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Drouyer A, Beaussire L, Jorda P, Leheurteur M, Guillemet C, Berghian A, Georgescu D, Di Fiore F, Perdrix A, Clatot F. Clinical relevance of circulating ESR1 mutations during endocrine therapy for advanced hormone-dependent endometrial carcinoma. BMC Cancer 2023; 23:1061. [PMID: 37924026 PMCID: PMC10625264 DOI: 10.1186/s12885-023-11559-x] [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: 05/07/2023] [Accepted: 10/22/2023] [Indexed: 11/06/2023] Open
Abstract
OBJECTIVE Endocrine therapy is frequently administered in patients with hormone dependent (HR+) metastatic endometrial cancer. ESR1 mutations have emerged as a key mechanism of aromatase inhibitor (AI) resistance in HR + metastatic breast cancer and can be monitored using circulating tumor DNA (ctDNA). The aim of this study was to explore the incidence and clinical relevance of circulating ESR1 mutations in patients treated by AI or megestrol acetate (M) for advanced endometrial carcinoma. METHODOLOGY This single-center retrospective study was performed at the Henri Becquerel Center (Rouen) and looked for circulating ESR1 gene mutations by droplet digital PCR (E380Q, L536R, Y537S, Y537N, Y537C, D538G, S463P) in patients with advanced HR + endometrial carcinoma treated between 2008 and 2020 for at least 30 days by AI or M. Analyses were performed before exposure and at progression/during endocrine therapy. RESULTS Twenty-two patients were included: 13 were treated with AI, 12 of whom progressed; 9 patients were treated with M, 8 of whom progressed. 68.1% of the patients had low-grade endometrial carcinoma and 54.5% had received chemotherapy in the metastatic setting. The median duration of treatment was 152 days (min 47 - max 629) with AI and 155 days (min 91-max 1297) with M. Under AI, there was no ESR1 mutation at baseline, and one Y537C mutation at progression with a variant allele frequency (VAF) of 0.14%. Under M, one patient had a Y537C (VAF 0.2%) at baseline that disappeared during treatment. Another patient had a Y537S mutation emergence at progression after 91 days of treatment (VAF 1.83%). There was no significant difference between the circulating DNA concentration before and after hormone therapy (p = 0.16). CONCLUSION ESR1 mutations do not seem to be involved in the mechanisms of resistance to AI or M in HR+ endometrial cancer. The clinical relevance of their detection is not demonstrated.
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Affiliation(s)
- Aurélien Drouyer
- Department of Gynecology, Henri Becquerel Cancer Institute, Rouen, France.
| | - Ludivine Beaussire
- Rouen Institute for Research and Innovation in Biomedicine, INSERM 1245, IRON group, Rouen, France
| | - Pauline Jorda
- Department of Gynecology, Henri Becquerel Cancer Institute, Rouen, France
| | - Marianne Leheurteur
- Department of Medical Oncology, Henri Becquerel Cancer Institute, Rouen, France
| | - Cécile Guillemet
- Department of Medical Oncology, Henri Becquerel Cancer Institute, Rouen, France
| | - Anca Berghian
- Department of Pathology, Henri Becquerel Cancer Institute, Rouen, France
| | - Dragos Georgescu
- Department of Surgery, Henri Becquerel Cancer Institute, Rouen, France
| | - Frédéric Di Fiore
- Rouen Institute for Research and Innovation in Biomedicine, INSERM 1245, IRON group, Rouen, France
- Department of Medical Oncology, Henri Becquerel Cancer Institute, Rouen, France
| | - Anne Perdrix
- Rouen Institute for Research and Innovation in Biomedicine, INSERM 1245, IRON group, Rouen, France
- Department of Biopathology, Henri Becquerel Cancer Institute, Rouen, France
| | - Florian Clatot
- Rouen Institute for Research and Innovation in Biomedicine, INSERM 1245, IRON group, Rouen, France
- Department of Medical Oncology, Henri Becquerel Cancer Institute, Rouen, France
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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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3
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Noeuveglise A, Sarafan-Vasseur N, Beaussire L, Marguet F, Modzelewski R, Hanzen C, Alexandru C, Magne N, Langlois O, Di Fiore F, Clatot F, Thureau S, Fontanilles M. Impact of EGFR A289T/V mutation on relapse pattern in glioblastoma. ESMO Open 2023; 8:100740. [PMID: 36566697 PMCID: PMC10024094 DOI: 10.1016/j.esmoop.2022.100740] [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: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Molecular factors influence relapse patterns in glioblastoma. The hotspot mutation located at position 289 of the extracellular domain of the epidermal growth factor receptor (EGFRA289mut) is associated with a more infiltrative phenotype. The primary objective of this study was to explore the impact of the EGFRA289 mutation on the pattern of relapse after chemoradiotherapy-based treatment of patients suffering from newly diagnosed glioblastoma. PATIENTS AND METHODS An ancillary study from a prospective cohort of patients suffering from glioblastoma was conducted. All patients received radiotherapy and concomitant temozolomide. The population was divided into two groups according to EGFRA289 status (mutated versus wild-type). The primary endpoint was the overlap score (varying from 0 to 1) between the initial irradiated tumor volume (Vinit) and the relapse volume (Vr). Secondary endpoints explored the impact of EGFRA289mut on survival. RESULTS One hundred twenty-eight patients were included and analyzed: 11% had EGFRA289mut glioblastoma (n = 14/128). EGFRA289mut glioblastomas had a relapse pattern that was more marginal than EGFRA289wt glioblastomas: a median overlap score Vinit/Vr of 0.96 was observed in the EGFRA289mut group versus 1 in the EGFRA289wt group (P = 0.05). Half of the population with EGFRA289mut tumor (n = 7/14) had a marginal relapse (i.e. overlap scoreVr/Vinit ≤ 0.95) compared to 23.7% (n = 27/114) in the EGFRA289wt group, P = 0.035. EGFRA289mut did not influence survival. CONCLUSION We highlighted a link between the EGFRA289 mutation and the relapse pattern in glioblastoma. The independent role of EGFRA289mut and its clinical implication should now be explored in further studies.
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Affiliation(s)
- A Noeuveglise
- Radiotherapy Department, Henri Becquerel Cancer Center, Rouen
| | - N Sarafan-Vasseur
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen
| | - L Beaussire
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen
| | - F Marguet
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen; Department of Pathology, Rouen University Hospital, Rouen
| | - R Modzelewski
- Nuclear Medicine Department, Henri Becquerel Center, Rouen
| | - C Hanzen
- Radiotherapy Department, Henri Becquerel Cancer Center, Rouen
| | - C Alexandru
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, Rouen
| | - N Magne
- Department of Radiology, Rouen University Hospital, Rouen
| | - O Langlois
- Department of Neurosurgery, Rouen University Hospital, Rouen
| | - F Di Fiore
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen; Department of Gastroenterology, Rouen University Hospital, Rouen
| | - F Clatot
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen; Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, Rouen
| | - S Thureau
- Radiotherapy Department, Henri Becquerel Cancer Center, Rouen; QuantIF-LITIS EA4108, University of Rouen, Rouen, France
| | - M Fontanilles
- Univ Rouen Normandie, Inserm U1245, Cancer And Brain Genomics, Rouen; Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, Rouen.
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Grancher A, Beaussire L, Manfredi S, Le Malicot K, Dutherage M, Verdier V, Mulot C, Bouché O, Phelip JM, Levaché CB, Deguiral P, Coutant S, Sefrioui D, Emile JF, Laurent-Puig P, Bibeau F, Michel P, Sarafan-Vasseur N, Lepage C, Di Fiore F. Postoperative circulating tumor DNA detection is associated with the risk of recurrence in patients resected for a stage II colorectal cancer. Front Oncol 2022; 12:973167. [PMID: 36439476 PMCID: PMC9685416 DOI: 10.3389/fonc.2022.973167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is reported to be promising in localized colorectal cancer (CRC). The present study aimed to retrospectively evaluate the impact of ctDNA in patients with a resected stage II CRC from the PROGIGE 13 trial with available paired tumor and blood samples. A group of recurrent patients were matched one-to-one with nonrecurrent patients according to sex, tumor location, treatment sequence, and blood collection timing. CtDNA was analyzed by digital PCR according to NGS of tumors. Disease-free survival (DFS) and overall survival (OS) were analyzed based on ctDNA, and the risks of recurrence and death were determined. A total of 134 patients were included, with 67 patients in each group. At least one alteration was identified in 115/134 tumors. Postoperative ctDNA was detected in 10/111 (9.0%) informative samples and was detected more frequently in the recurrent group (16.7% versus 1.8%; p = 0.02). The median DFS of ctDNA+ versus ctDNA- patients was 16.8 versus 54 months (p = 0.002), respectively, and the median OS was 51.3 versus 69.5 months (p = 0.03), respectively. CtDNA was associated with recurrence (ORa = 11.13, p = 0.03) and death (HRa = 3.15, p = 0.01). In conclusion, the presence of postoperative ctDNA is associated with both recurrence and survival in stage II CRC.
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Affiliation(s)
- Adrien Grancher
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- *Correspondence: Adrien Grancher,
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, Rouen, France
| | - Sylvain Manfredi
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Karine Le Malicot
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Marie Dutherage
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Vincent Verdier
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Claire Mulot
- Paris University, Biology Resources Center EPIGENETEC, Paris, France
| | - Olivier Bouché
- Department of Digestive Oncology, University Hospital of Reims, Reims, France
| | - Jean-Marc Phelip
- Department of Gastroenterology and Digestive Oncology, University Hospital of Saint Etienne, Saint Etienne, France
| | - Charles-Briac Levaché
- Department of Radiotherapy and Medical Oncology, Polyclinique Francheville, Périgueux, France
| | - Philippe Deguiral
- Department of Gastroenterology, St Nazaire Hospital, Saint-Nazaire, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Jean-François Emile
- Department of Pathology, Hôpital Ambroise-Paré, Boulogne-Billancourt, France
| | - Pierre Laurent-Puig
- Department of Biology, Georges Pompidou Hospital, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
| | - Frédéric Bibeau
- Department of Pathology, Caen University Hospital, Caen, France
| | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Côme Lepage
- Burgundy Digestive Cancer Registry, INSERM, Lipides, Nutrition, Cancers (LNC)-UMR1231, University Bourgogne Franche-Comté, Dijon, France
| | - Frederic Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, Rouen, France
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5
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Fontanilles M, Deniel A, Marguet F, Beaussire L, Magne N, Derrey S, Blanchard F, Alexandru C, Coutant S, Laquerrière A, Clatot F, Di Fiore F, Sarafan-Vasseur N. Usefulness of circulating tumor DNA from cerebrospinal fluid in recurrent high-grade glioma. Rev Neurol (Paris) 2022; 178:975-980. [PMID: 35871016 DOI: 10.1016/j.neurol.2022.02.462] [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: 08/02/2021] [Revised: 01/01/2022] [Accepted: 02/21/2022] [Indexed: 10/17/2022]
Abstract
Molecular documentation at relapse of high-grade glioma is an urgent need for patient care. A prospective pilot study was conducted to assess the rate of mutation detection using targeted deep sequencing on circulating tumor DNA from cerebrospinal fluid (CSF) after chemo-radiotherapy based treatment. Fifteen patients were included: 13 patients with glioblastoma, 1 patient with gliosarcoma and 1 patient with anaplastic astrocytoma. At progression, 10/15 patients (67%) had detectable mutations in the CSF. Among them, 5/10 patients harbored at least one common mutation between initial tumor and ctDNA. CSF protein level and cfDNA concentration were higher, although not significant, in the ctDNA positive group versus ctDNA negative group (1.17g/L vs. 0.79g/L). Molecular documentation obtained from ctDNA in CSF at the time of relapse is informative in around two-thirds of the patients.
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Affiliation(s)
- M Fontanilles
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France; Department of Medical Oncology, Cancer Centre Henri Becquerel, 76000 Rouen, France.
| | - A Deniel
- Department of Medical Oncology, Cancer Centre Henri Becquerel, 76000 Rouen, France
| | - F Marguet
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France; Department of Pathology, Rouen University Hospital, 76031 Rouen, France
| | - L Beaussire
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France
| | - N Magne
- Department of Radiology, Rouen University Hospital, 76031 Rouen, France
| | - S Derrey
- Department of Neurosurgery, Rouen University Hospital, 76031 Rouen, France
| | - F Blanchard
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France; Department of Pathology, Rouen University Hospital, 76031 Rouen, France
| | - C Alexandru
- Department of Medical Oncology, Cancer Centre Henri Becquerel, 76000 Rouen, France
| | - S Coutant
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France
| | - A Laquerrière
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France; Department of Pathology, Rouen University Hospital, 76031 Rouen, France
| | - F Clatot
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France; Department of Medical Oncology, Cancer Centre Henri Becquerel, 76000 Rouen, France
| | - F Di Fiore
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France; Department of Medical Oncology, Cancer Centre Henri Becquerel, 76000 Rouen, France; Department of Hepatogastroenterology, Rouen University Hospital, 76031 Rouen, France
| | - N Sarafan-Vasseur
- UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Normandie university, Rouen University Hospital, 76031 Rouen, France
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6
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Maxime F, Noeuveglise A, Vasseur N, Beaussire L, Marguet F, Modzelewski R, Hanzen C, Alexandru C, Magne N, Langlois O, Di Fiore F, Clatot F, Thureau S. Impact of EGFRA289T/Vmutation on relapse pattern in glioblastoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2046 Background: The prediction of the relapse pattern is an important issue in glioblastoma for personalized approach. Molecular factors, such as MGMT promoter methylation, influence relapse in- or out-field of the initial radiotherapy volume. Recently, a recurrent mutation located at position 289 of the extracellular domain of the epidermal growth factor receptor ( EGFRA289mut) has been associated with a more infiltrative phenotype in glioblastoma. The primary objective of the present study was to explore the impact of EGFRA289mut on the pattern of relapse after a chemo-radiotherapy based treatment of patients suffering from glioblastoma. Methods: An ancillary study from a monocentric prospective cohort of patients suffering from glioblastoma was conducted. All patients received radiotherapy and concomitant temozolomide. The population was divided into two groups according to EGFRA289 status (mutated versus wild-type). Primary endpoint was the overlap score (varying from 0 to 1) between initial irradiated tumor volume (Vinit) and relapse volume (Vr). Vinit was the initial 95% isodose of the radiotherapy and Vr was delineated using the enhanced MRI T1-weighted part of the relapse tumor. Secondary endpoints explored the impact of other EGFR extracellular mutations, EGFR amplification and EGFRvIII on the relapse pattern, as well as the impact of EGFRA289mut on survival. EGFR alterations were identified using next-generation sequencing or droplet-digital PCR based methods on formalin-fixed paraffin-embedded samples collected at initial diagnosis. Results: One hundred patients were included: 11% of the population had EGFRA289mut glioblastoma (n = 11/100). EGFRA289mut glioblastomas had a relapse pattern more marginal compared to EGFRA289wt glioblastomas: a mean overlap score Vinit/Vr of 0.78 was observed in the EGFRA289mut group versus 0.94 in the EGFRA289wt group (p = 0.021). The proportion of EGFR A289mut glioblastomas in the outfield relapse (overlap score < 0.8) has a trend to be higher than in the infield relapse (overlap score > 0.8): 25% (n = 2/8) versus 9.8% (n = 9/92) for the EGFRA289wt population, p = 0.21. Neither EGFR amplification nor EGFRvIII did influence overlap score Vinit/Vr. In our population, EGFRA289mut did not influence survival. Conclusions: EGFR A289mut influences the relapse pattern in a population of patients suffering from glioblastoma. The role of EGFRA289mut as a decision-making biomarker for personalized radiotherapy should now be investigated in dedicated clinical trial. Clinical trial information: NCT02617745.
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Affiliation(s)
| | | | - Nasrin Vasseur
- INSERM, U1079, IRON Group, University of Normandy, Rouen, France
| | - Ludivine Beaussire
- Institute of Research Onco-Normand (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | | | | | | | | | - Nicolas Magne
- Rouen University Hospital Charles Nicolle, Rouen, France
| | | | - Frédéric Di Fiore
- INSERM U1245, IRON Group, Centre Henri Becquerel, University Hospital, University of Normandy, Rouen, France
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
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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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8
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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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9
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Sefrioui D, Verdier V, Savoye-Collet C, Beaussire L, Ghomadi S, Gangloff A, Goria O, Riachi G, Montialoux H, Schwarz L, Tuech JJ, Frebourg T, Michel P, Sarafan-Vasseur N, Di Fiore F. Circulating DNA changes are predictive of disease progression after transarterial chemoembolization. Int J Cancer 2021; 150:532-541. [PMID: 34622951 DOI: 10.1002/ijc.33829] [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: 12/13/2020] [Revised: 04/25/2021] [Accepted: 05/12/2021] [Indexed: 11/09/2022]
Abstract
Transarterial chemoembolization (TACE) is used to treat patients with unresectable hepatocellular carcinoma (HCC). We evaluated the clinical impact of a-fetoprotein (AFP) and circulating cell-free and tumor DNA (cfDNA and ctDNA) changes around the TACE procedure. Our prospective monocentric study enrolled consecutive patients treated with TACE, with samples collected at baseline (D - 1), Day 2 (D + 2) and 1 month (M + 1) after TACE. cfDNA was quantified by the fluorometric method, and ctDNA was quantified by digital polymerase chain reaction designed for two hotspot TERT mutations. Computerized tomography scans or magnetic resonance imaging were performed at M + 1 every 3 months following TACE and independently reviewed. The objective was to identify thresholds of cfDNA, ctDNA and AFP changes associated with progressive disease (PD) using receiver operating characteristic curves. Thirty-eight patients were included from March 2018 to March 2019. All markers significantly increased from D - 1 to D + 2 (P < .005), and cfDNA and ctDNA significantly decreased from D + 2 to M + 1 (P < .0001). The analysis of changes from D - 1 to M + 1 identified thresholds at +31.4% for cfDNA and 0% for ctDNA that were significantly associated with PD at M + 1 (44.4% [>+31.4%] vs 3.8% [≤+31.4%] and 50.0% [>0%] vs 5.0% [≤0%], respectively). No significant threshold was identified for AFP. Using a score combining cfDNA and ctDNA, the patients were classified into high- or low-risk PD groups at M + 1, with PD rates of 80.0% vs 4.3% (P = .001) and median progression-free survival times of 1.3 vs 10.3 months (P = .002). Our study suggests that cfDNA and ctDNA increases around the TACE procedure and are associated with therapeutic failure.
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Affiliation(s)
- David Sefrioui
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Vincent Verdier
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Céline Savoye-Collet
- UNIROUEN, Quantif-LITIS EA 4108, Normandie Univ, Rouen, France.,Department of Radiology, Rouen University Hospital, Rouen, France
| | | | - Slim Ghomadi
- Department of Radiology, Rouen University Hospital, Rouen, France.,UNIROUEN, Normandie Univ, Rouen, France
| | - Alice Gangloff
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Odile Goria
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Ghassan Riachi
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Hélène Montialoux
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | - Lilian Schwarz
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Digestive Surgery Department, Rouen University Hospital, Rouen, France
| | - Jean-Jacques Tuech
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Digestive Surgery Department, Rouen University Hospital, Rouen, France
| | - Thierry Frebourg
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Pierre Michel
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
| | | | - Frédéric Di Fiore
- UNIROUEN, Inserm 1245, IRON group, Normandie Univ, Rouen, France.,Department of Hepatogastroenterology, Rouen University Hospital, Rouen, France
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10
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Sefrioui D, Beaussire L, Gillibert A, Blanchard F, Toure E, Bazille C, Perdrix A, Ziegler F, Gangloff A, Hassine M, Elie C, Bignon AL, Parzy A, Gomez P, Thill C, Clatot F, Sabourin JC, Frebourg T, Benichou J, Bouhier-Leporrier K, Gallais MP, Sarafan-Vasseur N, Michel P, Di Fiore F. CEA, CA19-9, circulating DNA and circulating tumour cell kinetics in patients treated for metastatic colorectal cancer (mCRC). Br J Cancer 2021; 125:725-733. [PMID: 34112948 PMCID: PMC8405627 DOI: 10.1038/s41416-021-01431-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 07/31/2020] [Revised: 04/17/2021] [Accepted: 04/28/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND We previously reported that CEA kinetics are a marker of progressive disease (PD) in metastatic colorectal cancer (mCRC). This study was specifically designed to confirm CEA kinetics for predicting PD and to evaluate CA19-9, cell-free DNA (cfDNA), circulating tumour DNA (ctDNA) and circulating tumour cell (CTC) kinetics. METHODS Patients starting a chemotherapy (CT) with pre-treatment CEA > 5 ng/mL and/or CA19.9 > 30 UI/mL were prospectively included. Samples were collected from baseline to cycle 4 for CEA and CA19-9 and at baseline and the sixth week for other markers. CEA kinetics were calculated from the first to the third or fourth CT cycle. RESULTS A total of 192 mCRC patients were included. CEA kinetics based on the previously identified >0.05 threshold was significantly associated with PD (p < 0.0001). By dichotomising by the median value, cfDNA, ctDNA and CA19-9 were associated with PD, PFS and OS in multivariate analysis. A circulating scoring system (CSS) combining CEA kinetics and baseline CA19-9 and cfDNA values classified patients based on high (n = 58) and low risk (n = 113) of PD and was independently associated with PD (ORa = 4.6, p < 0.0001), PFS (HRa = 2.07, p < 0.0001) and OS (HRa = 2.55, p < 0.0001). CONCLUSIONS CEA kinetics alone or combined with baseline CA19-9 and cfDNA are clinically relevant for predicting outcomes in mCRC. TRIAL REGISTRATION NUMBER NCT01212510.
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Affiliation(s)
- David Sefrioui
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Ludivine Beaussire
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - André Gillibert
- grid.41724.34Department of Biostatistics, Normandie Univ, UNIROUEN, Rouen University Hospital, Rouen, France
| | - France Blanchard
- grid.41724.34Department of Pathology, Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Emmanuel Toure
- grid.41724.34Department of Pathology, Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Céline Bazille
- grid.411149.80000 0004 0472 0160Department of Pathology, Caen University Hospital, Caen, France
| | - Anne Perdrix
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Biopathology, Henri Becquerel Centre, Rouen, France
| | - Frédéric Ziegler
- grid.7429.80000000121866389Normandie Univ, UNIROUEN, INSERM U1073, Rouen University Hospital and General Biochemistry Laboratory, Institute of Clinical Biology, Rouen, France
| | - Alice Gangloff
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Mélanie Hassine
- Department of Hepatogastroenterology, Elbeuf Hospital, Elbeuf, France
| | - Caroline Elie
- Department of Hepatogastroenterology, Elbeuf Hospital, Elbeuf, France
| | - Anne-Laure Bignon
- grid.411149.80000 0004 0472 0160Department of Hepatogastroenterology, Caen University Hospital, Caen, France
| | - Aurélie Parzy
- Department of Hepatogastroenterology, Francois Baclesse Centre, Caen, France
| | - Philippe Gomez
- Department of Medical Oncology, Frédéric Joliot Centre, Rouen, France
| | - Caroline Thill
- grid.41724.34Department of Biostatistics, Normandie Univ, UNIROUEN, Rouen University Hospital, Rouen, France
| | - Florian Clatot
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | - Jean-Christophe Sabourin
- grid.41724.34Department of Pathology, Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Genetics, Rouen, France
| | - Jacques Benichou
- grid.41724.34Department of Biostatistics, Normandie Univ, UNIROUEN, Rouen University Hospital, Rouen, France
| | - Karine Bouhier-Leporrier
- grid.411149.80000 0004 0472 0160Department of Hepatogastroenterology, Caen University Hospital, Caen, France
| | | | - Nasrin Sarafan-Vasseur
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pierre Michel
- grid.41724.34Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Hepatogastroenterology, Rouen, France
| | - Frédéric Di Fiore
- grid.41724.34Department of Hepatogastroenterology and Department of Medical Oncology, Henri Becquerel Centre, Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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11
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Cassinari K, Alessandri-Gradt E, Chambon P, Charbonnier F, Gracias S, Beaussire L, Alexandre K, Sarafan-Vasseur N, Houdayer C, Etienne M, Caron F, Plantier JC, Frebourg T. Assessment of Multiplex Digital Droplet RT-PCR as a Diagnostic Tool for SARS-CoV-2 Detection in Nasopharyngeal Swabs and Saliva Samples. Clin Chem 2021; 67:736-741. [PMID: 33331864 PMCID: PMC7799276 DOI: 10.1093/clinchem/hvaa323] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Reverse transcription-quantitative PCR on nasopharyngeal swabs is currently the reference COVID-19 diagnosis method but exhibits imperfect sensitivity. METHODS We developed a multiplex reverse transcription-digital droplet PCR (RT-ddPCR) assay, targeting 6 SARS-CoV-2 genomic regions, and evaluated it on nasopharyngeal swabs and saliva samples collected from 130 COVID-19 positive or negative ambulatory individuals, who presented symptoms suggestive of mild or moderate SARS-CoV2 infection. RESULTS For the nasopharyngeal swab samples, the results obtained using the 6-plex RT-ddPCR and RT-qPCR assays were all concordant. The 6-plex RT-ddPCR assay was more sensitive than RT-qPCR (85% versus 62%) on saliva samples from patients with positive nasopharyngeal swabs. CONCLUSION Multiplex RT-ddPCR represents an alternative and complementary tool for the diagnosis of COVID-19, in particular to control RT-qPCR ambiguous results. It can also be applied to saliva for repetitive sampling and testing individuals for whom nasopharyngeal swabbing is not possible.
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Affiliation(s)
- Kévin Cassinari
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Elodie Alessandri-Gradt
- Virology Laboratory, Rouen University Hospital, Rouen, France.,Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France
| | - Pascal Chambon
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Françoise Charbonnier
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Ségolène Gracias
- Virology Laboratory, Rouen University Hospital, Rouen, France.,Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France
| | - Ludivine Beaussire
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Kevin Alexandre
- Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France.,Department of Infectious Diseases, Rouen University Hospital, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Claude Houdayer
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Manuel Etienne
- Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France.,Department of Infectious Diseases, Rouen University Hospital, Rouen, France
| | - François Caron
- Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France.,Department of Infectious Diseases, Rouen University Hospital, Rouen, France
| | - Jean Christophe Plantier
- Virology Laboratory, Rouen University Hospital, Rouen, France.,Research Group on Microbial Adaptation, GRAM, UNIROUEN, Normandie University, Rouen, France
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital and Inserm U1245, UNIROUEN, Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
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12
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Fontanilles M, Marguet F, Beaussire L, Magne N, Pépin LF, Alexandru C, Tennevet I, Hanzen C, Langlois O, Jardin F, Laquerrière A, Sarafan-Vasseur N, Di Fiore F, Clatot F. Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma. Acta Neuropathol Commun 2020; 8:179. [PMID: 33148330 PMCID: PMC7641818 DOI: 10.1186/s40478-020-01057-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/26/2020] [Accepted: 10/10/2020] [Indexed: 01/28/2023] Open
Abstract
The clinical implications of plasmatic cell-free and tumor DNA (cfDNA and ctDNA) are challenging in glioblastoma. This prospective study included 52 consecutive newly diagnosed glioblastoma (n = 49) or gliosarcoma (n = 3) patients treated with concomitant temozolomide and radiotherapy (RT-TMZ), followed by a TMZ maintenance phase. Plasma samples were collected at baseline, before RT-TMZ (pre-RT-TMZ) and at the end of adjuvant TMZ, or at the time of progression in cases of progressive disease (PD). The cfDNA concentration was measured with a fluorometric method, and ctDNA was detected using targeted droplet digital PCR. The main objectives were to analyze the associations between cfDNA and ctDNA measurements during the course of treatment with PD and survival. There was a significant decrease in median cfDNA concentration from baseline to pre-RT-TMZ—19.4 versus 9.7 ng/mL (p < 0.0001)—in the entire cohort. In patients with PD, a significant increase in cfDNA concentration from pre-RT-TMZ to time of PD was observed, from 9.7 versus 13.1 ng/mL (p = 0.037), respectively, while no difference was observed for nonprogressive patients. Neither the cfDNA concentration at baseline nor its kinetics correlated with survival. ctDNA was detected in 2 patients (3.8%) and only in gliosarcoma subtypes. Trial registration ClinicalTrial, NCT02617745. Registered 1 December 2015, https://clinicaltrials.gov/ct2/show/NCT02617745?term=glioplak&draw=2&rank=1.
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13
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Sefrioui D, Verdier V, Savoye-Collet C, Beaussire L, Ghomadi S, Gangloff A, Goria O, Riachi G, Montialoux H, Schwarz L, Tuech JJ, Frebourg T, Michel P, Vasseur NS, Di Fiore F. 1007P cfDNA and ctDNA variations are predictive of disease progression to conventional transarterial chemoembolization (cTACE) in patients with hepatocellular carcinoma (HCC). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1123] [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: 11/27/2022] Open
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14
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Fontanilles M, Deniel A, Marguet F, Beaussire L, Magne N, Derrey S, Richard D, Alexandru C, Clatot F, Laquerrière A, Vasseur NS, Di Fiore F. 371MO Usefulness of circulating tumour DNA detection from cerebrospinal fluid in recurrent high-grade glioma. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.480] [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: 10/23/2022] Open
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15
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Clatot F, Perdrix A, Beaussire L, Lequesne J, Lévy C, Emile G, Bubenheim M, Lacaille S, Calbrix C, Augusto L, Guillemet C, Alexandru C, Fontanilles M, Sefrioui D, Burel L, Guénot S, Richard D, Sarafan-Vasseur N, Di Fiore F. Risk of early progression according to circulating ESR1 mutation, CA-15.3 and cfDNA increases under first-line anti-aromatase treatment in metastatic breast cancer. Breast Cancer Res 2020; 22:56. [PMID: 32466779 PMCID: PMC7254698 DOI: 10.1186/s13058-020-01290-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 01/14/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background Endocrine therapy is recommended as a first-line treatment for hormone receptor-positive metastatic breast cancer (HR+MBC) patients. No biomarker has been validated to predict tumor progression in that setting. We aimed to prospectively compare the risk of early progression according to circulating ESR1 mutations, CA-15.3, and circulating cell-free DNA in MBC patients treated with a first-line aromatase inhibitor (AI). Methods Patients with MBC treated with a first-line AI were prospectively included. Circulating biomarker assessment was performed every 3 months. The primary objective was to determine the risk of progression or death at the next follow-up visit (after 3 months) in case of circulating ESR1 mutation detection among patients treated with a first-line AI for HR+MBC. Results Overall, 103 patients were included, and 70 (68%) had progressive disease (PD). Circulating ESR1 mutations were detected in 22/70 patients with PD and in 0/33 patients without progression (p < 0.001). Among the ESR1-mutated patients, 18/22 had a detectable mutation prior to progression, with a median delay of 110 days from first detection to PD. The detection of circulating ESR1 mutations was associated with a 4.9-fold (95% CI 3.0–8.0) increase in the risk of PD at 3 months. Using a threshold value of 25% or 100%, a CA-15.3 increase was also correlated with progression (p < 0.001 and p = 0.003, respectively). In contrast to ESR1, the CA-15.3 increase occurred concomitantly with PD in most cases, in 27/47 (57%) with a 25% threshold and in 21/25 (84%) with a 100% threshold. Using a threshold value of either 25% or 100%, cfDNA increase was not correlated with progression. Conclusion The emergence of circulating ESR1 mutations is associated with a 4.9-fold increase in the risk of early PD during AI treatment in HR+MBC. Our results also highlighted that tracking circulating ESR1 mutations is more relevant than tracking CA-15.3 or cfDNA increase to predict progression in this setting. Trial registration ClinicalTrials.gov, NCT02473120. Registered 16 June 2015—retrospectively registered after one inclusion (first inclusion 1 June 2015)
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France. .,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Christelle Lévy
- Institut Normand du Sein, Centre François Baclesse, Caen, France
| | - George Emile
- Institut Normand du Sein, Centre François Baclesse, Caen, France
| | - Michael Bubenheim
- Department of Clinical Research and Innovation, Rouen University Hospital, Rouen, France
| | - Sigrid Lacaille
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Céline Calbrix
- Department of Biopathology, Centre Henri Becquerel, Rouen, France
| | - Laetitia Augusto
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Cécile Guillemet
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | | | - Maxime Fontanilles
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Lucie Burel
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Sabine Guénot
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Doriane Richard
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France.,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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16
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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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Chebbi A, Sarafon-Vasseur S, Beaussire L, Blanchard F, Gobet F, Sabourin JC, Pfister C, Di Fiore F, Nouhaud FX. Étude de l’impact clinique des variations de copies de gènes identifiées pour un panel de gènes d’intérêt par droplet digital PCR chez des patients traités par thérapie ciblée pour un cancer du rein métastatique. Prog Urol 2019. [DOI: 10.1016/j.purol.2019.08.048] [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: 11/26/2022]
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18
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Deniel A, Marguet F, Beaussire L, Tobenas-Dujardin AC, Peillon C, Gambirasio MA, Veresezan O, Magne N, Di Fiore F, Laquerrière A, Sarafan-Vasseur N, Fontanilles M. TERTp Mutation Detection in Plasma by Droplet-Digital Polymerase Chain Reaction in Spinal Myxopapillary Ependymoma with Lung Metastases. World Neurosurg 2019; 130:405-409. [PMID: 31330336 DOI: 10.1016/j.wneu.2019.07.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/25/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Spinal myxopapillary ependymoma (SP-MPE) is a subgroup of ependymomas in which after initial gross tumor resection, recurrences occur in more than half of the patients. Anaplastic transformation may also occur and contributes to intraneural and extraneural metastatic dissemination. Extraneural metastases from SP-MPE are rare and worsen the prognosis. In this situation, the noninvasive detection of recurrent somatic mutations in the circulating tumor DNA (ctDNA) from plasma is challenging. Telomerase-reverse transcriptase gene promoter (TERTp) mutation has been identified in a subset of ependymomas with aggressive behavior. CASE DESCRIPTION We report on a patient with TERTp mutated SP-MPE presenting with an extraneural anaplastic metastatic dissemination after iterative local recurrences. From the initial SP-MPE to pleural anaplastic lesion, TERTp C228T mutation was present with allele frequency varying from 33% to 39%. Interestingly, TERTp mutation was also detected by droplet digital polymerase chain reaction in the plasma with a frequency of 2.1% at the time of pleural metastases, highlighting that ctDNA is released in plasma of patients suffering from SP-MPE with extraneural metastatic dissemination. CONCLUSIONS Despite the rarity of this evolution, plasmatic liquid biopsy appears to be a useful diagnostic and follow-up tool in a subset of primary brain tumors.
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Affiliation(s)
- Anne Deniel
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rouen, France
| | - Florent Marguet
- Department of Pathology, Rouen University Hospital, Rouen, France
| | - Ludivine Beaussire
- IRON Group, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | | | - Christophe Peillon
- Department of Thoracic Surgery, Rouen University Hospital, Rouen, France
| | | | - Ovidiu Veresezan
- Department of Radiation Oncology and Medical Physics, Cancer Centre Henri Becquerel, Rouen, France
| | - Nicolas Magne
- Department of Radiology, Rouen University Hospital, Rouen, France
| | - Frederic Di Fiore
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rouen, France; IRON Group, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | | | - Nasrin Sarafan-Vasseur
- IRON Group, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Maxime Fontanilles
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rouen, France; IRON Group, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France.
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19
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Cassinari K, Quenez O, Joly-Hélas G, Beaussire L, Le Meur N, Castelain M, Goldenberg A, Guerrot AM, Brehin AC, Deleuze JF, Boland A, Rovelet-Lecrux A, Campion D, Saugier-Veber P, Gruchy N, Frebourg T, Nicolas G, Sarafan-Vasseur N, Chambon P. A Simple, Universal, and Cost-Efficient Digital PCR Method for the Targeted Analysis of Copy Number Variations. Clin Chem 2019; 65:1153-1160. [PMID: 31292136 DOI: 10.1373/clinchem.2019.304246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/13/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Rare copy number variations (CNVs) are a major cause of genetic diseases. Simple targeted methods are required for their confirmation and segregation analysis. We developed a simple and universal CNV assay based on digital PCR (dPCR) and universal locked nucleic acid (LNA) hydrolysis probes. METHODS We analyzed the mapping of the 90 LNA hydrolysis probes from the Roche Universal ProbeLibrary (UPL). For each CNV, selection of the optimal primers and LNA probe was almost automated; probes were reused across assays and each dPCR assay included the CNV amplicon and a reference amplicon. We assessed the assay performance on 93 small and large CNVs and performed a comparative cost-efficiency analysis. RESULTS UPL-LNA probes presented nearly 20000000 occurrences on the human genome and were homogeneously distributed with a mean interval of 156 bp. The assay accurately detected all the 93 CNVs, except one (<200 bp), with coefficient of variation <10%. The assay was more cost-efficient than all the other methods. CONCLUSIONS The universal dPCR CNV assay is simple, robust, and cost-efficient because it combines a straightforward design allowed by universal probes and end point PCR, the advantages of a relative quantification of the target to the reference within the same reaction, and the high flexibility of the LNA hydrolysis probes. This method should be a useful tool for genomic medicine, which requires simple methods for the interpretation and segregation analysis of genomic variations.
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Affiliation(s)
- Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Quenez
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Géraldine Joly-Hélas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nathalie Le Meur
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Mathieu Castelain
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Marie Guerrot
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Claire Brehin
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Génomique, CEA, Evry, France
| | - Anne Rovelet-Lecrux
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Dominique Campion
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lés-Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nicolas Gruchy
- Caen University Hospital, Department of Genetics, F 14000, Normandy Center for Genomic and Personalized Medicine, Caen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Pascal Chambon
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France;
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20
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Augusto L, Beaussire L, Lequesne J, Perdrix A, Sefrioui D, Fontanilles M, Leheurteur M, Di Fiore F, Sarafan-Vasseur N, Clatot F. Prognostic values of cell free DNA, CA 15.3, and ESR1 circulating mutations variations in hormone receptor (HR)-positive metastatic breast cancer (MBC) patients under aromatase inhibitor (AI). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e12534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e12534 Background: Circulating cell free DNA (cfDNA), CA 15.3 and circulating tumor DNA (ctDNA) have been associated with survival in MBC. These 3 biomarkers have never been compared. Methods: We retrospectively included all patients treated in our center between 2010 and 2012 for a HR+ MBC, who had clinical progression during the first line of aromatase inhibitor (AI) and available plasma samples. CfDNA level (ng/mL), CA 15.3 level (U/mL) and ESR1 circulating mutation level (Y537N, Y537S, Y537C and D538G, identified by ddPCR) were determined at time of clinical progression (Tp) and 3 months before (Tp-3). Biomarkers values at Tp and Tp-3 as well as their variations were analyzed according to clinical progression and overall survival (OS). Results: 91 patients were analyzed. CA 15.3 was elevated ( > 30 U/mL) in 71/91 (78%) at Tp and 62/91 (68%) at Tp-3. Higher CA 15.3 was associated with worse OS, especially at Tp (HR = 1.0006/unit at both times, p = 0.009 at Tp; p = 0.08 at Tp-3). Higher cfDNA was associated with worse OS, both at Tp and Tp-3 (HR = 1.006/unit, p < 0.0001 and HR = 1.007/unit, p = 0.02, respectively). An ESR1 mutation was detected in 14/91 at Tp-3 (15%) and 28/91 at Tp (31%). ESR1 mutation detection was strongly correlated with OS both at Tp and Tp-3 (HR = 2.4, p = 0.0005 and HR = 1.97, p = 0.03, respectively). Between Tp-3 and Tp, overall median CA 15.3 and ESR1 mutation level increased (p < 0.0001 and p = 0.007, respectively) and were related to poorer OS (HR = 1.007/unit, p = 0.0002 and HR = 3.1, p = 0.05). In contrast, CfDNA was not correlated at all with clinical progression (36/91 increase, 36/91 decrease, and 19/91 stable cfDNA). ROC curve analysis identified a 59% CA 15.3 increase as the best cut-off for predicting progression, but with poor performance (AUC = 0.64). Multivariate analysis showed that CA 15.3 at Tp (HR = 1.0006/unit, p = 0.006), cfDNA at Tp (HR = 1.005/unit, p = 0.01), ESR1 detection at Tp (HR = 2.7, p = 0.0002) and CA 15.3 increase between Tp-3 and Tp (HR = 1.006/unit, p = 0.003) were associated with poor OS. Conclusions: All 3 biomarkers are correlated with OS in MBC treated with AI. CfDNA variation is poorly related to clinical progression while CA 15.3 variation or ESR1 mutation detection are much more reliable. Overall the better performance is observed with ESR1 mutation detection.
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Affiliation(s)
- Laetitia Augusto
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Ludivine Beaussire
- Institute of Research Onco-Normand (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | | | - Anne Perdrix
- Department of Bio-Pathology, IRON Group, Centre Henri Becquerel, Rouen, France
| | - David Sefrioui
- Digestive Oncology Unit, Iron Group, Rouen University Hospital, Rouen, France
| | | | | | - Frédéric Di Fiore
- Digestive Oncology Unit, IRON group, Rouen Hospital, University of Normandy, Rouen, France
| | | | - Florian Clatot
- INSERM U1245, IRON Group, Centre Henri Becquerel, University Hospital, University of Normandy, Rouen, France
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21
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Duplaquet L, Figeac M, Leprêtre F, Frandemiche C, Villenet C, Sebda S, Sarafan-Vasseur N, Bénozène M, Vinchent A, Goormachtigh G, Wicquart L, Rousseau N, Beaussire L, Truant S, Michel P, Sabourin JC, Galateau-Sallé F, Copin MC, Zalcman G, De Launoit Y, Fafeur V, Tulasne D. Functional Analysis of Somatic Mutations Affecting Receptor Tyrosine Kinase Family in Metastatic Colorectal Cancer. Mol Cancer Ther 2019; 18:1137-1148. [PMID: 30926633 DOI: 10.1158/1535-7163.mct-18-0582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/08/2018] [Accepted: 03/21/2019] [Indexed: 11/16/2022]
Abstract
Besides the detection of somatic receptor tyrosine kinases (RTK) mutations in tumor samples, the current challenge is to interpret their biological relevance to give patients effective targeted treatment. By high-throughput sequencing of the 58 RTK exons of healthy tissues, colorectal tumors, and hepatic metastases from 30 patients, 38 different somatic mutations in RTKs were identified. The mutations in the kinase domains and present in both tumors and metastases were reconstituted to perform an unbiased functional study. Among eight variants found in seven RTKs (EPHA4-Met726Ile, EPHB2-Val621Ile, ERBB4-Thr731Met, FGFR4-Ala585Thr, VEGFR3-Leu1014Phe, KIT-Pro875Leu, TRKB-Leu584Val, and NTRK2-Lys618Thr), none displayed significantly increased tyrosine kinase activity. Consistently, none of them induced transformation of NIH3T3 fibroblasts. On the contrary, two RTK variants (FGFR4-Ala585Thr and FLT4-Leu1014Phe) caused drastic inhibition of their kinase activity. These findings indicate that these RTK variants are not suitable targets and highlight the importance of functional studies to validate RTK mutations as potential therapeutic targets.
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Affiliation(s)
- Leslie Duplaquet
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Martin Figeac
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Charline Frandemiche
- TCBN - Tumorothèque Caen Basse-Normandie, Caen, France.,Réseau Régional de Cancérologie, OncoBasseNormandie, Caen, France
| | - Céline Villenet
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, Plateau de génomique fonctionnelle et structurale, CHU Lille, Lille, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Mélanie Bénozène
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Audrey Vinchent
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | | | | | | | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Stéphanie Truant
- Department of Digestive Surgery and Transplantation, CHU Lille, Univ Lille, Lille Cedex, France
| | - Pierre Michel
- Department of Hepato-Gastroenterology, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandy University, INSERM 1245, Rouen University Hospital, Rouen, France
| | | | - Marie-Christine Copin
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France.,Tumorothèque du C2RC de Lille, Lille, France
| | - Gérard Zalcman
- Thoracic Oncology Department, CIC1425/CLIP2 Paris-Nord, Hôpital Bichat-Claude Bernard, Paris, France
| | - Yvan De Launoit
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - Véronique Fafeur
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France
| | - David Tulasne
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T, Lille, France.
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22
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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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23
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Allouchery V, Beaussire L, Perdrix A, Sefrioui D, Augusto L, Guillemet C, Sarafan-Vasseur N, Di Fiore F, Clatot F. Circulating ESR1 mutations at the end of aromatase inhibitor adjuvant treatment and after relapse in breast cancer patients. Breast Cancer Res 2018; 20:40. [PMID: 29769099 PMCID: PMC5956618 DOI: 10.1186/s13058-018-0968-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 01/13/2023] Open
Abstract
Background Detection of circulating ESR1 mutations is associated with acquired resistance to aromatase inhibitor (AI) in metastatic breast cancer. Until now, the presence of circulating ESR1 mutations at the end of adjuvant treatment by AI in early breast cancer had never been clearly established. In this context, the aim of the present study was to evaluate the circulating ESR1 mutation frequency at the end of adjuvant treatment and after relapse. Methods This monocentric retrospective study was based on available stored plasmas and included all early breast cancer patients who completed at least 2 years of AI adjuvant treatment and experienced a documented relapse after the end of their treatment. Circulating ESR1 mutations (D538G, Y537S/N/C) were assessed by droplet digital PCR in plasma samples taken at the end of adjuvant treatment, at time of relapse and at time of progression under first line metastatic treatment. Results A total of 42 patients were included, with a median adjuvant AI exposure of 60 months (range 41–85). No circulating ESR1 mutation was detectable at the end of AI adjuvant therapy. At first relapse, 5.3% of the patients (2/38) had a detectable circulating ESR1 mutation. At time of progression on first-line metastatic treatment, 33% of the patients (7/21) under AI had a detectable circulating ESR1 mutation compared to none of the patients under chemotherapy (0/10). The two patients with a detectable ESR1 mutation at relapse were treated by AI and had an increase of their variant allele fraction at time of progression on first-line metastatic treatment. Conclusions Circulating ESR1 mutation detection at the end of AI-based adjuvant treatment is not clinically useful. Circulating ESR1 mutation could be assessed as soon as first relapse to guide interventional studies.
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Affiliation(s)
- Violette Allouchery
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen cedex 1, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | - Laetitia Augusto
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen cedex 1, France
| | - Cécile Guillemet
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen cedex 1, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen cedex 1, France.,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen cedex 1, France. .,Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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Clatot F, Perdrix A, Augusto L, Beaussire L, Delacour J, Calbrix C, Sefrioui D, Viailly PJ, Bubenheim M, Moldovan C, Alexandru C, Tennevet I, Rigal O, Guillemet C, Leheurteur M, Gouérant S, Petrau C, Théry JC, Picquenot JM, Veyret C, Frébourg T, Jardin F, Sarafan-Vasseur N, Di Fiore F. Kinetics, prognostic and predictive values of ESR1 circulating mutations in metastatic breast cancer patients progressing on aromatase inhibitor. Oncotarget 2018; 7:74448-74459. [PMID: 27801670 PMCID: PMC5342678 DOI: 10.18632/oncotarget.12950] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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] [Indexed: 11/25/2022] Open
Abstract
Purpose To assess the prognostic and predictive value of circulating ESR1 mutation and its kinetics before and after progression on aromatase inhibitor (AI) treatment. Patients and methods ESR1 circulating D538G and Y537S/N/C mutations were retrospectively analyzed by digital droplet PCR after first-line AI failure in patients treated consecutively from 2010 to 2012 for hormone receptor-positive metastatic breast cancer. Progression-free survival (PFS) and overall survival (OS) were analyzed according to circulating mutational status and subsequent lines of treatment. The kinetics of ESR1 mutation before (3 and 6 months) and after (3 months) AI progression were determined in the available archive plasmas. Results Circulating ESR1 mutations were found at AI progression in 44/144 patients included (30.6%). Median follow-up from AI initiation was 40 months (range 4-94). The median OS was decreased in patients with circulating ESR1 mutation than in patients without mutation (15.5 versus 23.8 months, P=0.0006). The median PFS was also significantly decreased in patients with ESR1 mutation than in patients without mutation (5.9 vs 7 months, P=0.002). After AI failure, there was no difference in outcome for patients receiving chemotherapy (n = 58) versus non-AI endocrine therapy (n=51) in patients with and without ESR1 mutation. ESR1 circulating mutations were detectable in 75% of all cases before AI progression, whereas the kinetics 3 months after progression did not correlate with outcome. Conclusion ESR1 circulating mutations are independent risk factors for poor outcome after AI failure, and are frequently detectable before clinical progression. Interventional studies based on ESR1 circulating status are warranted.
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France.,INSERM U918, Henri Becquerel Centre, Rouen, France.,EquIpe de Recherche en Oncologie, Rouen, France
| | - Anne Perdrix
- EquIpe de Recherche en Oncologie, Rouen, France.,Department of Biopathology, Henri Becquerel Centre, Rouen, France
| | - Laetitia Augusto
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | - Ludivine Beaussire
- EquIpe de Recherche en Oncologie, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France
| | - Julien Delacour
- EquIpe de Recherche en Oncologie, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France
| | - Céline Calbrix
- Department of Biopathology, Henri Becquerel Centre, Rouen, France
| | - David Sefrioui
- EquIpe de Recherche en Oncologie, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | | | - Michael Bubenheim
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - Cristian Moldovan
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | | | - Isabelle Tennevet
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | - Olivier Rigal
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | - Cécile Guillemet
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | | | - Sophie Gouérant
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | - Camille Petrau
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France.,EquIpe de Recherche en Oncologie, Rouen, France
| | - Jean-Christophe Théry
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France
| | - Jean-Michel Picquenot
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France.,INSERM U918, Henri Becquerel Centre, Rouen, France.,Department of Biopathology, Henri Becquerel Centre, Rouen, France
| | - Corinne Veyret
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France
| | | | | | - Nasrin Sarafan-Vasseur
- EquIpe de Recherche en Oncologie, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Henri Becquerel Centre, Rouen, France.,EquIpe de Recherche en Oncologie, Rouen, France.,INSERM U1079, Faculty of Medecine, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
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25
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Sefrioui D, Beaussire L, Perdrix A, Clatot F, Michel P, Frebourg T, Di Fiore F, Sarafan-Vasseur N. Direct circulating tumor DNA detection from unpurified plasma using a digital PCR platform. Clin Biochem 2017. [DOI: 10.1016/j.clinbiochem.2017.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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26
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Allouchery V, Beaussire L, Perdrix A, Sefrioui D, Augusto L, Guillemet C, Sarafan-Vasseur N, Di Fiore F, Clatot F. Circulating ESR1 mutations at the end of aromatase inhibitor adjuvant treatment and after relapse in breast cancer patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx362.040] [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: 11/13/2022] Open
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27
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Sefrioui D, Beaussire L, Clatot F, Perdrix A, Michel P, Di Fiore F, Sarafan-Vasseur N. Heparinase enables reliable quantification of circulating tumor DNA from heparin plasma samples by droplet digital PCR. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx363.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Hassine M, Savoye-Collet C, Sefrioui D, Beaussire L, Gillibert A, Gangloff A, Sarafan-Vasseur N, Michel P, Di Fiore F. Relationship between pretreatment levels of circulating DNA, circulating tumor cells, CEA, CA19.9 and tumor burden on CT scan in patients treated for a metastatic colorectal cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx393.064] [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: 11/12/2022] Open
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29
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Sefrioui D, Beaussire L, Clatot F, Delacour J, Perdrix A, Frebourg T, Michel P, Di Fiore F, Sarafan-Vasseur N. Heparinase enables reliable quantification of circulating tumor DNA from heparinized plasma samples by droplet digital PCR. Clin Chim Acta 2017; 472:75-79. [PMID: 28729136 DOI: 10.1016/j.cca.2017.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 05/25/2017] [Accepted: 07/15/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND Heparin is often used as a blood anticoagulant for tumor marker analysis but results in the inhibition of PCR detection of circulating tumor DNA (ctDNA), which has been deemed a potential "liquid biopsy". We aimed to evaluate the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. METHODS Plasma samples were collected in heparinized (n=194) and EDTA (n=8) tubes from hormone receptor-positive metastatic breast cancer (HR+MBC) (n=144) and pancreatic adenocarcinoma (PA) patients (n=50). Circulating ESR1 and KRAS mutations were detected with or without heparinase by digital PCR in HR+MBC and PA patients, respectively. Patients were classified into 2 subgroups i) inhibition, I+ and ii) no inhibition, I- based on a threshold of 200copies/μL for PCR inhibition by heparin. RESULTS In the I+ subgroup (91/144 HR+MBC and 26/50 PA), heparinase treatment significantly improved PCR efficacy, enabling ctDNA detection in 22/91 and 13/26 patients. Moreover, comparable results for ctDNA detection (4/8) were obtained with heparinized and EDTA PA samples. In the I- subgroup, heparinase addition did not quantitatively and qualitatively alter ctDNA detection. CONCLUSION Heparinase addition removes the heparin inhibition and allows accurate ctDNA detection in heparinized samples. These findings could make the samples from heparinized blood suitable for ctDNA analysis.
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Affiliation(s)
- David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Florian Clatot
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Julien Delacour
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Biopathology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Frédéric Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Digestive Oncology Unit and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France.
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30
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Sefrioui D, Vermeulin T, Blanchard F, Chapusot C, Beaussire L, Armengol-Debeir L, Sesboué R, Gangloff A, Hebbar M, Copin MC, Houivet E, Schwarz L, Clatot F, Tuech JJ, Bénichou J, Martin L, Bouvier AM, Sabourin JC, Sarafan-Vasseur N, Frébourg T, Lepage C, Michel P, Di Fiore F. Copy number variations inDCC/18q andERBB2/17q are associated with disease-free survival in microsatellite stable colon cancer. Int J Cancer 2017; 140:1653-1661. [DOI: 10.1002/ijc.30584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/23/2016] [Indexed: 01/05/2023]
Affiliation(s)
- David Sefrioui
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Thomas Vermeulin
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - France Blanchard
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Pathology; Rouen University Hospital; Rouen France
| | - Caroline Chapusot
- Department of Pathology; Dijon University Hospital, University of Burgundy; Dijon France
| | - Ludivine Beaussire
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
| | - Laura Armengol-Debeir
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
| | - Richard Sesboué
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Alice Gangloff
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Mohamed Hebbar
- Department of Medical Oncology; Lille University Hospital; Lille France
| | | | - Estelle Houivet
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - Lilian Schwarz
- Department of Surgery; Rouen University Hospital; Rouen France
| | - Florian Clatot
- Department of Medical Oncology; Centre Henri Becquerel; Rouen France
| | | | - Jacques Bénichou
- Department of Biostatistics; Rouen University Hospital; Rouen France
| | - Laurent Martin
- Department of Pathology; Dijon University Hospital, University of Burgundy; Dijon France
| | - Anne-Marie Bouvier
- Digestive Cancer Registry of Burgundy, INSERM U866, University Hospital Dijon, University of Burgundy; Dijon France
| | - Jean-Christophe Sabourin
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Pathology; Rouen University Hospital; Rouen France
| | - Nasrin Sarafan-Vasseur
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Thierry Frébourg
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
| | - Côme Lepage
- Digestive Cancer Registry of Burgundy, INSERM U866, University Hospital Dijon, University of Burgundy; Dijon France
| | - Pierre Michel
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
| | - Frédéric Di Fiore
- Digestive Oncology Unit, Department of Hepato-Gastroenterology; Rouen University Hospital; Rouen France
- Inserm U1079, University of Rouen, Institute for Biomedical Research and Innovation; Rouen France
- EquIpe de Recherche en ONcogie (IRON), Rouen University Hospital; Rouen France
- Department of Medical Oncology; Centre Henri Becquerel; Rouen France
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31
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Sefrioui D, Mauger F, Leclere L, Beaussire L, Di Fiore F, Deleuze JF, Sarafan-Vasseur N, Tost J. Comparison of the quantification of KRAS mutations by digital PCR and E-ice-COLD-PCR in circulating-cell-free DNA from metastatic colorectal cancer patients. Clin Chim Acta 2016; 465:1-4. [PMID: 27940131 DOI: 10.1016/j.cca.2016.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 10/23/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA (ccfDNA) bears great promise as biomarker for personalized medicine, but ccfDNA is present only at low levels in the plasma or serum of cancer patients. E-ice-COLD-PCR is a recently developed enrichment method to detect and identify mutations present at low-abundance in clinical samples. However, recent studies have shown the importance to accurately quantify low-abundance mutations as clinically important decisions will depend on certain mutation thresholds. The possibility for an enrichment method to accurately quantify the mutation levels remains a point of concern and might limit its clinical applicability. In the present study, we compared the quantification of KRAS mutations in ccfDNA from metastatic colorectal cancer patients by E-ice-COLD-PCR with two digital PCR approaches. For the quantification of mutations by E-ice-COLD-PCR, cell lines with known mutations diluted into WT genomic DNA were used for calibration. E-ice-COLD-PCR and the two digital PCR approaches showed the same range of the mutation level and were concordant for mutation levels below the clinical relevant threshold. E-ice-COLD-PCR can accurately detect and quantify low-abundant mutations in ccfDNA and has a shorter time to results making it compatible with the requirements of analyses in a clinical setting without the loss of quantitative accuracy.
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Affiliation(s)
- David Sefrioui
- Digestive Oncology Unit, Rouen University Hospital, France; Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Laurence Leclere
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Ludivine Beaussire
- Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Frédéric Di Fiore
- Digestive Oncology Unit, Rouen University Hospital, France; Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
| | - Nasrin Sarafan-Vasseur
- Inserm U1079, Iron group, IRIB, University of Rouen, Normandy University, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France.
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Sefrioui D, Vasseur N, Toure E, Blanchard F, Delacour J, Thill C, Beaussire L, Gillibert A, Ziegler F, Gangloff A, Bouhier-Leporrier K, Lefebvre AC, Parzy A, Gallais MP, Clatot F, Perdrix A, Sabourin JC, Frebourg T, Michel P, Di Fiore F. Prospective analysis of CEA, CA19.9, circulating DNA (cDNA) and circulating tumor cells (CTC) in patients (pts) treated for a metastatic colorectal cancer (mCRC)_Results of COCA-COLON study. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw363.19] [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: 11/14/2022] Open
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33
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Sefrioui D, Blanchard F, Basile P, Toure E, Dolfus C, Beaussire L, Vasseur N, Perdrix A, Gangloff A, Schwarz L, Clatot F, Tuech JJ, Sabourin JC, Frebourg T, Michel P, Di Fiore F. Diagnostic performance of liquid biopsy for pancreatic solid lesion as alternative to endoscopic ultrasound-guided fine needle aspiration (EUS-FNA). Ann Oncol 2016. [DOI: 10.1093/annonc/mdw363.18] [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: 11/13/2022] Open
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34
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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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35
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Sefrioui D, Sarafan-Vasseur N, Toure E, Delacour J, Ziegler F, Thill C, Gangloff A, Blanchard F, Beaussire L, Bouhier Leporrier K, Galais MP, Perdrix A, Clatot F, Jardin F, Sabourin JC, Frébourg T, Michel P, Di Fiore F. Prospective analysis of CEA, circulating DNA (cDNA) and circulating tumor cells (CTC) kinetics in patients (pts) treated for a metastatic colorectal cancer (mCRC). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.3560] [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)
- David Sefrioui
- Digestive Oncology Unit, IRON group, Rouen Hospital, University of Normandy, Rouen, France
| | | | - Emmanuel Toure
- Department of Pathology, University of Normandy, Rouen, France
| | - Julien Delacour
- Inserm U1079, IRON group, University of Normandy, Rouen, France
| | - Frederic Ziegler
- Institute of Clinical Biology, INSERM UMR 1073, University of Normandy, Rouen, France
| | - Caroline Thill
- Department of Biostatistics, University of Normandy, Rouen, France
| | - Alice Gangloff
- Digestive Oncology Unit, IRON group, Rouen Hospital, University of Normandy, Rouen, France
| | - France Blanchard
- Department of Pathology, IRON group, University Hospital, Rouen, France
| | | | | | - Marie-Pierre Galais
- Digestive Oncology Unit, Centre Francois Baclesse, University of Normandy, Caen, France
| | - Anne Perdrix
- Department of Bio-Pathology,IRON group, Centre Henri Becquerel, Rouen, France
| | - Florian Clatot
- INSERM U918, IRON group, Centre Henri Becquerel, University of Normandy, Rouen, France
| | - Fabrice Jardin
- Department of hematology, Inserm U918, Centre henri Becquerel, University of Normandy, Rouen, France
| | | | | | - Pierre Michel
- Digestive Oncology Unit, IRON group, CHU Rouen, University of Normandy, Rouen, France
| | - Frédéric Di Fiore
- Digestive Oncology Unit, IRON group, Rouen Hospital, University of Normandy, Rouen, France
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Augusto L, Sarafan-Vasseur N, Perdrix A, Beaussire L, Delacour J, Sefrioui D, Calbrix C, Picquenot JM, Frébourg T, Jardin F, Di Fiore F, Clatot F. Prognostic and predictive value of circulating ESR1 mutations in metastatic breast cancer patients (mBC) progressing under aromatase inhibitor (AI) treatment. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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)
- Laetitia Augusto
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | | | - Anne Perdrix
- Department of Bio-Pathology,IRON group, Centre Henri Becquerel, Rouen, France
| | | | | | - David Sefrioui
- Digestive Oncology Unit, Department of Hepato-Gastroenterology, Rouen University Hospital, Rouen, France
| | - Céline Calbrix
- Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | | | | | | | - Frédéric Di Fiore
- Institute of Research Onco-Normand (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | - Florian Clatot
- INSERM U918, IRON group, Centre Henri Becquerel, University of Normandy, Rouen, France
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Sefrioui D, Vasseur C, Sesboué R, Blanchard F, Gangloff A, Baretti M, Beaussire L, Clatot F, Dolfus C, Sabourin J, Michel P, Frebourg T, Di Fiore F. Clinical Interest of Digital Pcr for Routine Detection of Circulating Dna in Metastatic Colorectal Cancer. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu358.48] [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: 11/14/2022] Open
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