen, France
| | - David Tonnelet
- Department of Nuclear Medicine and QuantIF-LITIS-EA4108, University of Rouen, Centre Henri Becquerel, Rouen, France
| | | | - Philippe Gaulard
- Department of Pathology, Henri Mondor University Hospital, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Hervé Tilly
- Department of Hematology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Thierry Jo Molina
- Department of Pathology, Université Paris Cité, Assistance Publique-Hôpitaux de Paris, Necker and Robert Debré, Paris, France
| | | | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
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Lanic MD, Guérin R, Wassef M, Durdilly P, Rainville V, Sater V, Jardin F, Ruminy P, Costes-Martineau V, Laé M. Detection of salivary gland and sinonasal fusions by a next-generation sequencing based, ligation-dependent, multiplex RT-PCR assay. Histopathology 2023; 83:685-699. [PMID: 37350081 DOI: 10.1111/his.14971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
AIMS The discovery of tumour type-specific gene fusion oncogenes in benign and malignant salivary gland and sinonasal (SGSN) tumours has significantly increased our knowledge about their molecular pathology and classification. METHODS AND RESULTS We developed a new targeted multiplexed next-generation sequencing (NGS)-based method that utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR) to detect oncogenic fusion transcripts involving 116 genes, leading to 96 gene fusions known to be recurrently rearranged in these tumours. In all, 180 SGSN tumours (formalin-fixed, paraffin-embedded samples, 141 specimens and 39 core needle biopsies) from the REFCORpath (French network for rare head and neck cancers) with previously identified fusion genes by fluorescent in situ hybridisation (FISH), RT-PCR, or molecular immunohistochemistry were selected to test its specificity and sensitivity and validate its diagnostic use. Tested tumours encompassed 14 major tumours types, including secretory carcinoma, mucoepidermoid carcinoma, adenoid cystic carcinoma, salivary gland intraductal carcinoma, clear cell carcinoma, pleomorphic adenoma, adamantinoma-like Ewing Sarcoma, EWSR1::COLCA2 sinonasal sarcoma, DEK::AFF2 sinonasal carcinoma, and biphenotypic sinonasal sarcoma. In-frame fusion transcripts were detected in 97.8% of cases (176/180). Gene fusion assay results correlated with conventional techniques (immunohistochemistry [IHC], FISH, and RT-PCR) in 176/180 tumours (97.8%). CONCLUSION This targeted multiplexed NGS-based LD-RT-PCR method is a robust, highly sensitive method for the detection of recurrent gene fusions from routine clinical SGSN tumours. It can be easily customized to cover new fusions. These results are promising for implementing an integrated NGS system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses, and accelerate time to precision therapies in SGSN tumours.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - René Guérin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | | | - Vinciane Rainville
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Vincent Sater
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | | | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
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Camus V, Etancelin P, Drieux F, Veresezan E, Picquenot J, Penther D, Viennot M, Ruminy P, Contentin N, Lemasle E, Leprêtre S, Dubois S, Penichoux J, Stamatoullas A, Zduniak A, Lanic H, Jardin F. Complete hematologic response after belinostat treatment and allogeneic stem cell transplantation for multiple relapsed/refractory angioimmunoblastic T-cell lymphoma: A case report. Clin Case Rep 2023; 11:e7623. [PMID: 37361652 PMCID: PMC10290197 DOI: 10.1002/ccr3.7623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Key Clinical Message This case report highlights the potential of belinostat for the treatment of relapsed/refractory peripheral T-cell lymphomas, for which effective therapies are still scarce. Abstract Peripheral T-cell lymphomas have an aggressive disease course associated with poor outcomes. We report a young patient with highly pretreated relapsed/refractory nodal follicular helper T-cell lymphoma (angioimmunoblastic-type [nTFHL-AI]), who successfully received an allogeneic stem cell transplantation following belinostat therapy. The complete hematologic response achieved has lasted more than 2 years.
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Affiliation(s)
- Vincent Camus
- Department of HematologyCentre Henri BecquerelRouenFrance
| | | | - Fanny Drieux
- Department of PathologyCentre Henri BecquerelRouenFrance
| | | | | | | | | | | | | | - Emilie Lemasle
- Department of HematologyCentre Henri BecquerelRouenFrance
| | | | - Sydney Dubois
- Department of HematologyCentre Henri BecquerelRouenFrance
| | | | | | | | - Hélène Lanic
- Department of HematologyCentre Henri BecquerelRouenFrance
| | - Fabrice Jardin
- Department of HematologyCentre Henri BecquerelRouenFrance
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7
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Levacher C, Viennot M, Drouet A, Beaussire L, Coutant S, Théry JC, Baert-Desurmont S, Laé M, Ruminy P, Houdayer C. Disequilibrium between BRCA1 and BRCA2 Circular and Messenger RNAs Plays a Role in Breast Cancer. Cancers (Basel) 2023; 15:cancers15072176. [PMID: 37046838 PMCID: PMC10093293 DOI: 10.3390/cancers15072176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Breast cancer is a frequent disease for which the discovery of markers that enable early detection or prognostic assessment remains challenging. Circular RNAs (circRNAs) are single-stranded structures in closed loops that are produced by backsplicing. CircRNA and messenger RNA (mRNA) are generated co-transcriptionally, and backsplicing and linear splicing compete against each other. As mRNAs are key players in tumorigenesis, we hypothesize that a disruption of the balance between circRNAs and mRNAs could promote breast cancer. Hence, we developed an assay for a simultaneous study of circRNAs and mRNAs, which we have called splice and expression analyses by exon ligation and high-throughput sequencing (SEALigHTS). Following SEALigHTS validation for BRCA1 and BRCA2, our hypothesis was tested using an independent research set of 95 pairs from tumor and adjacent normal breast tissues. In this research set, ratios of BRCA1 and BRCA2 circRNAs/mRNAs were significantly lower in the tumor breast tissue compared to normal tissue (p = 1.6 × 10-9 and p = 4.4 × 10-5 for BRCA1 and BRCA2, respectively). Overall, we developed an innovative method to study linear splicing and backsplicing, described the repertoire of BRCA1 and BRCA2 circRNAs, including 15 novel ones, and showed for the first time that a disequilibrium between BRCA1 and BRCA2 circRNAs and mRNAs plays a role in breast cancer.
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Affiliation(s)
- Corentin Levacher
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Mathieu Viennot
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
| | - Aurélie Drouet
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Ludivine Beaussire
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
- Department of Pathology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
| | - Jean-Christophe Théry
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique, 76000 Rouen, France
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Stéphanie Baert-Desurmont
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
| | - Marick Laé
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
- Department of Pathology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038 Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, 76000 Rouen, France
| | - Claude Houdayer
- Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, Department of Genetics, 76000 Rouen, France
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Lanic MD, Guérin R, Sater V, Durdilly P, Ruminy P, Skálová A, Laé M. A novel SMARCA2-CREM fusion expending the molecular spectrum of salivary gland hyalinazing clear cell carcinoma beyond the FET genes. Genes Chromosomes Cancer 2023; 62:231-236. [PMID: 36504225 DOI: 10.1002/gcc.23114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Hyalinizing clear cell carcinoma (HCCC) is a rare salivary gland carcinoma with a generally indolent behavior, characterized by recurrent chromosomal translocation involving EWSR1 (22q12.2) leading to two fusion genes EWSR1::ATF1 or EWSR1::CREM. We report one case of HCCC with a novel SMARCA2::CREM fusion, identified by targeted RNA next generation sequencing by LD-RT-PCR, which has until now never been described in salivary glands. The exon 4 of SMARCA2 is fused to exon 5 of CREM. This fusion has been described previously in only one tumor, a central nervous system tumor (intracranial mesenchymal tumor) but not in other FET::CREB fused tumors. This fusion was confirmed by CREM break-apart FISH and reverse transcriptase polymerase chain reaction (RT-PCR). The tumor cells showed retained expression of INI1, SMARCA2, and SMARCA4 by immunohistochemistry. We compare its clinical, histopathological, immunophenotypic, genetic features with those previously described in HCCC, FET::CREB fusion-positive. Our results added data suggesting that different histomolecular tumor subtypes seem to be included within the terminology "HCCC, FET::CREB fusion-positive," and that further series of cases are needed to better characterize them.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - René Guérin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Vincent Sater
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France.,Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Alena Skálová
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Plzen, Czech Republic.,Bioptic Laboratory, Ltd, Plzen, Czech Republic
| | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France.,Department of Pathology, Centre Henri Becquerel, Rouen, France
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9
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de Nattes T, Beadle J, Toulza F, Candon E, Ruminy P, François A, Bertrand D, Guerrot D, Drieux F, Roufosse C, Candon S. A Simple Molecular Tool for the Assessment of Kidney Transplant Biopsies. Clin J Am Soc Nephrol 2023; 18:499-509. [PMID: 36723289 PMCID: PMC10103338 DOI: 10.2215/cjn.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND The Banff Classification for Allograft Pathology recommendations for the diagnosis of kidney transplant rejection includes molecular assessment of the transplant biopsy. However, implementation of molecular tools in clinical practice is still limited, partly due to the required expertise and financial investment. The reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) assay is a simple, rapid, and inexpensive assay that permits simultaneous evaluation of a restricted gene panel using paraffin-embedded tissue blocks. The aim of this study was to develop and validate a RT-MLPA assay for diagnosis and classification of rejection. METHODS A retrospective cohort of 220 kidney transplant biopsies from two centers, which included 52 antibody-mediated rejection, 51 T-cell-mediated rejection, and 117 no-rejection controls, was assessed. A 17-gene panel was identified on the basis of relevant pathophysiological pathways. A support vector machine classifier was developed. A subset of 109 biopsies was also assessed using the Nanostring Banff Human Organ Transplant panel to compare the two assays. RESULTS The support vector machine classifier train and test accuracy scores were 0.84 and 0.83, respectively. In the test cohort, the F1 score for antibody-mediated rejection, T-cell-mediated rejection, and control were 0.88, 0.86, and 0.69, respectively. Using receiver-operating characteristic curves, the area under the curve for class predictions was 0.96, 0.89, and 0.91, respectively, with a weighted average at 0.94. Classifiers' performances were highest for antibody-mediated rejection diagnosis with 94% correct predictions, compared with 88% correct predictions for control biopsies and 60% for T-cell-mediated rejection biopsies. Gene expression levels assessed by RT-MLPA and Nanostring were correlated: r = 0.68, P < 0.001. Equivalent gene expression profiles were obtained with both assays in 81% of the samples. CONCLUSIONS The 17-gene panel RT-MLPA assay, developed here for formalin-fixed paraffin-embedded kidney transplant biopsies, classified kidney transplant rejection with an overall accurate prediction ratio of 0.83. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_04_10_CJN10100822.mp3.
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Affiliation(s)
- Tristan de Nattes
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
- Univ Rouen Normandie, INSERM U1234, Rouen, France
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Jack Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Frederic Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
| | - Edvin Candon
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Arnaud François
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Dominique Bertrand
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Dominique Guerrot
- Nephrology – Kidney Transplant Unit, Rouen University Hospital, Rouen, France
| | - Fanny Drieux
- Univ Rouen Normandie, INSERM U1245, Centre Henri Becquerel, Rouen, France
- Pathology Department, Rouen University Hospital, Rouen, France
| | - Candice Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Imperial College, London, United Kingdom
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10
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Lan X, Ruminy P, Bohers E, Marchand V, Viennot M, Viailly PJ, Etancelin P, Tilly H, Mihailescu S, Bouclet F, Leprêtre S, Jardin F. 5’ Rapid amplification of cDNA ends (5’RACE): A simpler method to analyze immunoglobulin genes and discover the value of the light chain in chronic lymphocytic leukemia. Leuk Res 2022; 123:106952. [DOI: 10.1016/j.leukres.2022.106952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022]
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11
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Lanic MD, Le Loarer F, Rainville V, Sater V, Viennot M, Beaussire L, Viailly PJ, Angot E, Hostein I, Jardin F, Ruminy P, Laé M. Detection of sarcoma fusions by a next-generation sequencing based-ligation-dependent multiplex RT-PCR assay. Mod Pathol 2022; 35:649-663. [PMID: 35075283 DOI: 10.1038/s41379-021-00980-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Morphological, immunohistochemical, and molecular methods often need to be combined for accurate diagnosis and optimal clinical management of sarcomas. Here, we have developed, a new molecular diagnostic assay, for the detection of gene fusions in sarcomas. This targeted multiplexed next-generation sequencing (NGS)-based method utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR-NGS) to detect oncogenic fusion transcripts involving 137 genes, leading to 139 gene fusions known to be recurrently rearranged in soft-tissue and bone tumors. 158 bone and soft-tissue tumors with previously identified fusion genes by fluorescent in situ hybridization (FISH) or RT-PCR were selected to test the specificity and the sensitivity of this assay. RNA were extracted from formalin-fixed paraffin-embedded (n = 143) or frozen (n = 15) material (specimen; n = 42 or core needle biopsies; n = 116). Tested tumors encompassed 23 major translocation-related sarcomas types, including Ewing and Ewing-like sarcomas, rhabdomyosarcomas, desmoplastic small round-cell tumors, clear-cell sarcomas, infantile fibrosarcomas, endometrial stromal sarcomas, epithelioid hemangioendotheliomas, alveolar soft-part sarcomas, biphenotypic sinonasal sarcomas, extraskeletal myxoid chondrosarcomas, myxoid/round-cell liposarcomas, dermatofibrosarcomas protuberans and solitary fibrous tumors. In-frame fusion transcripts were detected in 98.1% of cases (155/158). Gene fusion assay results correlated with conventional techniques (FISH and RT-PCR) in 155/158 tumors (98.1%). These data demonstrate that this assay is a rapid, robust, highly sensitive, and multiplexed targeted RNA sequencing assay for the detection of recurrent gene fusions on RNA extracted from routine clinical specimens of sarcomas (formalin-fixed paraffin-embedded or frozen). It facilitates the precise diagnosis and identification of tumors with potential targetable fusions. In addition, this assay can be easily customized to cover new fusions.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - François Le Loarer
- Department of Pathology, Institut Bergonié, cours de l'Argonne, 33000, Bordeaux, France
| | - Vinciane Rainville
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Vincent Sater
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Mathieu Viennot
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Ludivine Beaussire
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France.,Department of Pathology, Centre Henri Becquerel, rue d'Amiens, 76038, Rouen, France
| | - Pierre-Julien Viailly
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Emilie Angot
- Department of Pathology, Rouen University Hospital, 76031, Rouen, France
| | - Isabelle Hostein
- Department of Pathology, Institut Bergonié, cours de l'Argonne, 33000, Bordeaux, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France.
| | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France. .,Department of Pathology, Centre Henri Becquerel, rue d'Amiens, 76038, Rouen, France.
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12
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Steimlé T, Dourthe ME, Alcantara M, Touzart A, Simonin M, Mondesir J, Lhermitte L, Bond J, Graux C, Grardel N, Cayuela JM, Arnoux I, Gandemer V, Balsat M, Vey N, Macintyre E, Ifrah N, Dombret H, Petit A, Baruchel A, Ruminy P, Boissel N, Asnafi V. Clinico-biological features of T-cell acute lymphoblastic leukemia with fusion proteins. Blood Cancer J 2022; 12:14. [PMID: 35082269 PMCID: PMC8791998 DOI: 10.1038/s41408-022-00613-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
T-cell acute lymphoblastic leukemias (T-ALL) represent 15% of pediatric and 25% of adult ALL. Since they have a particularly poor outcome in relapsed/refractory cases, identifying prognosis factors at diagnosis is crucial to adapting treatment for high-risk patients. Unlike acute myeloid leukemia and BCP ALL, chromosomal rearrangements leading to chimeric fusion-proteins with strong prognosis impact are sparsely reported in T-ALL. To address this issue an RT-MPLA assay was applied to a consecutive series of 522 adult and pediatric T-ALLs and identified a fusion transcript in 20% of cases. PICALM-MLLT10 (4%, n = 23), NUP214-ABL1 (3%, n = 19) and SET-NUP214 (3%, n = 18) were the most frequent. The clinico-biological characteristics linked to fusion transcripts in a subset of 235 patients (138 adults in the GRAALL2003/05 trials and 97 children from the FRALLE2000 trial) were analyzed to identify their prognosis impact. Patients with HOXA trans-deregulated T-ALLs with MLLT10, KMT2A and SET fusion transcripts (17%, 39/235) had a worse prognosis with a 5-year EFS of 35.7% vs 63.7% (HR = 1.63; p = 0.04) and a trend for a higher cumulative incidence of relapse (5-year CIR = 45.7% vs 25.2%, HR = 1.6; p = 0.11). Fusion transcripts status in T-ALL can be robustly identified by RT-MLPA, facilitating risk adapted treatment strategies for high-risk patients.
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Affiliation(s)
- Thomas Steimlé
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Marie-Emilie Dourthe
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
| | - Marion Alcantara
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Aurore Touzart
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris (AP-HP), GH HUEP, Armand Trousseau Hospital, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 938, CDR Saint-Antoine, GRC n°07, GRC MyPAC, Paris, France
| | - Johanna Mondesir
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Ludovic Lhermitte
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Carlos Graux
- Department of Hematology, Université catholique de Louvain, CHU UCL Namur - site Godinne, Yvoir, Belgium
| | - Nathalie Grardel
- Laboratory of Hematology, CHRU Lille, Lille, France and U1172, INSERM, Lille, France
| | - Jean-Michel Cayuela
- Laboratory of Hematology and EA 3518 University Hospital Saint-Louis, AP-HP and Université de Paris, Paris, France
| | - Isabelle Arnoux
- Hematology Laboratory, Marseille University Hospital Timone, Marseille, France
| | - Virginie Gandemer
- Department of Pediatric Hematology and Oncology, University Hospital of Rennes, Rennes, France
| | - Marie Balsat
- Service d'hématologie clinique, Hôpital Lyon Sud, Marseille, France
| | - Norbert Vey
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers service des Maladies du Sang et CRCINA INSERM, Angers, France
| | - Hervé Dombret
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris (AP-HP), GH HUEP, Armand Trousseau Hospital, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 938, CDR Saint-Antoine, GRC n°07, GRC MyPAC, Paris, France
| | - André Baruchel
- Department of Pediatric Hematology and Immunology, Robert Debré University Hospital (AP-HP), Université de Paris, Paris, France
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
| | - Philippe Ruminy
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Nicolas Boissel
- Institut de Recherche Saint-Louis, Université de Paris, EA-3518, Paris, France
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
- AP-HP, Hôpital Saint Louis, Unité d'Hématologie Adolescents et Jeunes Adultes, Paris, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France.
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13
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Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data. Methods Mol Biol 2022; 2493:235-245. [PMID: 35751818 DOI: 10.1007/978-1-0716-2293-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rapid transition from traditional sequencing methods to Next-Generation Sequencing (NGS) has allowed for a faster and more accurate detection of somatic variants (Single-Nucleotide Variant (SNV) and Copy Number Variation (CNV)) in tumor cells. NGS technologies require a succession of steps during which false variants can be silently added at low frequencies. Filtering these artifacts can be a rather difficult task especially when the experiments are designed to look for very low frequency variants. Recently, adding unique molecular barcodes called UMI (Unique Molecular Identifier) to the DNA fragments appears to be a very effective strategy to specifically filter out false variants from the variant calling results (Kukita et al. DNA Res 22(4):269-277, 2015; Newman et al. Nat Biotechnol 34(5):547-555, 2016; Schmitt et al. Proc Natl Acad Sci U S A 109(36):14508-14513). Here, we describe UMI-VarCal (Sater et al. Bioinformatics 36:2718-2724, 2020), which can use the UMI information from UMI-tagged reads to offer a faster and more accurate variant calling analysis.
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Affiliation(s)
- Vincent Sater
- Normandie Univ, UNIROUEN, LITIS EA 4108, Rouen, France.
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | | | | | - Élodie Bohers
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | - Mathieu Viennot
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
| | | | - Pierre Vera
- Normandie Univ, UNIROUEN, LITIS EA 4108, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
- INSERM U1245, University of Normandie UNIROUEN, Rouen, France
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14
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Csanyi-Bastien M, Lanic MD, Beaussire L, Ferric S, François A, Meseure D, Jardin F, Wassef M, Ruminy P, Laé M. Pan-TRK Immunohistochemistry Is Highly Correlated With NTRK3 Gene Rearrangements in Salivary Gland Tumors. Am J Surg Pathol 2021; 45:1487-1498. [PMID: 33899788 DOI: 10.1097/pas.0000000000001718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Secretory carcinoma (SC) is characterized by ETV6 rearrangements, most often ETV6-NTRK3 fusion. Given its histologic overlap with other salivary gland tumors (SGTs), SCs can be difficult to diagnose without genetic confirmation. A recently developed pan-TRK (tropomyosin receptor kinase) antibody shows promise for identifying tumors with NTRK (neurotrophic tyrosine kinase receptor 3) fusions. The aim of this study was to evaluate the utility of pan-TRK immunohistochemistry in distinguishing SCs from mimics and selecting patients eligible for TRK inhibitor clinical trials. We examined whole-tissue sections from 111 SGTs with molecular characterization, including 26 SCs (23 with ETV6-NTRK3 fusion and 3 with ETV6-RET fusion detected by ligation-dependent reverse transcription-polymerase chain reaction, next-generation sequencing and 85 non-SC SGTs (no ETV6-NTRK3 fusion). Immunohistochemistry was performed with a pan-TRK rabbit monoclonal antibody. When any pan-TRK staining (nuclear or cytoplasmic with any staining intensity) was considered to indicate positivity, 22 of 23 SCs with ETV6-NTRK3 fusion (95.7%) and 33 of 85 non-SC (38.8%) salivary neoplasms were positive, mainly basal cell adenoma, pleomorphic adenomas, adenoid cystic carcinomas, and epithelial-myoepithelial carcinomas. All SCs with ETV6-RET fusion were entirely negative. When only nuclear pan-TRK staining with any staining intensity was considered positive, 18 of 23 SCs with ETV6-NTRK3 fusion (78.3%) were positive, 11 among them with diffuse staining (>30% of cells). All non-SCs and SCs with ETV6-RET fusion were entirely negative. In comparison to molecular analysis (ligation-dependent reverse transcription-polymerase chain reaction, next-generation sequencing), nuclear pan-TRK IHC has a sensitivity of 78.3% and a specificity of 100% for diagnosing SCs with ETV6-NTRK3 fusion, 69% and 100% for SCs (all fusions). Pan-TRK is a reasonable screening test for diagnosing SCs among SGTs when taking only nuclear staining into account. Although pan-TRK expression is not entirely sensitive for SCs, nuclear staining is highly specific for SCs with ETV6-NTRK3 fusion. The lack of pan-TRK immunoreactivity in a subset of SCs is suggestive of atypical exons 4 to 14 or exons 5 to 14 ETV6-NTRK3 fusion or non-NTRK alternative fusion partners such as ETV6-RET. Pan-TRK staining can serve as a strong diagnostic marker to distinguish SC from it mimics and to select patients eligible for TRK inhibitor clinical trials.
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Affiliation(s)
| | | | | | | | | | - Didier Meseure
- Platform of Experimental Pathology, Department of Diagnostic and Theranostic Medicine, Curie Institute
| | | | - Michel Wassef
- Department of Pathology, Lariboisière Hospital, Paris, France
| | | | - Marick Laé
- Department of Pathology, Centre Henri Becquerel
- INSERM 1245, Rouen Normandy Uniiversity
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15
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Gros A, Menguy S, Bobée V, Ducharme O, Cassaigne IC, Vergier B, Parrens M, Beylot-Barry M, Pham-Ledard A, Ruminy P, Jardin F, Merlio JP. Classification of primary cutaneous large B-cell lymphomas according to cell of origin is clinically relevant. Eur J Cancer 2021. [DOI: 10.1016/s0959-8049(21)00675-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Dubois S, Ruminy P, Bohers E, Viailly P, Veresezan L, Picquenot J, Bobée V, Viennot M, Penther D, Camus V, Thieblemont C, Pouaty C, Tilly H, Jardin F. Concomitant occurrence of genetically distinct Hodgkin lymphoma and primary mediastinal lymphoma. Clin Case Rep 2021; 9:e04504. [PMID: 34429980 PMCID: PMC8365538 DOI: 10.1002/ccr3.4504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Sydney Dubois
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Philippe Ruminy
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Elodie Bohers
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | | | - Liana Veresezan
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | | | | | - Mathieu Viennot
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Dominique Penther
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Vincent Camus
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | | | - Camille Pouaty
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Hervé Tilly
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
| | - Fabrice Jardin
- Department of Clinical HematologyCentre Henri Becquerel, INSERM U1245RouenFrance
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17
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Drieux F, Ruminy P, Sater V, Marchand V, Fataccioli V, Lanic MD, Viennot M, Viailly PJ, Sako N, Robe C, Dupuy A, Vallois D, Veresezan L, Poullot E, Picquenot JM, Bossard C, Parrens M, Lemonnier F, Jardin F, de Leval L, Gaulard P. Detection of Gene Fusion Transcripts in Peripheral T-Cell Lymphoma Using a Multiplexed Targeted Sequencing Assay. J Mol Diagn 2021; 23:929-940. [PMID: 34147695 DOI: 10.1016/j.jmoldx.2021.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022] Open
Abstract
The genetic basis of peripheral T-cell lymphoma (PTCL) is complex and encompasses several recurrent fusion transcripts discovered over the past years by means of massive parallel sequencing. However, there is currently no affordable and rapid technology for their simultaneous detection in clinical samples. Herein, we developed a multiplex ligation-dependent RT-PCR-based assay, followed by high-throughput sequencing, to detect 33 known PTCL-associated fusion transcripts. Anaplastic lymphoma kinase (ALK) fusion transcripts were detected in 15 of 16 ALK-positive anaplastic large-cell lymphomas. The latter case was further characterized by a novel SATB1_ALK fusion transcript. Among 239 other PTCLs, representative of nine entities, non-ALK fusion transcripts were detected in 24 samples, mostly of follicular helper T-cell (TFH) derivation. The most frequent non-ALK fusion transcript was ICOS_CD28 in nine TFH-PTCLs, one PTCL not otherwise specified, and one adult T-cell leukemia/lymphoma, followed by VAV1 rearrangements with multiple partners (STAP2, THAP4, MYO1F, and CD28) in five samples (three PTCL not otherwise specified and two TFH-PTCLs). The other rearrangements were CTLA4_CD28 (one TFH-PTCL), ITK_SYK (two TFH-PTCLs), ITK_FER (one TFH-PTCL), IKZF2_ERBB4 (one TFH-PTCL and one adult T-cell leukemia/lymphoma), and TP63_TBL1XR1 (one ALK-negative anaplastic large-cell lymphoma). All fusions detected by our assay were validated by conventional RT-PCR and Sanger sequencing in 30 samples with adequate material. The simplicity and robustness of this targeted multiplex assay make it an attractive tool for the characterization of these heterogeneous diseases.
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Affiliation(s)
- Fanny Drieux
- INSERM U1245, Centre Henri Becquerel, Rouen, France; Pathology Department, Centre Henri Becquerel, Rouen, France; INSERM U955, Université Paris-Est, Créteil, France
| | | | | | | | - Virginie Fataccioli
- INSERM U955, Université Paris-Est, Créteil, France; Pathology Department, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | | | | | | | - Nouhoum Sako
- INSERM U955, Université Paris-Est, Créteil, France
| | | | | | - David Vallois
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | - Elsa Poullot
- INSERM U955, Université Paris-Est, Créteil, France; Pathology Department, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | | | | | - Marie Parrens
- Pathology Department, Hôpital Haut-Lévêque, Bordeaux, France
| | - François Lemonnier
- INSERM U955, Université Paris-Est, Créteil, France; Hematology Department, Lymphoma Unit, Henri Mondor Hospital, Public Assistance Hospital of Paris, Créteil, France
| | | | - Laurence de Leval
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Philippe Gaulard
- INSERM U955, Université Paris-Est, Créteil, France; Pathology Department, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France.
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18
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Piton N, Lanic MD, Marguet F, Lamy A, Blanchard F, Guisier F, Viennot M, Salaün M, Thiberville L, Jardin F, Sabourin JC, Ruminy P. An improved assay for detection of theranostic gene translocations and MET exon 14 skipping in thoracic oncology. J Transl Med 2021; 101:648-660. [PMID: 33495574 DOI: 10.1038/s41374-021-00536-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 01/15/2023] Open
Abstract
Theranostic translocations may be difficult to detect by routine techniques, especially when specimens are exiguous. We recently demonstrated in a series of translocated lung adenocarcinomas that LD-RT-PCR (ligation-dependent reverse transcription polymerase chain reaction) assay could identify ALK, ROS1 and RET rearrangements with 64% sensitivity and 100% specificity. Here, we report an upgraded version of this assay used in a routine prospective cohort of lung carcinomas. Newly diagnosed lung carcinomas referred to the Rouen molecular platform between 15/05/2018 and 15/05/2019 for ALK and ROS1 IHC, genotyping (SNaPshot© +/- high-throughput genotyping) and sometimes FISH (standard routine process) were tested prospectively in parallel with the LD-RT-PCR assay designed to detect at one go ALK, ROS1 and RET translocations and MET exon 14 skipping. 413 tumors from 396 patients were included. LD-RT-PCR had a global sensitivity of 91.43% (standard routine process: 80%), with a specificity of 100%. It detected 15/18 ALK and 4/4 ROS1 translocated tumors, but also 6/6 tumors with MET exon 14 skipping retrieved by genotyping. In addition, it retrieved 7 alterations missed by the routine process, then confirmed by other means: 5 MET exon 14 skipping and 2 RET translocated tumors. Finally, it allowed to deny an effect on MET exon 14 skipping for 8 mutations detected by routine genotyping. We successfully implemented LD-RT-PCR in routine analysis. This technique is cheap, fast, sensitive, specific, and easily upgradable (e.g., NTRK translocations), but still requires IHC to be performed in parallel. Owing to its advantages, we recommend considering it, in parallel with IHC and genotyping, as an excellent cost-effective alternative, for the systematic testing of lung adenocarcinoma, to FISH and to more expensive and complex assays such as RNA-seq.
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Affiliation(s)
- Nicolas Piton
- Normandie Univ, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Pathology, F76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France, F-76000, Rouen, France.
| | - Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, Rouen, France
| | - Florent Marguet
- Normandie Univ, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Pathology, F76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France, F-76000, Rouen, France
| | - Aude Lamy
- Normandie Univ, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Pathology, F76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France, F-76000, Rouen, France
| | - France Blanchard
- Normandie Univ, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Pathology, F76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France, F-76000, Rouen, France
| | - Florian Guisier
- Normandie Univ, UNIROUEN, EA4108 LITIS lab, CHU Rouen, Department of Pneumology and Inserm CIC-CRB 1404, F-76000, Rouen, France
| | - Mathieu Viennot
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, Rouen, France
| | - Mathieu Salaün
- Normandie Univ, UNIROUEN, EA4108 LITIS lab, CHU Rouen, Department of Pneumology and Inserm CIC-CRB 1404, F-76000, Rouen, France
| | - Luc Thiberville
- Normandie Univ, UNIROUEN, EA4108 LITIS lab, CHU Rouen, Department of Pneumology and Inserm CIC-CRB 1404, F-76000, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, Rouen, France
| | - Jean-Christophe Sabourin
- Normandie Univ, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Pathology, F76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France, F-76000, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, Rouen, France
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19
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Viailly PJ, Sater V, Viennot M, Bohers E, Vergne N, Berard C, Dauchel H, Lecroq T, Celebi A, Ruminy P, Marchand V, Lanic MD, Dubois S, Penther D, Tilly H, Mareschal S, Jardin F. Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. BMC Bioinformatics 2021; 22:120. [PMID: 33711922 PMCID: PMC7971104 DOI: 10.1186/s12859-021-04060-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
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.
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Affiliation(s)
- Pierre-Julien Viailly
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France. .,Centre Henri Becquerel, Rouen, France.
| | - Vincent Sater
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France.,LITIS EA 4108, Normandie Univ, UNIROUEN, Rouen, France
| | - Mathieu Viennot
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Elodie Bohers
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | | | | | | | | | - Alison Celebi
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France.,Master Bioinformatique BIM, Normandie Univ, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Vinciane Marchand
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Marie-Delphine Lanic
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Sydney Dubois
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Dominique Penther
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
| | - Sylvain Mareschal
- INSERM U1052 UMR CNRS 5286, Cancer Research Center of Lyon, Lyon, France
| | - Fabrice Jardin
- INSERM U1245, Team Genomics and Biomarkers of Lymphoma and Solid Tumors, Normandie Univ, UNIROUEN, Rouen, France.,Centre Henri Becquerel, Rouen, France
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20
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Oberic L, Peyrade F, Puyade M, Bonnet C, Dartigues-Cuillères P, Fabiani B, Ruminy P, Maisonneuve H, Abraham J, Thieblemont C, Feugier P, Salles G, Bijou F, Pica GM, Damaj G, Haioun C, Casasnovas RO, Farhat H, Le Calloch R, Waultier-Rascalou A, Malak S, Paget J, Gat E, Tilly H, Jardin F. Subcutaneous Rituximab-MiniCHOP Compared With Subcutaneous Rituximab-MiniCHOP Plus Lenalidomide in Diffuse Large B-Cell Lymphoma for Patients Age 80 Years or Older. J Clin Oncol 2021; 39:1203-1213. [PMID: 33444079 DOI: 10.1200/jco.20.02666] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE The prognosis of elderly patients with diffuse large B-cell lymphoma (DLBCL) is worse than that of young patients. An attenuated dose of chemotherapy-cyclophosphamide, doxorubicin, vincristine, and prednisone plus rituximab (R-miniCHOP)-is a good compromise between efficacy and safety in very elderly patients. In combination with R-CHOP (R2-CHOP), lenalidomide has an acceptable level of toxicity and may mitigate the negative prognosis of the non-germinal center B-cell-like phenotype. The Lymphoma Study association conducted a multicentric, phase III, open-label, randomized trial to compare R-miniCHOP and R2-miniCHOP. PATIENTS AND METHODS Patients of age 80 years or older with untreated DLBCL were randomly assigned into the R-miniCHOP21 group or the R2-miniCHOP21 group for six cycles and stratified according to CD10 expression and age. The first cycle of rituximab was delivered by IV on D1 after a prephase and then delivered subcutaneously on D1 of cycles 2-6. Lenalidomide was delivered at a dose of 10 mg once daily on D1-D14 of each cycle. The primary end point was overall survival (OS). RESULTS A total of 249 patients with new DLBCL were randomly assigned (127 R-miniCHOP and 122 R2-miniCHOP). The median age was 83 years (range, 80-96), and 55% of the patients were classified as non-GCB. The delivered dose for each R-miniCHOP compound was similar in both arms. Over a median follow-up of 25.1 months, the intention-to-treat analysis revealed that R2-miniCHOP did not improve OS (2-year OS 66% in R-miniCHOP and 65.7% in R2-miniCHOP arm, P = .98) in the overall population or in the non-GCB population. Grade 3-4 adverse events occurred in 53% of patients with R-miniCHOP and in 81% of patients with R2-miniCHOP. CONCLUSION The addition of lenalidomide to R-miniCHOP does not improve OS. Rituximab delivered subcutaneously was safe in this population.
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Affiliation(s)
- Lucie Oberic
- Department of Hematology, Institut Universitaire du Cancer, Toulouse-Oncopole, Toulouse, France
| | - Frederic Peyrade
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | - Mathieu Puyade
- Department of Oncology-Haematology and Cell Therapy, CHU, Poitiers, INSERM, Inserm CIC 1402, Poitiers, France
| | - Christophe Bonnet
- Clinical Hematology Unit, CHU Liège, Liège Université, Campus Universitaire de Sart Tilman, Liège, Belgique
| | - Peggy Dartigues-Cuillères
- Anapath Research Unit (EA) EA4340 and Pathology Laboratory, Versailles University and APHP, Ambroise Paré Hospital, Boulogne, France
| | - Bettina Fabiani
- Department of Pathology, Hopital Saint-Antoine, APHP, Paris, France
| | | | - Hervé Maisonneuve
- Department of Clinical Hematology, Centre Hospitalier Départemental Vendée, La Roche-sur-Yon, France
| | - Julie Abraham
- Department of Hematology, CHU Dupuytren, Limoges, France
| | - Catherine Thieblemont
- APHP, Hopital Saint-Louis, Hemato-oncologie; Université de Paris, Paris Diderot, Paris, France
| | - Pierre Feugier
- Department of Haematology, Centre Hospitalier Régional Universitaire de Nancy, Vandoeuvre Les Nancy, France
| | - Gilles Salles
- Department of Hematology, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Benite, France
| | - Fontanet Bijou
- Department of Hematology, Hospital Bergonié, Bordeaux, France
| | - Gian-Matteo Pica
- Department of Hematology, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Gandhi Damaj
- Department of Hematology, CHU Caen, Caen, France
| | - Corinne Haioun
- Department of Hematology, Henri Mondor University Hospital, UPEC, Creteil, France
| | | | - Hassan Farhat
- Department of Hematology, Centre Hospitalier de Versailles André Mignot, Versailles, France
| | - Ronan Le Calloch
- Centre hospitalier de Quimper Cornouaille/Université de Bretagne Occidentale, France
| | | | - Sandra Malak
- Department of Hematology, CLCC Rene Huguenin Institut Curie, Saint-Cloud, France
| | - Jerome Paget
- LYSARC, The Lymphoma Academic Research Organisation, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
| | - Elodie Gat
- LYSARC, The Lymphoma Academic Research Organisation, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
| | - Hervé Tilly
- Department of Hematology, Centre Henri Becquerel, UNIROUEN, University of Normandy, INSERM U1245, Rouen, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, UNIROUEN, University of Normandy, INSERM U1245, Rouen, France
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21
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Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. Bioinformatics 2020; 36:2718-2724. [PMID: 31985795 DOI: 10.1093/bioinformatics/btaa053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/18/2019] [Accepted: 01/20/2020] [Indexed: 01/03/2023] Open
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.
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Affiliation(s)
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | | | | | - Élodie Bohers
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Mathieu Viennot
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Hélène Dauchel
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
| | - Pierre Vera
- University of Normandie UNIROUEN, LITIS EA 4108.,Department of Pathology, Centre Henri Becquerel
| | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel.,INSERM U1245, University of Normandie UNIROUEN, Rouen 76000, France
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22
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Decazes P, Camus V, Bohers E, Viailly PJ, Tilly H, Ruminy P, Viennot M, Hapdey S, Gardin I, Becker S, Vera P, Jardin F. Correlations between baseline 18F-FDG PET tumour parameters and circulating DNA in diffuse large B cell lymphoma and Hodgkin lymphoma. EJNMMI Res 2020; 10:120. [PMID: 33029662 PMCID: PMC7541805 DOI: 10.1186/s13550-020-00717-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
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 < 0.001 for [ctDNA] of DLBLC), the tumour median distance between the periphery and the centroid (medPCD) describing the tumour’s massiveness (e.g. ρ = 0.81 p < 0.001 for [ctDNA] of DLBLC) and the volume of the bounding box including tumours (TumBB) describing the disease’s dispersion (e.g. ρ = 0.83 p < 0.001 for [ctDNA] of DLBLC). Conclusions Some PET parameters describing tumour burden, fragmentation/massiveness and dispersion are significantly correlated with circulating DNA parameters of DLBCL and cHL patients. These results could help to understand the pathophysiology of B cell malignancies.
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Affiliation(s)
- Pierre Decazes
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France. .,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France.
| | - Vincent Camus
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Elodie Bohers
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Pierre-Julien Viailly
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Hervé Tilly
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Philippe Ruminy
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Mathieu Viennot
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Sébastien Hapdey
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Isabelle Gardin
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Stéphanie Becker
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Pierre Vera
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Fabrice Jardin
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
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23
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Sater V, Viailly PJ, Lecroq T, Ruminy P, Bérard C, Prieur-Gaston É, Jardin F. UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries. Comput Struct Biotechnol J 2020; 18:2270-2280. [PMID: 32952940 PMCID: PMC7484502 DOI: 10.1016/j.csbj.2020.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 11/02/2022] Open
Abstract
Motivation With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. Multiple variant callers are publicly available and are usually efficient at calling out variants. However, when frequencies begin to drop under 1%, the specificity of these tools suffers greatly as true variants at very low frequencies can be easily confused with sequencing or PCR artifacts. The recent use of Unique Molecular Identifiers (UMI) in NGS experiments has offered a way to accurately separate true variants from artifacts. UMI-based variant callers are slowly replacing raw-read based variant callers as the standard method for an accurate detection of variants at very low frequencies. However, benchmarking done in the tools publication are usually realized on real biological data in which real variants are not known, making it difficult to assess their accuracy. Results We present UMI-Gen, a UMI-based read simulator for targeted sequencing paired-end data. UMI-Gen generates reference reads covering the targeted regions at a user customizable depth. After that, using a number of control files, it estimates the background error rate at each position and then modifies the generated reads to mimic real biological data. Finally, it will insert real variants in the reads from a list provided by the user. Availability The entire pipeline is available at https://gitlab.com/vincent-sater/umigen under MIT license.
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Affiliation(s)
- Vincent Sater
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Pierre-Julien Viailly
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Thierry Lecroq
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France
| | - Philippe Ruminy
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
| | - Caroline Bérard
- University of Rouen Normandy UNIROUEN, LITIS EA 4108, 76000 Rouen, France
| | | | - Fabrice Jardin
- Department of Pathology, Centre Henri Becquerel, 76000 Rouen, France.,INSERM U1245, University of Rouen Normandy UNIROUEN, 76000 Rouen, France
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24
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Fontanilles M, Marguet F, Ruminy P, Basset C, Noel A, Beaussire L, Viennot M, Viailly PJ, Cassinari K, Chambon P, Richard D, Alexandru C, Tennevet I, Langlois O, Di Fiore F, Laquerrière A, Clatot F, Sarafan-Vasseur N. Simultaneous detection of EGFR amplification and EGFRvIII variant using digital PCR-based method in glioblastoma. Acta Neuropathol Commun 2020; 8:52. [PMID: 32303258 PMCID: PMC7165387 DOI: 10.1186/s40478-020-00917-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/13/2020] [Indexed: 12/20/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) amplification and EGFR variant III (EGFRvIII, deletion of exons 2-7) are of clinical interest for glioblastoma. The aim was to develop a digital PCR (dPCR)-based method using locked nucleic acid (LNA)-based hydrolysis probes, allowing the simultaneous detection of the EGFR amplification and EGFRvIII variant. Sixty-two patients were included. An exploratory cohort (n = 19) was used to develop the dPCR assay using three selected amplicons within the EGFR gene, targeting intron 1 (EGFR1), junction of exon 3 and intron 3 (EGFR2) and intron 22 (EGFR3). The copy number of EGFR was estimated by the relative quantification of EGFR1, EGFR2 and EGFR3 amplicon droplets compared to the droplets of a reference gene. EGFRvIII was identified by comparing the copy number of the EGFR2 amplicon to either the EGFR1 or EGFR3 amplicon. dPCR results were compared to fluorescence in situ hybridization (FISH) and next-generation sequencing for amplification; and to RT-PCR-based method for EGFRvIII. The dPCR assay was then tested in a validation cohort (n = 43). A total of 8/19 EGFR-amplified and 5/19 EGFRvIII-positive tumors were identified in the exploratory cohort. Compared to FISH, the EGFR3 dPCR assay detected all EGFR-amplified tumors (8/8, 100%) and had the highest concordance with the copy number estimation by NGS. The concordance between RT-PCR and dPCR was also 100% for detecting EGFRvIII using an absolute difference of 10.8 for the copy number between EGFR2 and EGFR3 probes. In the validation cohort, the sensitivity and specificity of dPCR using EGFR3 probes were 100% for the EGFR amplification detection compared to FISH (19/19). EGFRvIII was detected by dPCR in 8 EGFR-amplified patients and confirmed by RT-PCR. Compared to FISH, the EGFR2/EGFR3 dPCR assay was estimated with a one-half cost value. These results highlight that dPCR allowed the simultaneous detection of EGFR amplification and EGFRvIII for glioblastoma.
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25
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Ducourneau B, Fenwarth L, Duployez N, Lambert J, Struski S, Luquet I, Daudignon A, Helevaut N, Ruminy P, Preudhomme C, Terre C. Cytogenetically masked CBFB-MYH11 fusion and concomitant TP53 deletion in a case of acute myeloid leukemia with a complex karyotype. Leuk Lymphoma 2020; 61:1772-1774. [PMID: 32223488 DOI: 10.1080/10428194.2020.1742905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Benoît Ducourneau
- Chu de Lille, Laboratory of Hematology, Lille, France.,Laboratory of Hematology, Centre Hospitalier de Valenciennes, Valenciennes, France
| | - Laurène Fenwarth
- Chu de Lille, Laboratory of Hematology, Lille, France.,University of Lille, CNRS, INSERM, Lille, France
| | - Nicolas Duployez
- Chu de Lille, Laboratory of Hematology, Lille, France.,University of Lille, CNRS, INSERM, Lille, France
| | - Juliette Lambert
- Department of Hematology, Centre Hospitalier de Versailles, Le Chesnay, France
| | | | | | | | - Nathalie Helevaut
- Chu de Lille, Laboratory of Hematology, Lille, France.,University of Lille, CNRS, INSERM, Lille, France
| | - Philippe Ruminy
- Institute for Research and Innovation in Biomedicine, Centre Henri Becquerel and Rouen University, Rouen, France
| | - Claude Preudhomme
- Chu de Lille, Laboratory of Hematology, Lille, France.,University of Lille, CNRS, INSERM, Lille, France
| | - Christine Terre
- Laboratory of Hematology, Centre Hospitalier deVersailles, Le Chesnay, France.,Laboratory of Cytogenetics, Centre Hospitalier deVersailles, Le Chesnay, France
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26
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Adam N, Coutance G, Viailly PJ, Drieux F, Ruminy P, Sater AA, Toquet C, Rouvier P, François A, Chenard MP, Epailly E, Guillemain R, Pattier S, Gay A, Varnous S, Taupin JL, Rabant M, Loupy A, Bruneval P, Duong Van Huyen JP. Reverse transcriptase multiplex ligation-dependent probe amplification in endomyocardial biopsies for the diagnosis of cardiac allograft rejection. J Heart Lung Transplant 2020; 39:115-124. [DOI: 10.1016/j.healun.2019.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022] Open
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27
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Dubois S, Tesson B, Mareschal S, Viailly PJ, Bohers E, Ruminy P, Etancelin P, Peyrouze P, Copie-Bergman C, Fabiani B, Petrella T, Jais JP, Haioun C, Salles G, Molina TJ, Leroy K, Tilly H, Jardin F. Refining diffuse large B-cell lymphoma subgroups using integrated analysis of molecular profiles. EBioMedicine 2019; 48:58-69. [PMID: 31648986 PMCID: PMC6838437 DOI: 10.1016/j.ebiom.2019.09.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 12/23/2022] Open
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.
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Affiliation(s)
- Sydney Dubois
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Sylvain Mareschal
- Cancer Research Center of Lyon, INSERM U1052 UMR CNRS 5286, Lyon, France
| | - Pierre-Julien Viailly
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France; Normandie Univ, EdN BISE 497, Normandy, France
| | - Elodie Bohers
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Ruminy
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Pascaline Etancelin
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Christiane Copie-Bergman
- Department of Pathology, Henri Mondor Hospital, APHP, INSERM U955, Université Paris-Est, Créteil, France
| | - Bettina Fabiani
- Laboratoire de Pathologie, AP-HP Hôpital Saint Antoine, Paris, France
| | - Tony Petrella
- Department of Pathology, Hôpital Maisonneuve-Rosemont, Montréal, Quebec, Canada
| | - Jean-Philippe Jais
- Institut Imagine HGID, Inserm U1163, AP-HP Hôpital Necker, Université Paris Descartes, Paris, France
| | - Corinne Haioun
- Unité Hémopathies Lymphoïdes, AP-HP Hôpital Henri Mondor, Créteil, France
| | - Gilles Salles
- Cancer Research Center of Lyon, INSERM U1052 UMR CNRS 5286, Lyon, France
| | - Thierry Jo Molina
- Pathology, AP-HP, Hôpital Necker, Université Paris Descartes, Paris, France
| | - Karen Leroy
- Inserm U1016 - CNRS UMR8104 - Université Paris Descartes Groupe Hospitalier Cochin, Paris, France
| | - Hervé Tilly
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Fabrice Jardin
- Inserm U1245, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.
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28
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Drieux F, Ruminy P, Abdel-Sater A, Lemonnier F, Viailly PJ, Fataccioli V, Marchand V, Bisig B, Letourneau A, Parrens M, Bossard C, Bruneau J, Dobay P, Veresezan L, Dupuy A, Pujals A, Robe C, Sako N, Copie-Bergman C, Delfau-Larue MH, Picquenot JM, Tilly H, Delarue R, Jardin F, de Leval L, Gaulard P. Defining signatures of peripheral T-cell lymphoma with a targeted 20-marker gene expression profiling assay. Haematologica 2019; 105:1582-1592. [PMID: 31488561 PMCID: PMC7271600 DOI: 10.3324/haematol.2019.226647] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022] Open
Abstract
Peripheral T-cell lymphoma comprises a heterogeneous group of mature non-Hodgkin lymphomas. Their diagnosis is challenging, with up to 30% of cases remaining unclassifiable and referred to as “not otherwise specified”. We developed a reverse transcriptase-multiplex ligation-dependent probe amplification gene expression profiling assay to differentiate the main T-cell lymphoma entities and to study the heterogeneity of the “not specified” category. The test evaluates the expression of 20 genes, including 17 markers relevant to T-cell immunology and lymphoma biopathology, one Epstein-Barr virus-related transcript, and variants of RHOA (G17V) and IDH2 (R172K/T). By unsupervised hierarchical clustering, our assay accurately identified 21 of 21 ALK-positive anaplastic large cell lymphomas, 16 of 16 extranodal natural killer (NK)/T-cell lymphomas, 6 of 6 hepatosplenic T-cell lymphomas, and 13 of 13 adult T-cell leukemia/lymphomas. ALK-negative anaplastic lymphomas (n=34) segregated into one cytotoxic cluster (n=10) and one non-cytotoxic cluster expressing Th2 markers (n=24) and enriched in DUSP22-rearranged cases. The 63 TFH-derived lymphomas divided into two subgroups according to a predominant TFH (n=50) or an enrichment in Th2 (n=13) signatures. We next developed a support vector machine predictor which attributed a molecular class to 27 of 77 not specified T-cell lymphomas: 17 TFH, five cytotoxic ALK-negative anaplastic and five NK/T-cell lymphomas. Among the remaining cases, we identified two cell-of-origin subgroups corresponding to cytotoxic/Th1 (n=19) and Th2 (n=24) signatures. A reproducibility test on 40 cases yielded a 90% concordance between three independent laboratories. This study demonstrates the applicability of a simple gene expression assay for the classification of peripheral T-cell lymphomas. Its applicability to routinely-fixed samples makes it an attractive adjunct in diagnostic practice.
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Affiliation(s)
- Fanny Drieux
- INSERM U1245, Centre Henri Becquerel, Rouen, France.,Service d'Anatomie et Cytologie Pathologiques, Centre Henri Becquerel, Rouen, France.,INSERM U955 and Université Paris-Est, Créteil, France
| | | | | | - François Lemonnier
- INSERM U955 and Université Paris-Est, Créteil, France.,Unité Hémopathies Lymphoïdes, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | | | | | | | - Bettina Bisig
- Institut de Pathologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Audrey Letourneau
- Institut de Pathologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Marie Parrens
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Haut-Lévêque, CHU de Bordeaux, France
| | - Céline Bossard
- Service d'Anatomie et Cytologie Pathologiques, CHU de Nantes, France
| | - Julie Bruneau
- Service d'Anatomie et Cytologie Pathologiques, Hôpital Universitaire Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Pamela Dobay
- Institut de Pathologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Liana Veresezan
- INSERM U1245, Centre Henri Becquerel, Rouen, France.,Service d'Anatomie et Cytologie Pathologiques, Centre Henri Becquerel, Rouen, France
| | - Aurélie Dupuy
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Anaïs Pujals
- INSERM U955 and Université Paris-Est, Créteil, France.,Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | - Cyrielle Robe
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Nouhoum Sako
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Christiane Copie-Bergman
- INSERM U955 and Université Paris-Est, Créteil, France.,Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | - Marie-Hélène Delfau-Larue
- INSERM U955 and Université Paris-Est, Créteil, France.,Département d'Hématologie et Immunologie Biologique, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
| | - Jean-Michel Picquenot
- INSERM U1245, Centre Henri Becquerel, Rouen, France.,Service d'Anatomie et Cytologie Pathologiques, Centre Henri Becquerel, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - Richard Delarue
- Service Hématologie Adultes, Hôpital Universitaire Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | | | - Laurence de Leval
- Institut de Pathologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Philippe Gaulard
- INSERM U955 and Université Paris-Est, Créteil, France .,Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
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29
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Bossard C, Laghmari O, Le Bris Y, Bonnet A, Moreau A, El Alami Thomas W, Pavageau A, Guerzider P, Maisonneuve H, Ruminy P, Bene M, Casasnovas O, Canioni D, Thieblemont C, Petrella T, Jardin F, Salles G, Tilly H, Gaulard P, Haioun C, Brière J, Le Gouill S, Copie Bergman C, Molina T. REFINEMENT OF MUM1 EXPRESSION THRESHOLD FOR DOUBLE POSITIVE CD10+ MUM1+ DIFFUSE LARGE B CELL LYMPHOMA ALLOWS A BETTER CELL OF ORIGIN CLASSIFICATION FOR GCB SUBTYPE. Hematol Oncol 2019. [DOI: 10.1002/hon.11_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- C. Bossard
- Department of Pathology; University Hospital of Nantes; Nantes France
| | - O. Laghmari
- Department of Pathology; University Hospital of Nantes; Nantes France
| | - Y. Le Bris
- Department of Hematology Biology; University Hospital of Nantes; Nantes France
| | - A. Bonnet
- Department of Hematology; University Hospital of Nantes; Nantes France
| | - A. Moreau
- Department of Pathology; University Hospital of Nantes; Nantes France
| | | | - A. Pavageau
- Department of Pathology; Centre Hospitalier de la Roche sur Yon; La Roche sur Yon France
| | - P. Guerzider
- Department of Pathology; Centre Hospitalier de Saint Nazaire; Saint Nazaire France
| | - H. Maisonneuve
- Department of Hematology; Centre Hospitalier de la Roche sur Yon; La Roche sur Yon France
| | - P. Ruminy
- INSERM U918; Centre Henri Becquerel; Rouen France
| | - M. Bene
- Department of Hematology Biology; University Hospital of Nantes; Nantes France
| | - O. Casasnovas
- Department of Hematology; University Hospital; Dijon France
| | - D. Canioni
- Department of Pathology; Hopital Necker Enfants Malades; Paris France
| | - C. Thieblemont
- Hemato-oncology Department; Hopital Saint Louis; Paris France
| | - T. Petrella
- Department of Medical Oncology; Odette Cancer Center; Toronto Canada
| | - F. Jardin
- Department of Hematology; Centre Henri Becquerel; Rouen France
| | - G. Salles
- Department of Hematology; Hospice Civils de Lyon; Lyon France
| | - H. Tilly
- Department of Hematology; Centre Henri Becquerel; Rouen France
| | - P. Gaulard
- Department of Pathology; Groupe Hospitalier Henri Mondor; Creteil France
| | - C. Haioun
- Department of Hematology; Groupe Hospitalier Henri Mondor; Creteil France
| | - J. Brière
- Hemato-oncology Department; Hopital Saint Louis; Paris France
| | - S. Le Gouill
- Department of Hematology; University Hospital of Nantes; Nantes France
| | - C. Copie Bergman
- Department of Pathology; Groupe Hospitalier Henri Mondor; Creteil France
| | - T.J. Molina
- Department of Pathology; Hopital Necker Enfants Malades; Paris France
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30
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Penther D, Viailly PJ, Latour S, Etancelin P, Bohers E, Vellemans H, Camus V, Menard AL, Coutant S, Lanic H, Lemasle E, Drieux F, Veresezan L, Ruminy P, Raimbault A, Soulier J, Frebourg T, Tilly H, Jardin F. A recurrent clonally distinct Burkitt lymphoma case highlights genetic key events contributing to oncogenesis. Genes Chromosomes Cancer 2019; 58:595-601. [PMID: 30779244 PMCID: PMC6790587 DOI: 10.1002/gcc.22743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/07/2023] Open
Abstract
Burkitt lymphoma (BL) is characterized by a translocation of the MYC oncogene that leads to the upregulation of MYC expression, cell growth and proliferation. It is well-established that MYC translocation is not a sufficient genetic event to cause BL. Next-generation sequencing has recently provided a comprehensive analysis of the landscape of additional genetic events that contribute to BL lymphomagenesis. Refractory BL or relapsing BL are almost always incurable as a result of the selection of a highly chemoresistant clonally related cell population. Conversely, a few BL recurrence cases arising from clonally distinct tumors have been reported and were associated with a favorable outcome similar to that reported for first-line treatment. Here, we used an unusual case of recurrent but clonally distinct EBV+ BL to highlight the key genetic events that drive BL lymphomagenesis. By whole exome sequencing, we established that ID3 gene was targeted by distinct mutations in the two clonally unrelated diseases, highlighting the crucial role of this gene during lymphomagenesis. We also detected a heterozygous E1021K PIK3CD mutation, thus increasing the spectrum of somatic mutations altering the PI3K signaling pathway in BL. Interestingly, this mutation is known to be associated with activated phosphoinositide 3-kinase delta syndrome (APDS). Finally, we also identified an inherited heterozygous truncating c.5791CT FANCM mutation that may contribute to the unusual recurrence of BL.
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Affiliation(s)
| | | | - Sylvain Latour
- INSERM UMR_S1163, Institut Imagine Université Paris Descartes, Paris, France
| | | | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | - Hélène Vellemans
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Vincent Camus
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Anne Lise Menard
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Sophie Coutant
- Department of Genetics, Rouen University Hospital, F76000 and Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Hélène Lanic
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Emilie Lemasle
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fanny Drieux
- Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Liana Veresezan
- Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | - Anna Raimbault
- INSERM U944/CNRS UMR7212, Saint Louis Hospital, Paris, France
| | - Jean Soulier
- INSERM U944/CNRS UMR7212, Saint Louis Hospital, Paris, France
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital, F76000 and Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France.,Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France.,Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
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Houot R, Cartron G, Bijou F, de Guibert S, Salles GA, Fruchart C, Bouabdallah K, Maerevoet M, Feugier P, Le Gouill S, Tilly H, Casasnovas RO, Moluçon-Chabrot C, Van Den Neste E, Zachee P, Andre M, Bonnet C, Haioun C, Van Hoof A, Van Eygen K, Molina L, Nicolas-Virelizier E, Ruminy P, Morschhauser F. Obinutuzumab plus Lenalidomide (GALEN) for the treatment of relapse/refractory aggressive lymphoma: a phase II LYSA study. Leukemia 2018; 33:776-780. [PMID: 30291335 DOI: 10.1038/s41375-018-0282-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Roch Houot
- Department of Clinical Hematology, University Hospital of Rennes, Inserm 0203, University of Rennes, Rennes, France
| | - Guillaume Cartron
- Department of Clinical Hematology, University Hospital of Montpellier, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | | | - Sophie de Guibert
- Department of Clinical Hematology, University Hospital of Rennes, Inserm 0203, University of Rennes, Rennes, France
| | - Gilles A Salles
- Department of Hematology, Centre Hospitalier Lyon-Sud, Pierre Benite, France
| | | | | | | | - Pierre Feugier
- CHU et INSERM 954, Nancy Université, Vandoeuvre Les Nancy, France
| | - Steven Le Gouill
- Department of Hematology, Nantes University Hospital and UMR892 INSERM, Nantes, France
| | - Hervé Tilly
- Centre Henri Becquerel, Inserm U918, Université de Rouen, IRIB, Rouen, France
| | | | | | - Eric Van Den Neste
- Department of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | | | - Marc Andre
- Hematology Department, CHU UCL NAMUR, Yvoir, Belgium
| | | | - Corinne Haioun
- Hôpital Henri Mondor, Unité Hémopathies Lymphoide, Créteil, France
| | | | | | | | | | - Philippe Ruminy
- Centre Henri Becquerel, Inserm U918, Université de Rouen, IRIB, Rouen, France
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Bessi L, Viailly PJ, Bohers E, Ruminy P, Maingonnat C, Bertrand P, Vasseur N, Beaussire L, Cornic M, Etancelin P, Camus V, Picquenot JM, Tilly H, Stamatoullas A, Jardin F. Somatic mutations of cell-free circulating DNA detected by targeted next-generation sequencing and digital droplet PCR in classical Hodgkin lymphoma. Leuk Lymphoma 2018; 60:498-502. [DOI: 10.1080/10428194.2018.1492123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Lucile Bessi
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | | | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | | | - Philippe Bertrand
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | | | - Ludivine Beaussire
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
| | - Marie Cornic
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Vincent Camus
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | | | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Aspasia Stamatoullas
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel and Rouen University, Rouen, France
- Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
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33
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Bohers E, Viailly PJ, Becker S, Marchand V, Ruminy P, Maingonnat C, Bertrand P, Etancelin P, Picquenot JM, Camus V, Menard AL, Lemasle E, Contentin N, Leprêtre S, Lenain P, Stamatoullas A, Lanic H, Libraire J, Vaudaux S, Pepin LF, Vera P, Tilly H, Jardin F. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort. Blood Cancer J 2018; 8:74. [PMID: 30069017 PMCID: PMC6070497 DOI: 10.1038/s41408-018-0111-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/28/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Stéphanie Becker
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Vinciane Marchand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Philippe Bertrand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | | | - Vincent Camus
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Anne-Lise Menard
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Emilie Lemasle
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Nathalie Contentin
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Stéphane Leprêtre
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Pascal Lenain
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | | | - Hélène Lanic
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Julie Libraire
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | | | - Pierre Vera
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France.
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France.
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France.
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Mareschal S, Ruminy P, Alcantara M, Villenet C, Figeac M, Dubois S, Bertrand P, Bouzelfen A, Viailly PJ, Penther D, Tilly H, Bastard C, Jardin F. Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. Bioinformatics 2018; 33:2977-2985. [PMID: 28481978 DOI: 10.1093/bioinformatics/btx309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Motivation Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyze such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. Results The cghRA framework combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas. New algorithms for copy-number calling, polymorphism detection and minimal common region prioritization were also developed and validated. While their performances will only be demonstrated with aCGH, these algorithms could actually prove useful to any copy-number analysis, whatever the technique used. Availability and implementation R package and source for Linux, MS Windows and MacOS are freely available at http://bioinformatics.ovsa.fr/cghRA. Contact mareschal@ovsa.fr or fabrice.jardin@chb.unicancer.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylvain Mareschal
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Ruminy
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Marion Alcantara
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Céline Villenet
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France
| | - Martin Figeac
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France.,Cellule de Bioinformatique du Plateau Commun de Séquençage, CHRU de Lille, 59000 Lille, France
| | - Sydney Dubois
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Bertrand
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Abdelilah Bouzelfen
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Pierre-Julien Viailly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Dominique Penther
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Hervé Tilly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France
| | - Christian Bastard
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Fabrice Jardin
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
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Fontanilles M, Marguet F, Bohers É, Viailly PJ, Dubois S, Bertrand P, Camus V, Mareschal S, Ruminy P, Maingonnat C, Lepretre S, Veresezan EL, Derrey S, Tilly H, Picquenot JM, Laquerrière A, Jardin F. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma. Oncotarget 2018. [PMID: 28636991 PMCID: PMC5564634 DOI: 10.18632/oncotarget.18325] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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.
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Affiliation(s)
- Maxime Fontanilles
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Florent Marguet
- INSERM U1245 and Hôpital Charles Nicolle, NeoVasc Team, University of Normandy, UNIVROUEN, CHU-Hôpitaux de Rouen, 76031 Rouen, France.,Department of Neuropathology, Hôpital Charles Nicolle, Normandy Center for Genomic and Personalized Medicine, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Élodie Bohers
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Pierre-Julien Viailly
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Sydney Dubois
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Philippe Bertrand
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Vincent Camus
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Sylvain Mareschal
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Catherine Maingonnat
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Stéphane Lepretre
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France
| | | | - Stéphane Derrey
- Department of Neurosurgery, Hôpital Charles Nicolle, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Hervé Tilly
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | | | - Annie Laquerrière
- INSERM U1245 and Hôpital Charles Nicolle, NeoVasc Team, University of Normandy, UNIVROUEN, CHU-Hôpitaux de Rouen, 76031 Rouen, France.,Department of Neuropathology, Hôpital Charles Nicolle, Normandy Center for Genomic and Personalized Medicine, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Fabrice Jardin
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
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Petrella T, Copie-Bergman C, Brière J, Delarue R, Jardin F, Ruminy P, Thieblemont C, Figeac M, Canioni D, Feugier P, Fabiani B, Leroy K, Parrens M, André M, Haioun C, Salles GA, Gaulard P, Tilly H, Jais JP, Molina TJ. BCL2 expression but not MYC and BCL2 coexpression predicts survival in elderly patients with diffuse large B-cell lymphoma independently of cell of origin in the phase 3 LNH03-6B trial. Ann Oncol 2018; 28:1042-1049. [PMID: 28327893 DOI: 10.1093/annonc/mdx022] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Our aim was to evaluate whether the cell of origin (COO) as defined by the Hans algorithm and MYC/BCL2 coexpression, which are the two main biological risk factors in elderly patients treated with rituximab, cyclophosphamide, doxorubicin hydrochloride, vincristine, and prednisolone (R-CHOP), maintain their prognostic value in a large prospective clinical trial. Patients and methods We evaluated 285 paraffin-embedded samples from patients (60-80 years of age) enrolled in the Lymphoma Study Association trial LNH03-6B who were treated with R-CHOP. We correlated the COO defined by the transcriptome according to the Wright algorithm with that defined by the Hans algorithm in a subset of 62 tumors with available frozen tissue samples. Results The non-germinal center B-cell-like phenotype according to the Hans algorithm and BCL2 expression (but not MYC and BCL2 coexpression) predicted worse progression-free survival [hazard ratio (HR)=1.78, P = 0.003 and HR = 1.79, P = 0.003, respectively] and overall survival (HR = 1.85, P = 0.005 and HR = 1.67, P = 0.02, respectively) independently of the International Prognostic Index. The correlation between the Hans algorithm and the Wright algorithm was 91%, with an almost perfect concordance according to a kappa test (0.81). Conclusions Our results suggest that immunohistochemically defined COO remains a useful tool for predicting prognosis in diffuse large B-cell lymphoma when performed under optimized standardized conditions and that BCL2 expression may help to identify elderly patients at risk for relapse and who could potentially respond to anti-BCL2 targeted agents. In this prospective phase III trial, the coexpression of MYC and BCL2 does not appear to predict worse survival. Clinical trial Number NCT00144755.
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Affiliation(s)
| | - C Copie-Bergman
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - J Brière
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | - R Delarue
- Hematology, AP-HP, Necker Enfants-Malades, Paris
| | - F Jardin
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - P Ruminy
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - C Thieblemont
- Hemato-Oncology, AP-HP, Saint-Louis, Université Paris Diderot, Sorbonne Paris Cité and EA 7324, Paris Descartes, Sorbonne Paris Cité, Paris
| | - M Figeac
- Functional Genomic Platform, Cancer Research Institute, Lille
| | - D Canioni
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | | | - B Fabiani
- Pathology, AP-HP, Saint-Antoine, Paris
| | - K Leroy
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - M Parrens
- Pathology, CHU Bordeaux, Inserm U1053, Bordeaux, France
| | - M André
- Hematology, Université Catholique de Louvain, CHU UCL Namur, Yvoir, Belgium
| | - C Haioun
- Lymphoid Malignancies Unit, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil
| | - G A Salles
- Haematology, Hospices Civils de Lyon, Université Claude Bernard, Pierre Bénite
| | - P Gaulard
- Pathology, AP-HP, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Université Paris-Est Créteil, Créteil and IMRB, INSERM U955 Unité, Créteil
| | - H Tilly
- Hematology and UMR918, Centre Henri Becquerel, Université de Rouen, Rouen
| | - J P Jais
- Biostatistics, AP-HP, Necker Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, Paris
| | - T J Molina
- Pathology, AP-HP, Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris.,EA7324, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Piton N, Ruminy P, Gravet C, Marchand V, Colasse É, Lamy A, Naoures Mear CL, Bibeau F, Marguet F, Guisier F, Salaün M, Thiberville L, Jardin F, Sabourin JC. Ligation-dependent RT-PCR: a new specific and low-cost technique to detect ALK, ROS, and RET rearrangements in lung adenocarcinoma. J Transl Med 2018; 98:371-379. [PMID: 29251734 DOI: 10.1038/labinvest.2017.124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Detection of anaplastic lymphoma kinase (ALK), ROS proto-oncogene 1 (ROS1), and rearranged during transfection (RET) gene rearrangements in lung adenocarcinoma is usually performed by immunohistochemistry (IHC) screening followed by fluorescence in situ hybridization (FISH), which is an expensive and difficult technique. Ligation-dependent reverse transcription polymerase chain reaction (RT-PCR) multiplex technique can detect gene rearrangements using probes specifically hybridized to either side of the break point. PCR products are then sequenced by pyrosequencing or high throughput sequencing in order to identify the two genes involved. The reagent cost is <15 dollars per patient and results are available in 2 days. We have developed a 47-probe LD-RT-PCR kit especially for lung adenocarcinomas. Thirty-nine lung adenocarcinomas were studied: 24 ALK+, 14 ROS1+, and 1 RET+. ALK+ and ROS1+ were IHC+ (D5F3 Ventana for ALK and D4D6 Cell Signaling Technology for ROS1) and all cases were FISH+ (Vysis ALK Breakapart Probe Abbott for ALK, Zytolight SPEC ROS1 Dualcolor Breakapart Probe for ROS1 and Zytolight SPEC RET Dual Color Breakapart for RET); 14 wild type samples were included as negative controls. Using LD-RT-PCR, 15 rearrangements (63%) were detected in the ALK cases (gene partner: EML4 in all cases), 9 rearrangements (64%) in the ROS1 cases (gene partners: CD74 in 8 cases and SLC34A2 in 1 case) and 1 (100%) in the single RET case (gene partner: KIF5B). No rearrangement was found in the 14 negative control cases. Negative cases using LD-RT-PCR could be explained by the fact that some partner genes were not included in our assay and therefore could not be detected. Because it is an affordable, fast, and very simple technique, we propose using LD-RT-PCR when ALK immunostaining is positive. For LD-RT-PCR-negative cases, samples should then be analyzed by FISH.
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Affiliation(s)
- Nicolas Piton
- Rouen University Hospital, Department of Pathology, Rouen, France.,Normandie University, UNIROUEN, Inserm U1245, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- Normandie University, UNIROUEN, Inserm U1245, Rouen University Hospital, Rouen, France
| | - Claire Gravet
- Rouen University Hospital, Department of Pathology, Rouen, France
| | - Vinciane Marchand
- Normandie University, UNIROUEN, Inserm U1245, Rouen University Hospital, Rouen, France
| | - Élodie Colasse
- Rouen University Hospital, Department of Pathology, Rouen, France
| | - Aude Lamy
- Rouen University Hospital, Department of Pathology, Rouen, France
| | | | - Fréderic Bibeau
- Caen University Hospital, Department of Pathology, Caen, France
| | - Florent Marguet
- Rouen University Hospital, Department of Pathology, Rouen, France
| | - Florian Guisier
- Rouen University Hospital, Clinique Pneumologique, Rouen, France
| | - Mathieu Salaün
- Rouen University Hospital, Clinique Pneumologique, Rouen, France
| | - Luc Thiberville
- Rouen University Hospital, Clinique Pneumologique, Rouen, France
| | - Fabrice Jardin
- Caen University Hospital, Department of Pathology, Caen, France
| | - Jean-Christophe Sabourin
- Rouen University Hospital, Department of Pathology, Rouen, France.,Normandie University, UNIROUEN, Inserm U1245, Rouen University Hospital, Rouen, France
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Toledano MN, Desbordes P, Banjar A, Gardin I, Vera P, Ruminy P, Jardin F, Tilly H, Becker S. Combination of baseline FDG PET/CT total metabolic tumour volume and gene expression profile have a robust predictive value in patients with diffuse large B-cell lymphoma. Eur J Nucl Med Mol Imaging 2018; 45:680-688. [PMID: 29344718 DOI: 10.1007/s00259-017-3907-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/03/2017] [Indexed: 01/12/2023]
Abstract
PURPOSE This study evaluated the predictive significance of total metabolic tumour volume (TMTV) measured on baseline FDG PET/CT and its value in addition to gene expression profiling using a new method of gene analysis (rapid reverse transcriptase multiplex ligation-dependent probe amplification assay, RT-MLPA) in patients with diffuse large B-cell lymphoma treated with R-CHOP or R-CHOP-like chemotherapies. METHODS The analysis included 114 patients. TMTV was measured using a 41% SUVmax threshold and tumours were classified into GCB or ABC subtypes according to the RT-MLPA assay. RESULTS The median follow-up was 40 months. the 5-year progression-free survival (PFS) was 54% and the 5-year overall survival (OS) was 62%. The optimal TMTV cut-off value was 261 cm3. In 59 patients with a high TMTV the 5-year PFS and OS were 37% and 39%, respectively, in comparison with 72% and 83%, respectively, in 55 patients with a low TMTV (p = 0.0002 for PFS, p < 0.0001 for OS). ABC status was significantly associated with a worse prognosis. TMTV combined with molecular data identified three groups with very different outcomes: (1) patients with a low TMTV whatever their phenotype (n = 55), (2) patients with a high TMTV and GCB phenotype (n = 33), and (3) patients with a high TMTV and ABC phenotype (n = 26). In the three groups, 5-year PFS rates were 72%, 51% and 17% (p < 0.0001), and 5-year OS rates were 83%, 55% and 17% (p < 0.0001), respectively. In multivariate analysis, TMTV, ABC/GCB phenotype and International Prognostic Index were independent predictive factors for both PFS and OS (p < 0.05 for both). CONCLUSIONS This integrated risk model could lead to more accurate selection of patients that would allow better individualization of therapy.
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Affiliation(s)
- Mathieu Nessim Toledano
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France. .,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France.
| | - P Desbordes
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - A Banjar
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - I Gardin
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - P Vera
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - P Ruminy
- INSERM U918, Centre Henri Becquerel, Rouen, France
| | - F Jardin
- INSERM U918, Centre Henri Becquerel, Rouen, France.,Hematology Department, Centre Henri Becquerel, Rouen, France
| | - H Tilly
- INSERM U918, Centre Henri Becquerel, Rouen, France.,Hematology Department, Centre Henri Becquerel, Rouen, France
| | - S Becker
- Nuclear Medicine Department, Henri Becquerel Cancer Centre and Rouen University Hospital, Rouen, France.,QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
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Bobée V, Ruminy P, Marchand V, Viailly PJ, Abdel Sater A, Veresezan L, Drieux F, Bérard C, Bohers E, Mareschal S, Dubois S, Jais JP, Leroy K, Figeac M, Picquenot JM, Molina TJ, Salles G, Haioun C, Tilly H, Jardin F. Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier: A CALYM Study. J Mol Diagn 2017; 19:892-904. [PMID: 29054399 DOI: 10.1016/j.jmoldx.2017.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/11/2017] [Accepted: 07/28/2017] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Victor Bobée
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Biological Hematology, Rouen University Hospital, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France.
| | | | | | - Ahmad Abdel Sater
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; LITIS EA 4108, UNIROUEN, University of Normandie, Rouen, France
| | - Liana Veresezan
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fanny Drieux
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Caroline Bérard
- LITIS EA 4108, UNIROUEN, University of Normandie, Rouen, France
| | - Elodie Bohers
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | | | - Sydney Dubois
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | | | - Karen Leroy
- INSERM U955 Team 09, AP-HP Henri Mondor Hospital, Creteil, France
| | - Martin Figeac
- Functional Genomics Platform, Center for Biology and Pathology, University of Lille, Lille Cedex, France
| | - Jean-Michel Picquenot
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France; Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Thierry Jo Molina
- Department of Pathology, Necker Hospital, AP-HP, Université Paris Descartes Sorbonne Cité, Paris, France
| | - Gilles Salles
- Department of Hematology, University Claude Bernard Lyon 1, Hospices Civils de Lyon, Pierre-Benite, France
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Hospital Henri Mondor, Creteil, France
| | - Hervé Tilly
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
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40
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Jais JP, Molina TJ, Ruminy P, Gentien D, Reyes C, Scott DW, Rimsza LM, Wright G, Gascoyne RD, Staudt LM, Haioun C, Tilly H, Gaulard P, Salles GA, Jardin F, Leroy K. Reliable subtype classification of diffuse large B-cell lymphoma samples from GELA LNH2003 trials using the Lymph2Cx gene expression assay. Haematologica 2017; 102:e404-e406. [PMID: 28679653 DOI: 10.3324/haematol.2017.166827] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Jean-Philippe Jais
- AP-HP, Cochin and Necker Hospitals and Paris Descartes University, France
| | - Thierry Jo Molina
- AP-HP, Cochin and Necker Hospitals and Paris Descartes University, France.,Paris Descartes University, EA 7324, France
| | | | - David Gentien
- Institut Curie, PSL Research University, Translational Research Department, Genomic Platform, Paris, F-75248, France
| | - Cecile Reyes
- Institut Curie, PSL Research University, Translational Research Department, Genomic Platform, Paris, F-75248, France
| | | | | | - George Wright
- Center for Cancer Research, National Institute of Health, Bethesda, MD, USA
| | | | - Louis M Staudt
- Center for Cancer Research, National Institute of Health, Bethesda, MD, USA
| | | | - Herve Tilly
- INSERM U918, Centre Henri Becquerel, Rouen, France
| | | | | | | | - Karen Leroy
- AP-HP, Cochin and Necker Hospitals and Paris Descartes University, France
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41
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Ruminy P, Drieux F, Abdel Sater A, Fataccioli V, Marchand V, Parrens M, Bossard C, Dobay P, Viailly P, Veresezan L, Dupuy A, Pujals A, Picquenot J, Tilly H, De Leval L, Jardin F, Gaulard P. GENE EXPRESSION PROFILING USING a RTMLPA ASSAY ALLOWS FOR AN ACCURATE CLASSIFICATION OF PERIPHERAL T-CELL LYMPHOMA AND HIGHLIGHTS NOVEL SUBGROUPS WITHIN PTCLS-NOS. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- P. Ruminy
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - F. Drieux
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | | | | | - V. Marchand
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - M. Parrens
- Pathologie; Hopital Haut-Levêque; Pessac France
| | - C. Bossard
- Pathologie; Hotel Dieu de Nantes; Nantes France
| | - P. Dobay
- Pathologie; Centre Hospitalier Universitaire Vaudois; Lausanne Switzerland
| | - P. Viailly
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - L. Veresezan
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - A. Dupuy
- Inserm U955; Hopital Henri Mondor; Créteil France
| | - A. Pujals
- Inserm U955; Hopital Henri Mondor; Créteil France
| | - J. Picquenot
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - H. Tilly
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - L. De Leval
- Pathologie; Centre Hospitalier Universitaire Vaudois; Lausanne Switzerland
| | - F. Jardin
- Inserm U1245; Centre Henri Becquerel; Rouen France
| | - P. Gaulard
- Inserm U955; Hopital Henri Mondor; Créteil France
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42
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Jardin F, Mareschal S, Pham-Ledard A, Viailly P, Carlotti M, Dubois S, Bertrand P, Maingonnat C, Bohers E, Ruminy P, Tournier I, Courville P, Duval A, Andrieu E, Verneuil L, Fontanillles M, Vergier B, Tilly H, Joly P, Frebourg T, Beylot-Barry M, Merlio J. THE LANDSCAPE OF SOMATIC MUTATIONS OF PRIMARY CUTANEOUS DIFFUSE LARGE B-CELL LYMPHOMA, LEG-TYPE. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- F. Jardin
- Hematology; Henri Becquerel Center; Rouen France
| | - S. Mareschal
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - A. Pham-Ledard
- Inserm U1053, Team “Oncogenesis of Cutaneous Lymphoma”, CHU Bordeaux; Bordeaux France
| | - P. Viailly
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - M. Carlotti
- Inserm U1053, Team “Oncogenesis of Cutaneous Lymphoma”, CHU Bordeaux; Bordeaux France
| | - S. Dubois
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - P. Bertrand
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - C. Maingonnat
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - E. Bohers
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - P. Ruminy
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - I. Tournier
- Department of Genetics, Normandie Univ, UNIROUEN; Inserm U1245 and Rouen University Hospital; Rouen France
| | - P. Courville
- Departments of Dermatology and Pathology; Rouen University Hospital; Rouen France
| | - A. Duval
- Departments of Dermatology and Pathology; Rouen University Hospital; Rouen France
| | - E. Andrieu
- Departments of Dermatology and Pathology; Rouen University Hospital; Rouen France
| | - L. Verneuil
- Departments of Dermatology and Pathology, Caen CHU; Caen France
| | - M. Fontanillles
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - B. Vergier
- Inserm U1053, Team “Oncogenesis of Cutaneous Lymphoma”, CHU Bordeaux; Bordeaux France
| | - H. Tilly
- Team Genetics and Biomarkers in Lymphoma and Solid Tumors, INSERM U1245; Rouen France
| | - P. Joly
- Departments of Dermatology and Pathology; Rouen University Hospital; Rouen France
| | - T. Frebourg
- Department of Genetics, Normandie Univ, UNIROUEN; Inserm U1245 and Rouen University Hospital; Rouen France
| | - M. Beylot-Barry
- Inserm U1053, Team “Oncogenesis of Cutaneous Lymphoma”, CHU Bordeaux; Bordeaux France
| | - J. Merlio
- Inserm U1053, Team “Oncogenesis of Cutaneous Lymphoma”, CHU Bordeaux; Bordeaux France
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43
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Mareschal S, Pham-Ledard A, Viailly PJ, Dubois S, Bertrand P, Maingonnat C, Fontanilles M, Bohers E, Ruminy P, Tournier I, Courville P, Lenormand B, Duval AB, Andrieu E, Verneuil L, Vergier B, Tilly H, Joly P, Frebourg T, Beylot-Barry M, Merlio JP, Jardin F. Identification of Somatic Mutations in Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type by Massive Parallel Sequencing. J Invest Dermatol 2017; 137:1984-1994. [PMID: 28479318 DOI: 10.1016/j.jid.2017.04.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/27/2017] [Accepted: 04/01/2017] [Indexed: 12/16/2022]
Abstract
To determine whether the mutational profile of primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) is unique by comparison with other diffuse large B-cell lymphoma subtypes, we analyzed a total cohort of 20 PCLBCL-LT patients by using next-generation sequencing with a lymphoma panel designed for diffuse large B-cell lymphoma. We also analyzed 12 pairs of tumor and control DNA samples by whole-exome sequencing, which led us to perform resequencing of three selected genes not included in the lymphoma panel: TBL1XR1, KLHL6, and IKZF3. Our study clearly identifies an original mutational landscape of PCLBCL-LT with a very restricted set of highly recurrent mutations (>40%) involving MYD88 (p.L265P variant), PIM1, and CD79B. Other genes involved in B-cell signaling, NF-κB activation, or DNA modeling were found altered, notably TBL1XR1 (33%), MYC (26%) CREBBP (26%), and IRF4 (21%) or HIST1H1E (41%). MYD88L265P variant was associated with copy number variations or copy neutral loss of heterozygosity in 60% of patients. The most frequent genetic losses involved CDKN2A/2B, TNFAIP3/A20, PRDM1, TCF3, and CIITA. Together, these results show that PCLBCL-LT exhibits a unique mutational landscape, combining highly recurrent hotspot mutations in genes involved in NF-kB and B-cell signaling pathways, which provides a rationale for using selective inhibitors of the B-cell receptor.
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Affiliation(s)
- Sylvain Mareschal
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Anne Pham-Ledard
- Departments of Dermatology, Pathology, and Tumor Biology, CHU Bordeaux, Bordeaux, France; INSERM U1053, Team Oncogenesis of Cutaneous Lymphoma, University Bordeaux, Bordeaux, France
| | - Pierre Julien Viailly
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Sydney Dubois
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Philippe Bertrand
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Catherine Maingonnat
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Maxime Fontanilles
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Elodie Bohers
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Philippe Ruminy
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Isabelle Tournier
- Normandie Université, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Philippe Courville
- Rouen University Hospital, Departments of Dermatology and Pathology, Rouen, France
| | - Bernard Lenormand
- Rouen University Hospital, Departments of Dermatology and Pathology, Rouen, France
| | - Anne Bénédicte Duval
- Rouen University Hospital, Departments of Dermatology and Pathology, Rouen, France
| | - Emilie Andrieu
- Rouen University Hospital, Departments of Dermatology and Pathology, Rouen, France
| | | | - Beatrice Vergier
- Departments of Dermatology, Pathology, and Tumor Biology, CHU Bordeaux, Bordeaux, France; INSERM U1053, Team Oncogenesis of Cutaneous Lymphoma, University Bordeaux, Bordeaux, France
| | - Hervé Tilly
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France
| | - Pascal Joly
- Normandie Université, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- Normandie Université, UNIROUEN, INSERM U1245 and Rouen University Hospital, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Marie Beylot-Barry
- Departments of Dermatology, Pathology, and Tumor Biology, CHU Bordeaux, Bordeaux, France; INSERM U1053, Team Oncogenesis of Cutaneous Lymphoma, University Bordeaux, Bordeaux, France
| | - Jean-Philippe Merlio
- Departments of Dermatology, Pathology, and Tumor Biology, CHU Bordeaux, Bordeaux, France; INSERM U1053, Team Oncogenesis of Cutaneous Lymphoma, University Bordeaux, Bordeaux, France
| | - Fabrice Jardin
- Department of Hematology, Henri Becquerel Comprehensive Cancer Center and Normandie Université, UNIROUEN, INSERM U1245, Team Genomics and biomarkers in lymphoma and solid tumors, Rouen, France.
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44
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Rizzo D, Viailly PJ, Mareschal S, Bohers E, Picquenot JM, Penther D, Dubois S, Marchand V, Bertrand P, Maingonnat C, Etancelin P, Feuillard J, Bastard C, Tilly H, Jardin F, Ruminy P. Oncogenic events rather than antigen selection pressure may be the main driving forces for relapse in diffuse large B-cell lymphomas. Am J Hematol 2017; 92:68-76. [PMID: 27737507 DOI: 10.1002/ajh.24584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023]
Abstract
Little is known on the phylogenetic relationship between diagnostic and relapse clones of diffuse large B-cell lymphoma (DLBCL). We applied high throughput sequencing (HTS) of the VDJ locus of Immunoglobulin heavy chain (IGHV) on 14 DLBCL patients with serial samples, including tumor biopsies and/or peripheral blood mononuclear cells (PBMC). Phylogenetic data were consolidated with targeted sequencing and cytogenetics. Phylogeny clearly showed that DLBCL relapse could occur according either an early or a late divergent mode. These two modes of divergence were independent from the elapsed time between diagnosis and relapse. We found no significant features for antigen selection pressure in complementary determining region both at diagnosis and relapse for 9/12 pairs and a conserved negative selection pressure for the three remaining cases. Targeted HTS and conventional cytogenetics revealed a branched vs. linear evolution for 5/5 IGHV early divergent cases, but unexpected such "oncogenetic" branched evolution could be found in at least 2/7 IGHV late divergent cases. Thus, if BCR signaling is mandatory for DLBCL emergence, oncogenetic events under chemotherapy selection pressure may be the main driving forces at relapse. Finally, circulating subclones with divergent IGHV somatic hypermutations patterns from initial biopsy could be detected in PBMC at diagnosis for 4/6 patients and, for two of them, at least one was similar to the ones found at relapse. This study highlights that oncogenetic intraclonal diversity of DLBCL should be evaluated beyond the scope a single biopsy and represents a rationale for future investigations using peripheral blood for lymphoid malignancies genotyping. Am. J. Hematol. 92:68-76, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- David Rizzo
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of biological hematology; Centre Hospitalier Universitaire Dupuytren; Limoges France
| | - Pierre-Julien Viailly
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Sylvain Mareschal
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Elodie Bohers
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Jean-Michel Picquenot
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of pathology; Centre Henri Becquerel; Rouen France
| | - Dominique Penther
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Sydney Dubois
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Vinciane Marchand
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Philippe Bertrand
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Catherine Maingonnat
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Pascaline Etancelin
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Jean Feuillard
- Department of biological hematology; Centre Hospitalier Universitaire Dupuytren; Limoges France
- UMR CNRS 7276, University of Limoges; Limoges France
| | - Christian Bastard
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Hervé Tilly
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of clinical hematology; Centre Henri Becquerel; Rouen France
| | - Fabrice Jardin
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of clinical hematology; Centre Henri Becquerel; Rouen France
| | - Philippe Ruminy
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
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Dubois S, Viailly PJ, Bohers E, Bertrand P, Ruminy P, Marchand V, Maingonnat C, Mareschal S, Picquenot JM, Penther D, Jais JP, Tesson B, Peyrouze P, Figeac M, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Fabiani B, Delarue R, Peyrade F, André M, Ketterer N, Leroy K, Salles G, Molina TJ, Tilly H, Jardin F. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases. Clin Cancer Res 2016; 23:2232-2244. [PMID: 27923841 DOI: 10.1158/1078-0432.ccr-16-1922] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Purpose: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 NFκB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88-mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants.Experimental Design: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next-generation sequencing (NGS) focusing on 34 genes to analyze associated mutations and copy number variations, as well as gene expression profiling, 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 also segregated subgroups according to associated genetic alterations among patients with the same MYD88 mutation. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFκB pathway activation, although the majority of MYD88 L265P-mutant cases harbors downstream NFκB alterations, which can predict BTK inhibitor resistance. Finally, 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.Conclusions: This study highlights the relative heterogeneity of MYD88-mutant DLBCL, adding to the field's knowledge of the theranostic importance of MYD88 mutations, but also of associated alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. Clin Cancer Res; 23(9); 2232-44. ©2016 AACR.
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Affiliation(s)
- Sydney Dubois
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Pierre-Julien Viailly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,LITIS EA 4108, Normandie Université, Rouen, France
| | - Elodie Bohers
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Bertrand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Ruminy
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Vinciane Marchand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Sylvain Mareschal
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Dominique Penther
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | | | | | | | | | | | - Corinne Haioun
- Unité Hémopathies Lymphoïdes, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | | | - Bettina Fabiani
- Laboratoire de Pathologie, AP-HP Hôpital Saint Antoine, Paris, France
| | - Richard Delarue
- Department of Hematology, AP-HP Hôpital Necker, Paris, France
| | | | - Marc André
- CHU Dinant Godinne, UcL Namur, Yvoir, Belgium
| | | | - Karen Leroy
- Inserm U955 Team 09, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | - Thierry J Molina
- Pathology, AP-HP Hôpital Necker, Université Paris Descartes, Paris, France
| | - Hervé Tilly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Fabrice Jardin
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.
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Camus V, Sarafan-Vasseur N, Bohers E, Dubois S, Mareschal S, Bertrand P, Viailly PJ, Ruminy P, Maingonnat C, Lemasle E, Stamatoullas A, Picquenot JM, Cornic M, Beaussire L, Bastard C, Frebourg T, Tilly H, Jardin F. Digital PCR for quantification of recurrent and potentially actionable somatic mutations in circulating free DNA from patients with diffuse large B-cell lymphoma. Leuk Lymphoma 2016; 57:2171-9. [PMID: 26883583 DOI: 10.3109/10428194.2016.1139703] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Female
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Karyopherins/genetics
- Liquid Biopsy
- Lymphoma, Large B-Cell, Diffuse/diagnostic imaging
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Mutation
- Myeloid Differentiation Factor 88/genetics
- Neoplasm Staging
- Positron-Emission Tomography
- Real-Time Polymerase Chain Reaction
- Receptors, Cytoplasmic and Nuclear/genetics
- Recurrence
- Exportin 1 Protein
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Affiliation(s)
- Vincent Camus
- a Department of Hematology , Centre Henri Becquerel , Rouen , France
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | | | - Elodie Bohers
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | - Sydney Dubois
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | - Sylvain Mareschal
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | - Philippe Bertrand
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | | | - Philippe Ruminy
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | | | - Emilie Lemasle
- a Department of Hematology , Centre Henri Becquerel , Rouen , France
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | - Aspasia Stamatoullas
- a Department of Hematology , Centre Henri Becquerel , Rouen , France
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | | | - Marie Cornic
- d Department of Pathology , Centre Henri Becquerel , Rouen , France
| | | | - Christian Bastard
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
- e Department of Genetic Oncology , Centre Henri Becquerel , Rouen , France
| | | | - Hervé Tilly
- a Department of Hematology , Centre Henri Becquerel , Rouen , France
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
| | - Fabrice Jardin
- a Department of Hematology , Centre Henri Becquerel , Rouen , France
- b INSERM U918, Centre Henri Becquerel, University of Rouen , Rouen , France
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47
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Camus V, Stamatoullas A, Mareschal S, Viailly PJ, Sarafan-Vasseur N, Bohers E, Dubois S, Picquenot JM, Ruminy P, Maingonnat C, Bertrand P, Cornic M, Tallon-Simon V, Becker S, Veresezan L, Frebourg T, Vera P, Bastard C, Tilly H, Jardin F. Detection and prognostic value of recurrent exportin 1 mutations in tumor and cell-free circulating DNA of patients with classical Hodgkin lymphoma. Haematologica 2016; 101:1094-101. [PMID: 27479820 PMCID: PMC5060026 DOI: 10.3324/haematol.2016.145102] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, Rouen, France INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Aspasia Stamatoullas
- Department of Hematology, Centre Henri Becquerel, Rouen, France INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Sylvain Mareschal
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | | | - Elodie Bohers
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Sydney Dubois
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Jean Michel Picquenot
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Philippe Ruminy
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Philippe Bertrand
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Marie Cornic
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Stéphanie Becker
- Department of Nuclear Medicine and Radiology, Centre Henri Becquerel and QuantIF (Litis EA4108 - FR CNRS 3638), Rouen, France
| | - Liana Veresezan
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Pierre Vera
- Department of Nuclear Medicine and Radiology, Centre Henri Becquerel and QuantIF (Litis EA4108 - FR CNRS 3638), Rouen, France
| | - Christian Bastard
- INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France Department of Genetic Oncology, Centre Henri Becquerel, Rouen, France
| | - Hervé Tilly
- Department of Hematology, Centre Henri Becquerel, Rouen, France INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, Rouen, France INSERM U918, Centre Henri Becquerel, University of Rouen, Rouen, France
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Dubois S, Viailly PJ, Mareschal S, Bohers E, Bertrand P, Ruminy P, Maingonnat C, Jais JP, Peyrouze P, Figeac M, Molina TJ, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Brière J, Petrella T, Canioni D, Fabiani B, Coiffier B, Delarue R, Peyrade F, Bosly A, André M, Ketterer N, Salles G, Tilly H, Leroy K, Jardin F. Next-Generation Sequencing in Diffuse Large B-Cell Lymphoma Highlights Molecular Divergence and Therapeutic Opportunities: a LYSA Study. Clin Cancer Res 2016; 22:2919-28. [PMID: 26819451 DOI: 10.1158/1078-0432.ccr-15-2305] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/11/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Next-generation sequencing (NGS) has detailed the genomic characterization of diffuse large B-cell lymphoma (DLBCL) by identifying recurrent somatic mutations. We set out to design a clinically feasible NGS panel focusing on genes whose mutations hold potential therapeutic impact. Furthermore, for the first time, we evaluated the prognostic value of these mutations in prospective clinical trials. EXPERIMENTAL DESIGN A Lymphopanel was designed to identify mutations in 34 genes, selected according to literature and a whole exome sequencing study of relapsed/refractory DLBCL patients. The tumor DNA of 215 patients with CD20(+)de novo DLBCL in the prospective, multicenter, and randomized LNH-03B LYSA clinical trials was sequenced to deep, uniform coverage with the Lymphopanel. Cell-of-origin molecular classification was obtained through gene expression profiling with HGU133+2.0 Affymetrix GeneChip arrays. RESULTS The Lymphopanel was informative for 96% of patients. A clear depiction of DLBCL subtype molecular heterogeneity was uncovered with the Lymphopanel, confirming that activated B-cell-like (ABC), germinal center B-cell like (GCB), and primary mediastinal B-cell lymphoma (PMBL) are frequently affected by mutations in NF-κB, epigenetic, and JAK-STAT pathways, respectively. Novel truncating immunity pathway, ITPKB, MFHAS1, and XPO1 mutations were identified as highly enriched in PMBL. Notably, TNFAIP3 and GNA13 mutations in ABC patients treated with R-CHOP were associated with significantly less favorable prognoses. CONCLUSIONS This study demonstrates the contribution of NGS with a consensus gene panel to personalized therapy in DLBCL, highlighting the molecular heterogeneity of subtypes and identifying somatic mutations with therapeutic and prognostic impact. Clin Cancer Res; 22(12); 2919-28. ©2016 AACRSee related commentary by Lim and Elenitoba-Johnson, p. 2829.
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Affiliation(s)
- Sydney Dubois
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Pierre-Julien Viailly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France. LITIS EA 4108, Normandie Université, Rouen, France
| | - Sylvain Mareschal
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Elodie Bohers
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Bertrand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Ruminy
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | | | | | | | - Thierry J Molina
- Pathology, AP-HP, Hôpital Necker, Université Paris Descartes, Paris, France
| | | | | | - Corinne Haioun
- Unité Hémopathies Lymphoïdes, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | | | - Josette Brière
- Inserm U728, Université Paris Diderot, Sorbonne Paris Cité, Paris, France. Department of Pathology, AP-HP Hôpital Saint-Louis, Paris, France
| | - Tony Petrella
- Department of Pathology, Hôpital Maisonneuve-Rosemont, Montréal, Quebec, Canada
| | | | - Bettina Fabiani
- Laboratoire de Pathologie, AP-HP Hôpital Saint Antoine, Paris, France
| | | | - Richard Delarue
- Department of Hematology, AP-HP Hôpital Necker, Paris, France
| | | | - André Bosly
- CHU Dinant Godinne, UcL Namur, Yvoir, Belgium
| | - Marc André
- CHU Dinant Godinne, UcL Namur, Yvoir, Belgium
| | - Nicolas Ketterer
- Department of Oncology, Lausanne Hospital, Lausanne, Switzerland
| | | | - Hervé Tilly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Karen Leroy
- Inserm U955 Team 09, AP-HP Hôpital Henri Mondor, Créteil, France
| | - Fabrice Jardin
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.
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49
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Leroy K, Jais JP, Ruminy P, Gentien D, Reyes C, Scott DW, Rimsza LM, Wright G, Gascoyne RD, Staudt LM, Haioun C, Tilly H, Gaulard P, Salles GA, Molina T, Jardin F. Classification of diffuse large b-cell lymphoma (DLBCL) FFPE samples of the GELA LNH2003 program, using Lymph2Cx assay on the nCounter analysis system. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.7547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Karen Leroy
- Department of Molecular Biology, Cochin Hospital, Paris Descartes University, AP-HP, CARPEM, Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | | | | | | | | | | | | | | | | | - Louis M. Staudt
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
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50
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Dubois S, Mareschal S, Picquenot JM, Viailly PJ, Bohers E, Cornic M, Bertrand P, Veresezan EL, Ruminy P, Maingonnat C, Marchand V, Lanic H, Penther D, Bastard C, Tilly H, Jardin F. Immunohistochemical and genomic profiles of diffuse large B-cell lymphomas: implications for targeted EZH2 inhibitor therapy? Oncotarget 2016; 6:16712-24. [PMID: 25762637 PMCID: PMC4599301 DOI: 10.18632/oncotarget.3154] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/15/2015] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Sydney Dubois
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Sylvain Mareschal
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Jean-Michel Picquenot
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Elodie Bohers
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Marie Cornic
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Philippe Bertrand
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Elena Liana Veresezan
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Philippe Ruminy
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Vinciane Marchand
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Hélène Lanic
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Dominique Penther
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Christian Bastard
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Hervé Tilly
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
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